2025
Triebel, Sandra; Eulenfeld, Tom; Ontiveros-Palacios, Nancy; Sweeney, Blake; Tautz, Norbert; Marz, Manja
First full-genome alignment representative for the genus Pestivirus Journal Article
In: bioRxiv, 2025.
Abstract | Links | BibTeX | Tags: alignment, evolution, phylogenetics, RNA structure, RNA-RNA interactions, viruses
@article{nokey_77,
title = {First full-genome alignment representative for the genus \textit{Pestivirus}},
author = {Sandra Triebel and Tom Eulenfeld and Nancy Ontiveros-Palacios and Blake Sweeney and Norbert Tautz and Manja Marz},
url = {https://doi.org/10.5281/zenodo.15490752},
doi = {10.1101/2025.05.22.655560},
year = {2025},
date = {2025-05-27},
journal = {bioRxiv},
abstract = {The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3’ stem-loop essential for genome replication, had already been studied for a few individual pestiviruses.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.},
keywords = {alignment, evolution, phylogenetics, RNA structure, RNA-RNA interactions, viruses},
pubstate = {published},
tppubtype = {article}
}
The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3’ stem-loop essential for genome replication, had already been studied for a few individual pestiviruses.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.
Ontiveros-Palacios, Nancy; Cooke, Emma; Nawrocki, Eric P.; Triebel, Sandra; Marz, Manja; Rivas, Elena; Griffiths-Jones, Sam; Petrov, Anton I.; Bateman, Alex; Sweeney, Blake
Rfam 15: RNA families database in 2025 Journal Article
In: Nucleic Acids Research, 2025.
Abstract | Links | BibTeX | Tags: database, ncRNAs, RNA structure, RNA-RNA interactions
@article{nokey_67,
title = {Rfam 15: RNA families database in 2025},
author = {Nancy Ontiveros-Palacios and Emma Cooke and Eric P. Nawrocki and Sandra Triebel and Manja Marz and Elena Rivas and Sam Griffiths-Jones and Anton I. Petrov and Alex Bateman and Blake Sweeney},
doi = {10.1093/nar/gkae1023},
year = {2025},
date = {2025-01-06},
urldate = {2024-11-11},
journal = {Nucleic Acids Research},
abstract = {The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam’s coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org.},
keywords = {database, ncRNAs, RNA structure, RNA-RNA interactions},
pubstate = {published},
tppubtype = {article}
}
The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam’s coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org.
2024
Krautwurst, Sarah; Lamkiewicz, Kevin
RNA-protein interaction prediction without high-throughput data: An overview and benchmark of in silico tools Journal Article
In: Computational and Structural Biotechnology Journal, vol. 23, pp. 4036-4046, 2024, ISSN: 2001-0370.
Abstract | Links | BibTeX | Tags: ncRNAs, proteins, RNA / transcriptomics, RNA structure
@article{nokey_66,
title = {RNA-protein interaction prediction without high-throughput data: An overview and benchmark of \textit{in silico} tools},
author = {Sarah Krautwurst and Kevin Lamkiewicz},
doi = {10.1016/j.csbj.2024.11.015},
issn = {2001-0370},
year = {2024},
date = {2024-11-08},
journal = {Computational and Structural Biotechnology Journal},
volume = {23},
pages = {4036-4046},
abstract = {RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.},
keywords = {ncRNAs, proteins, RNA / transcriptomics, RNA structure},
pubstate = {published},
tppubtype = {article}
}
RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.
Triebel, Sandra; Lamkiewicz, Kevin; Ontiveros, Nancy; Sweeney, Blake; Stadler, Peter F.; Petrov, Anton I.; Niepmann, Michael; Marz, Manja
Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus Journal Article
In: Scientific Reports, vol. 14, iss. 1, 2024.
Abstract | Links | BibTeX | Tags: evolution, ncRNAs, phylogenetics, RNA structure, RNA-RNA interactions, virus host interaction, viruses
@article{nokey_62,
title = {Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus},
author = {Sandra Triebel and Kevin Lamkiewicz and Nancy Ontiveros and Blake Sweeney and Peter F. Stadler and Anton I. Petrov and Michael Niepmann and Manja Marz},
doi = {10.1038/s41598-024-62897-0},
year = {2024},
date = {2024-07-02},
urldate = {2024-07-02},
journal = {Scientific Reports},
volume = {14},
issue = {1},
abstract = {Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which—by trial and error—comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.},
keywords = {evolution, ncRNAs, phylogenetics, RNA structure, RNA-RNA interactions, virus host interaction, viruses},
pubstate = {published},
tppubtype = {article}
}
Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which—by trial and error—comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.
Ren, Sijia; Bai, Feng; Stanko, Clara; Ritsch, Muriel; Schenk, Tino; Barth, Emanuel; Pei, Xin-Hai; Bierhoff, Holger
PAPAS Suppresses Breast Carcinogenesis by Promoting Differentiation of Mammary Epithelial Cells Journal Article
In: Cell Reports, 2024.
Abstract | Links | BibTeX | Tags: cancer, ncRNAs, RNA structure
@article{nokey_42,
title = {PAPAS Suppresses Breast Carcinogenesis by Promoting Differentiation of Mammary Epithelial Cells},
author = {Sijia Ren and Feng Bai and Clara Stanko and Muriel Ritsch and Tino Schenk and Emanuel Barth and Xin-Hai Pei and Holger Bierhoff
},
doi = {10.2139/ssrn.4436847},
year = {2024},
date = {2024-01-23},
urldate = {2023-05-23},
journal = {Cell Reports},
abstract = {Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoid breast cancer development. Here we show that lactogenic differentiation of murine MECs requires epigenetic silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and, as revealed by transcriptomics, immune evasion potential. Mechanistically, we show that PAPAS transcription depends on R-loop formation at the 3’ end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS, and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings.},
keywords = {cancer, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoid breast cancer development. Here we show that lactogenic differentiation of murine MECs requires epigenetic silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and, as revealed by transcriptomics, immune evasion potential. Mechanistically, we show that PAPAS transcription depends on R-loop formation at the 3’ end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS, and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings.
2022
Lamkiewicz, Kevin
2022.
Links | BibTeX | Tags: RNA structure, RNA-RNA interactions, viruses
@phdthesis{nokey_36,
title = {RNA secondary structures in RNA viruses: Why viruses would not exist without RNA secondary structures},
author = {Kevin Lamkiewicz},
url = {https://suche.thulb.uni-jena.de/Record/1811938531},
year = {2022},
date = {2022-07-13},
howpublished = {Friedrich-Schiller-Universität Jena},
keywords = {RNA structure, RNA-RNA interactions, viruses},
pubstate = {published},
tppubtype = {phdthesis}
}
2020
Jordan-Paiz, Ana; Nevot, Maria; Lamkiewicz, Kevin; Lataretu, Marie; Franco, Sandra; Marz, Manja; Martinez, Miguel Angel
HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer Journal Article
In: J Virol, vol. 94, no. 21, 2020.
Abstract | Links | BibTeX | Tags: proteins, RNA structure, splicing, viruses
@article{Jordan-Paiz:20,
title = {HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer},
author = {Ana Jordan-Paiz and Maria Nevot and Kevin Lamkiewicz and Marie Lataretu and Sandra Franco and Manja Marz and Miguel Angel Martinez},
doi = {10.1128/jvi.01108-20},
year = {2020},
date = {2020-10-14},
urldate = {2020-01-01},
journal = {J Virol},
volume = {94},
number = {21},
publisher = {American Society for Microbiology},
abstract = {Synonymous genome recoding has been widely used to study different aspects of virus biology. Codon usage affects the temporal regulation of viral gene expression. In this study, we performed synonymous codon mutagenesis to investigate whether codon usage affected HIV-1 Env protein expression and virus viability. We replaced the codons AGG, GAG, CCU, ACU, CUC, and GGG of the HIV-1 env gene with the synonymous codons CGU, GAA, CCG, ACG, UUA, and GGA, respectively. We found that recoding the Env protein gp120 coding region (excluding the Rev response element [RRE]) did not significantly affect virus replication capacity, even though we introduced 15 new CpG dinucleotides. In contrast, changing a single codon (AGG to CGU) located in the gp41 coding region (HXB2 env position 2125 to 2127), which was included in the intronic splicing silencer (ISS), completely abolished virus replication and Env expression. Computational analyses of this mutant revealed a severe disruption in the ISS RNA secondary structure. A variant that restored ISS secondary RNA structure also reestablished Env production and virus viability. Interestingly, this codon variant prevented both virus replication and Env translation in a eukaryotic expression system. These findings suggested that disrupting mRNA splicing was not the only means of inhibiting translation. Our findings indicated that synonymous gp120 recoding was not always deleterious to HIV-1 replication. Importantly¸ we found that disrupting an external ISS loop strongly affected HIV-1 replication and Env translation.
},
keywords = {proteins, RNA structure, splicing, viruses},
pubstate = {published},
tppubtype = {article}
}
Synonymous genome recoding has been widely used to study different aspects of virus biology. Codon usage affects the temporal regulation of viral gene expression. In this study, we performed synonymous codon mutagenesis to investigate whether codon usage affected HIV-1 Env protein expression and virus viability. We replaced the codons AGG, GAG, CCU, ACU, CUC, and GGG of the HIV-1 env gene with the synonymous codons CGU, GAA, CCG, ACG, UUA, and GGA, respectively. We found that recoding the Env protein gp120 coding region (excluding the Rev response element [RRE]) did not significantly affect virus replication capacity, even though we introduced 15 new CpG dinucleotides. In contrast, changing a single codon (AGG to CGU) located in the gp41 coding region (HXB2 env position 2125 to 2127), which was included in the intronic splicing silencer (ISS), completely abolished virus replication and Env expression. Computational analyses of this mutant revealed a severe disruption in the ISS RNA secondary structure. A variant that restored ISS secondary RNA structure also reestablished Env production and virus viability. Interestingly, this codon variant prevented both virus replication and Env translation in a eukaryotic expression system. These findings suggested that disrupting mRNA splicing was not the only means of inhibiting translation. Our findings indicated that synonymous gp120 recoding was not always deleterious to HIV-1 replication. Importantly¸ we found that disrupting an external ISS loop strongly affected HIV-1 replication and Env translation.
Gerresheim, Gesche K.; Hess, Carolin S.; Shalamova, Lyudmila A.; Fricke, Markus; Marz, Manja; Andreev, Dmitri E.; Shatsky, Ivan N.; Niepmann, Michael
Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication Journal Article
In: Int J Mol Sci, vol. 21, no. 18, pp. 6955, 2020.
Abstract | Links | BibTeX | Tags: cancer, liver, ncRNAs, RNA structure, viruses
@article{Gerresheim:20,
title = {Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication},
author = {Gesche K. Gerresheim and Carolin S. Hess and Lyudmila A. Shalamova and Markus Fricke and Manja Marz and Dmitri E. Andreev and Ivan N. Shatsky and Michael Niepmann},
doi = {10.3390/ijms21186955},
year = {2020},
date = {2020-09-22},
urldate = {2020-09-22},
journal = {Int J Mol Sci},
volume = {21},
number = {18},
pages = {6955},
publisher = {MDPI AG},
abstract = {Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3′-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in cis, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome.
},
keywords = {cancer, liver, ncRNAs, RNA structure, viruses},
pubstate = {published},
tppubtype = {article}
}
Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3′-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in cis, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome.
2019
Gerresheim, Gesche; Bathke, Jochen; Michel, Audrey; Andreev, Dmitri E.; Shalamova, Lyudmila; Rossbach, Oliver; Hu, Pan; Glebe, Dieter; Fricke, Markus; Marz, Manja; Goesmann, Alexander; Kiniry, Stephen; Baranov, Pavel; Shatsky, Ivan; Niepmann, Michael
Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling Journal Article
In: Int J Mol Sci, vol. 20, no. 6, pp. 1321, 2019.
Abstract | Links | BibTeX | Tags: cancer, differential expression analysis, liver, RNA structure, virus host interaction, viruses
@article{Gerresheim:19,
title = {Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling},
author = {Gesche Gerresheim and Jochen Bathke and Audrey Michel and Dmitri E. Andreev and Lyudmila Shalamova and Oliver Rossbach and Pan Hu and Dieter Glebe and Markus Fricke and Manja Marz and Alexander Goesmann and Stephen Kiniry and Pavel Baranov and Ivan Shatsky and Michael Niepmann},
doi = {10.3390/ijms20061321},
year = {2019},
date = {2019-03-15},
urldate = {2019-03-15},
journal = {Int J Mol Sci},
volume = {20},
number = {6},
pages = {1321},
publisher = {MDPI AG},
abstract = {Background: Hepatitis C virus (HCV) infects human liver hepatocytes, often leading to liver cirrhosis and hepatocellular carcinoma (HCC). It is believed that chronic infection alters host gene expression and favors HCC development. In particular, HCV replication in Endoplasmic Reticulum (ER) derived membranes induces chronic ER stress. How HCV replication affects host mRNA translation and transcription at a genome wide level is not yet known. Methods: We used Riboseq (Ribosome Profiling) to analyze transcriptome and translatome changes in the Huh-7.5 hepatocarcinoma cell line replicating HCV for 6 days. Results: Established viral replication does not cause global changes in host gene expression—only around 30 genes are significantly differentially expressed. Upregulated genes are related to ER stress and HCV replication, and several regulated genes are known to be involved in HCC development. Some mRNAs (PPP1R15A/GADD34, DDIT3/CHOP, and TRIB3) may be subject to upstream open reading frame (uORF) mediated translation control. Transcriptional downregulation mainly affects mitochondrial respiratory chain complex core subunit genes. Conclusion: After establishing HCV replication, the lack of global changes in cellular gene expression indicates an adaptation to chronic infection, while the downregulation of mitochondrial respiratory chain genes indicates how a virus may further contribute to cancer cell-like metabolic reprogramming (“Warburg effect”) even in the hepatocellular carcinoma cells used here. },
keywords = {cancer, differential expression analysis, liver, RNA structure, virus host interaction, viruses},
pubstate = {published},
tppubtype = {article}
}
Background: Hepatitis C virus (HCV) infects human liver hepatocytes, often leading to liver cirrhosis and hepatocellular carcinoma (HCC). It is believed that chronic infection alters host gene expression and favors HCC development. In particular, HCV replication in Endoplasmic Reticulum (ER) derived membranes induces chronic ER stress. How HCV replication affects host mRNA translation and transcription at a genome wide level is not yet known. Methods: We used Riboseq (Ribosome Profiling) to analyze transcriptome and translatome changes in the Huh-7.5 hepatocarcinoma cell line replicating HCV for 6 days. Results: Established viral replication does not cause global changes in host gene expression—only around 30 genes are significantly differentially expressed. Upregulated genes are related to ER stress and HCV replication, and several regulated genes are known to be involved in HCC development. Some mRNAs (PPP1R15A/GADD34, DDIT3/CHOP, and TRIB3) may be subject to upstream open reading frame (uORF) mediated translation control. Transcriptional downregulation mainly affects mitochondrial respiratory chain complex core subunit genes. Conclusion: After establishing HCV replication, the lack of global changes in cellular gene expression indicates an adaptation to chronic infection, while the downregulation of mitochondrial respiratory chain genes indicates how a virus may further contribute to cancer cell-like metabolic reprogramming (“Warburg effect”) even in the hepatocellular carcinoma cells used here.
2018
Desiro, Daniel; Hölzer, Martin; Ibrahim, Bashar; Marz, Manja
SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs Journal Article
In: Virus Res, vol. 260, pp. 135-141, 2018.
Abstract | Links | BibTeX | Tags: RNA structure, RNA-RNA interactions, software, viruses
@article{Desiro:18,
title = {SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs},
author = {Daniel Desiro and Martin Hölzer and Bashar Ibrahim and Manja Marz},
url = {https://github.com/desiro/silentMutations},
doi = {10.1016/j.virusres.2018.11.005},
year = {2018},
date = {2018-11-12},
urldate = {2018-11-12},
journal = {Virus Res},
volume = {260},
pages = {135-141},
abstract = {A single nucleotide change in the coding region can alter the amino acid sequence of a protein. In consequence, natural or artificial sequence changes in viral RNAs may have various effects not only on protein stability, function and structure but also on viral replication. In recent decades, several tools have been developed to predict the effect of mutations in structured RNAs such as viral genomes or non-coding RNAs. Some tools use multiple point mutations and also take coding regions into account. However, none of these tools was designed to specifically simulate the effect of mutations on viral long-range interactions. Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate disruptive and compensatory mutants of two interacting single-stranded RNAs. This allows a fast and accurate assessment of key regions potentially involved in functional long-range RNA-RNA interactions and will eventually help virologists and RNA-experts to design appropriate experiments. SIM only requires two interacting single-stranded RNA regions as input. The output is a plain text file containing the most promising mutants and a graphical representation of all interactions. We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. The source code and documentation of SIM are freely available at github.com/desiro/silentMutations.},
keywords = {RNA structure, RNA-RNA interactions, software, viruses},
pubstate = {published},
tppubtype = {article}
}
A single nucleotide change in the coding region can alter the amino acid sequence of a protein. In consequence, natural or artificial sequence changes in viral RNAs may have various effects not only on protein stability, function and structure but also on viral replication. In recent decades, several tools have been developed to predict the effect of mutations in structured RNAs such as viral genomes or non-coding RNAs. Some tools use multiple point mutations and also take coding regions into account. However, none of these tools was designed to specifically simulate the effect of mutations on viral long-range interactions. Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate disruptive and compensatory mutants of two interacting single-stranded RNAs. This allows a fast and accurate assessment of key regions potentially involved in functional long-range RNA-RNA interactions and will eventually help virologists and RNA-experts to design appropriate experiments. SIM only requires two interacting single-stranded RNA regions as input. The output is a plain text file containing the most promising mutants and a graphical representation of all interactions. We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. The source code and documentation of SIM are freely available at github.com/desiro/silentMutations.
Fricke, Markus; Gerst, Ruman; Ibrahim, Bashar; Niepmann, Michael; Marz, Manja
Global importance of RNA secondary structures in protein coding sequences Journal Article
In: Bioinformatics, vol. 35, no. 4, pp. 579–583, 2018.
Abstract | Links | BibTeX | Tags: evolution, RNA / transcriptomics, RNA structure, viruses
@article{Fricke:18,
title = {Global importance of RNA secondary structures in protein coding sequences},
author = {Markus Fricke and Ruman Gerst and Bashar Ibrahim and Michael Niepmann and Manja Marz},
doi = {10.1093/bioinformatics/bty678},
year = {2018},
date = {2018-08-07},
urldate = {2018-08-07},
journal = {Bioinformatics},
volume = {35},
number = {4},
pages = {579–583},
abstract = {The protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing. We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.},
keywords = {evolution, RNA / transcriptomics, RNA structure, viruses},
pubstate = {published},
tppubtype = {article}
}
The protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing. We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.
2017
Madhugiri, Ramakanth; Karl, Nadja; Petersen, Daniel; Lamkiewicz, Kevin; Fricke, Markus; Wend, Ulrike; Scheuer, Robina; Marz, Manja; Ziebuhr, John
Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions Journal Article
In: Virology, vol. 517, pp. 44–55, 2017.
Abstract | Links | BibTeX | Tags: coronavirus, phylogenetics, RNA / transcriptomics, RNA structure, viruses
@article{Madhugiri:18,
title = {Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions},
author = {Ramakanth Madhugiri and Nadja Karl and Daniel Petersen and Kevin Lamkiewicz and Markus Fricke and Ulrike Wend and Robina Scheuer and Manja Marz and John Ziebuhr},
doi = {10.1016/j.virol.2017.11.025},
year = {2017},
date = {2017-12-06},
urldate = {2017-12-06},
journal = {Virology},
volume = {517},
pages = {44--55},
abstract = {Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.},
keywords = {coronavirus, phylogenetics, RNA / transcriptomics, RNA structure, viruses},
pubstate = {published},
tppubtype = {article}
}
Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.
Hölzer, Martin; Marz, Manja
Software Dedicated to Virus Sequence Analysis Journal Article
In: Adv Virus Res, vol. 99, pp. 233–257, 2017.
Abstract | Links | BibTeX | Tags: DNA / genomics, evolution, phylogenetics, review, RNA / transcriptomics, RNA structure, software, viruses
@article{Hoelzer:17,
title = {Software Dedicated to Virus Sequence Analysis },
author = {Martin Hölzer and Manja Marz},
doi = {10.1016/bs.aivir.2017.08.004},
year = {2017},
date = {2017-09-28},
urldate = {2017-09-28},
journal = {Adv Virus Res},
volume = {99},
pages = {233--257},
abstract = {Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.},
keywords = {DNA / genomics, evolution, phylogenetics, review, RNA / transcriptomics, RNA structure, software, viruses},
pubstate = {published},
tppubtype = {article}
}
Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.
2016
Gerresheim, Gesche K; Dünnes, Nadia; Nieder-Röhrmann, Anika; Shalamova, Lyudmila A; Fricke, Markus; Hofacker, Ivo; zu Siederdissen, Christian Höner; Marz, Manja; Niepmann, Michael
In: Cell Mol Life Sci, vol. 74, pp. 747–760, 2016.
Abstract | Links | BibTeX | Tags: liver, ncRNAs, RNA / transcriptomics, RNA structure, viruses
@article{Gerresheim:17,
title = {microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure},
author = {Gesche K Gerresheim and Nadia Dünnes and Anika Nieder-Röhrmann and Lyudmila A Shalamova and Markus Fricke and Ivo Hofacker and Christian {Höner zu Siederdissen} and Manja Marz and Michael Niepmann},
doi = {10.1007/s00018-016-2377-9},
year = {2016},
date = {2016-09-27},
urldate = {2016-09-27},
journal = {Cell Mol Life Sci},
volume = {74},
pages = {747--760},
abstract = {We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3' untranslated region (3'UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites. This suggests that the dynamics of miRNA/Ago2 binding not only depends on the target site itself but also on flanking sequence context to a considerable extent, in particular in a small viral genome in which strong selection constraints act on coding sequence and overlapping cis-signals and model the accessibility of cis-signals. In full-length genomes, single and combination mutations in the miR-122 target sites reveal that site 5B.2 is positively involved in regulating overall genome replication efficiency, whereas mutation of site 5B.3 showed a weaker effect. Mutation of the 3'UTR site and double or triple mutants showed no significant overall effect on genome replication, whereas in a translation reporter RNA, the 3'UTR target site inhibits translation directed by the HCV 5'UTR. Thus, the miR-122 target sites in the 3'-region of the HCV genome are involved in a complex interplay in regulating different steps of the HCV replication cycle.},
keywords = {liver, ncRNAs, RNA / transcriptomics, RNA structure, viruses},
pubstate = {published},
tppubtype = {article}
}
We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3' untranslated region (3'UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites. This suggests that the dynamics of miRNA/Ago2 binding not only depends on the target site itself but also on flanking sequence context to a considerable extent, in particular in a small viral genome in which strong selection constraints act on coding sequence and overlapping cis-signals and model the accessibility of cis-signals. In full-length genomes, single and combination mutations in the miR-122 target sites reveal that site 5B.2 is positively involved in regulating overall genome replication efficiency, whereas mutation of site 5B.3 showed a weaker effect. Mutation of the 3'UTR site and double or triple mutants showed no significant overall effect on genome replication, whereas in a translation reporter RNA, the 3'UTR target site inhibits translation directed by the HCV 5'UTR. Thus, the miR-122 target sites in the 3'-region of the HCV genome are involved in a complex interplay in regulating different steps of the HCV replication cycle.
Madhugiri, Ramakanth; Fricke, Markus; Marz, Manja; Ziebuhr, John
Coronavirus cis-Acting RNA Elements Book Section
In: Coronaviruses, vol. 96, pp. 127–163, Elsevier, 2016.
Abstract | Links | BibTeX | Tags: coronavirus, RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses
@incollection{Madhugiri:16,
title = {Coronavirus cis-Acting RNA Elements},
author = {Ramakanth Madhugiri and Markus Fricke and Manja Marz and John Ziebuhr},
doi = {10.1016/bs.aivir.2016.08.007},
year = {2016},
date = {2016-09-06},
urldate = {2016-09-06},
booktitle = {Coronaviruses},
volume = {96},
pages = {127--163},
publisher = {Elsevier},
abstract = {Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5′- and 3′-terminal genome regions and upstream of the open reading frames located in the 3′-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA–RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.},
keywords = {coronavirus, RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses},
pubstate = {published},
tppubtype = {incollection}
}
Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5′- and 3′-terminal genome regions and upstream of the open reading frames located in the 3′-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA–RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.
Fricke, Markus; Marz, Manja
Prediction of conserved long-range RNA-RNA interactions in full viral genomes Journal Article
In: Bioinformatics, vol. 32, no. 19, pp. 2928–2935, 2016.
Abstract | Links | BibTeX | Tags: alignment, RNA / transcriptomics, RNA structure, RNA-RNA interactions, software, viruses
@article{Fricke:16,
title = {Prediction of conserved long-range RNA-RNA interactions in full viral genomes},
author = {Markus Fricke and Manja Marz},
url = {http://www.rna.uni-jena.de/en/supplements/lriscan/},
doi = {10.1093/bioinformatics/btw323},
year = {2016},
date = {2016-06-10},
urldate = {2016-06-10},
journal = {Bioinformatics},
volume = {32},
number = {19},
pages = {2928--2935},
abstract = {Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools. We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs. Source code and binaries of LRIscan freely available for download at http://www.rna.uni-jena.de/en/supplements/lriscan/, implemented in Ruby/C ++ and supported on Linux and Windows. manja@uni-jena.de Supplementary data are available at Bioinformatics online.},
keywords = {alignment, RNA / transcriptomics, RNA structure, RNA-RNA interactions, software, viruses},
pubstate = {published},
tppubtype = {article}
}
Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools. We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs. Source code and binaries of LRIscan freely available for download at http://www.rna.uni-jena.de/en/supplements/lriscan/, implemented in Ruby/C ++ and supported on Linux and Windows. manja@uni-jena.de Supplementary data are available at Bioinformatics online.
Fricke, Markus
2016.
Links | BibTeX | Tags: RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses
@phdthesis{Fricke2016,
title = {RNA structure analysis and conserved long-range RNA-RNA interaction prediction of full viral RNA genomes},
author = {Markus Fricke},
url = {https://suche.thulb.uni-jena.de/Record/865455945},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
howpublished = {Friedrich-Schiller-Universität Jena},
keywords = {RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses},
pubstate = {published},
tppubtype = {phdthesis}
}
2015
Fricke, Markus; Dünnes, Nadia; Zayas, Margarita; Bartenschlager, Ralf; Niepmann, Michael; Marz, Manja
Conserved RNA secondary structures and long-range interactions in hepatitis C viruses Journal Article
In: RNA, vol. 21, pp. 1219–1232, 2015.
Abstract | Links | BibTeX | Tags: alignment, RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses
@article{Fricke:15,
title = {Conserved RNA secondary structures and long-range interactions in hepatitis C viruses},
author = {Markus Fricke and Nadia Dünnes and Margarita Zayas and Ralf Bartenschlager and Michael Niepmann and Manja Marz},
doi = {10.1261/rna.049338.114},
year = {2015},
date = {2015-05-11},
urldate = {2015-05-11},
journal = {RNA},
volume = {21},
pages = {1219--1232},
abstract = {Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.},
keywords = {alignment, RNA / transcriptomics, RNA structure, RNA-RNA interactions, viruses},
pubstate = {published},
tppubtype = {article}
}
Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.
2014
Wehner, Stefanie; Damm, Katrin; Hartmann, Roland K; Marz, Manja
Dissemination of 6S RNA among bacteria Journal Article
In: RNA Biol, vol. 11, pp. 1467–1478, 2014.
Abstract | Links | BibTeX | Tags: assembly, bacteria, ncRNAs, RNA / transcriptomics, RNA structure
@article{Wehner:14,
title = {Dissemination of 6S RNA among bacteria},
author = {Stefanie Wehner and Katrin Damm and Roland K Hartmann and Manja Marz},
doi = {10.4161/rna.29894},
year = {2014},
date = {2014-10-31},
urldate = {2014-10-31},
journal = {RNA Biol},
volume = {11},
pages = {1467--1478},
abstract = {6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.},
keywords = {assembly, bacteria, ncRNAs, RNA / transcriptomics, RNA structure},
pubstate = {published},
tppubtype = {article}
}
6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.
Madhugiri, Ramakanth; Fricke, Markus; Marz, Manja; Ziebuhr, John
RNA structure analysis of alphacoronavirus terminal genome regions Journal Article
In: Virus Res, vol. 194, pp. 76–89, 2014.
Abstract | Links | BibTeX | Tags: classification, coronavirus, evolution, RNA / transcriptomics, RNA structure, viruses
@article{Madhugiri:14,
title = {RNA structure analysis of alphacoronavirus terminal genome regions},
author = {Ramakanth Madhugiri and Markus Fricke and Manja Marz and John Ziebuhr},
doi = {10.1016/j.virusres.2014.10.001},
year = {2014},
date = {2014-10-13},
urldate = {2014-10-13},
journal = {Virus Res},
volume = {194},
pages = {76--89},
abstract = {Coronavirus genome replication is mediated by a multi-subunit protein complex that is comprised of more than a dozen virally encoded and several cellular proteins. Interactions of the viral replicase complex with cis-acting RNA elements located in the 5' and 3'-terminal genome regions ensure the specific replication of viral RNA. Over the past years, boundaries and structures of cis-acting RNA elements required for coronavirus genome replication have been extensively characterized in betacoronaviruses and, to a lesser extent, other coronavirus genera. Here, we review our current understanding of coronavirus cis-acting elements located in the terminal genome regions and use a combination of bioinformatic and RNA structure probing studies to identify and characterize putative cis-acting RNA elements in alphacoronaviruses. The study suggests significant RNA structure conservation among members of the genus Alphacoronavirus but also across genus boundaries. Overall, the conservation pattern identified for 5' and 3'-terminal RNA structural elements in the genomes of alpha- and betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements.},
keywords = {classification, coronavirus, evolution, RNA / transcriptomics, RNA structure, viruses},
pubstate = {published},
tppubtype = {article}
}
Coronavirus genome replication is mediated by a multi-subunit protein complex that is comprised of more than a dozen virally encoded and several cellular proteins. Interactions of the viral replicase complex with cis-acting RNA elements located in the 5' and 3'-terminal genome regions ensure the specific replication of viral RNA. Over the past years, boundaries and structures of cis-acting RNA elements required for coronavirus genome replication have been extensively characterized in betacoronaviruses and, to a lesser extent, other coronavirus genera. Here, we review our current understanding of coronavirus cis-acting elements located in the terminal genome regions and use a combination of bioinformatic and RNA structure probing studies to identify and characterize putative cis-acting RNA elements in alphacoronaviruses. The study suggests significant RNA structure conservation among members of the genus Alphacoronavirus but also across genus boundaries. Overall, the conservation pattern identified for 5' and 3'-terminal RNA structural elements in the genomes of alpha- and betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements.
Qin, Jing; Fricke, Markus; Marz, Manja; Stadler, Peter F; Backofen, Rolf
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures Journal Article
In: Algorithms Mol Biol, vol. 9, pp. 19, 2014.
Abstract | Links | BibTeX | Tags: RNA / transcriptomics, RNA structure, software, splicing, viruses
@article{Qin:14,
title = {Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures},
author = {Jing Qin and Markus Fricke and Manja Marz and Peter F Stadler and Rolf Backofen},
url = {http://www.rna.uni-jena.de/RNAgraphdist.html},
doi = {10.1186/1748-7188-9-19},
year = {2014},
date = {2014-09-11},
urldate = {2014-09-11},
journal = {Algorithms Mol Biol},
volume = {9},
pages = {19},
abstract = {Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between a fixed pair of nucleotides can be computed in polynomial time by means of dynamic programming. While a naïve implementation would yield recursions with a very high time complexity of O(n (6) D (5)) for sequence length n and D distinct distance values, it is possible to reduce this to O(n (4)) for practical applications in which predominantly small distances are of of interest. Further reductions, however, seem to be difficult. Therefore, we introduced sampling approaches that are much easier to implement. They are also theoretically favorable for several real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. The graph-distance distribution can be computed using a dynamic programming approach. Although a crude approximation of reality, our initial results indicate that the graph-distance can be related to the smFRET data. The additional file and the software of our paper are available from http://www.rna.uni-jena.de/RNAgraphdist.html.},
keywords = {RNA / transcriptomics, RNA structure, software, splicing, viruses},
pubstate = {published},
tppubtype = {article}
}
Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between a fixed pair of nucleotides can be computed in polynomial time by means of dynamic programming. While a naïve implementation would yield recursions with a very high time complexity of O(n (6) D (5)) for sequence length n and D distinct distance values, it is possible to reduce this to O(n (4)) for practical applications in which predominantly small distances are of of interest. Further reductions, however, seem to be difficult. Therefore, we introduced sampling approaches that are much easier to implement. They are also theoretically favorable for several real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. The graph-distance distribution can be computed using a dynamic programming approach. Although a crude approximation of reality, our initial results indicate that the graph-distance can be related to the smFRET data. The additional file and the software of our paper are available from http://www.rna.uni-jena.de/RNAgraphdist.html.
2013
Wehner, Stefanie; Dörrich, Anja K; Ciba, Philipp; Wilde, Annegret; Marz, Manja
pRNA: NoRC-associated RNA of rRNA operons Journal Article
In: RNA Biol, vol. 11, pp. 3–9, 2013.
Abstract | Links | BibTeX | Tags: alignment, assembly, ncRNAs, RNA / transcriptomics, RNA structure
@article{Wehner:14b,
title = {pRNA: NoRC-associated RNA of rRNA operons},
author = {Stefanie Wehner and Anja K Dörrich and Philipp Ciba and Annegret Wilde and Manja Marz},
doi = {10.4161/rna.27448},
year = {2013},
date = {2013-12-20},
urldate = {2013-12-20},
journal = {RNA Biol},
volume = {11},
pages = {3--9},
abstract = {Promoter-associated RNAs (pRNAs) are a family of ~90-100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon. pRNA transcripts interact with TIP5, a component of the chromatin remodeling complex NoRC, which recruits enzymes for heterochromatin formation and mediates silencing of rRNA genes. Here we present a comprehensive analysis of pRNA homologs, including different versions per species, as result of in silico studies in available metazoan genome assemblies. Comparative sequence analysis and secondary structure prediction ended up in two possible secondary structures, which let us assume a possible dual function of pRNAs for regulation of rRNA operons. Furthermore, we validated parts of our computational predictions experimentally by RT-PCR and sequencing. A representative seed alignment of the pRNA family, annotated with possible secondary structures was released to the Rfam database.},
keywords = {alignment, assembly, ncRNAs, RNA / transcriptomics, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Promoter-associated RNAs (pRNAs) are a family of ~90-100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon. pRNA transcripts interact with TIP5, a component of the chromatin remodeling complex NoRC, which recruits enzymes for heterochromatin formation and mediates silencing of rRNA genes. Here we present a comprehensive analysis of pRNA homologs, including different versions per species, as result of in silico studies in available metazoan genome assemblies. Comparative sequence analysis and secondary structure prediction ended up in two possible secondary structures, which let us assume a possible dual function of pRNAs for regulation of rRNA operons. Furthermore, we validated parts of our computational predictions experimentally by RT-PCR and sequencing. A representative seed alignment of the pRNA family, annotated with possible secondary structures was released to the Rfam database.
Vierna, Joaquin; Wehner, Stefanie; zu Siederdissen, Christian Höner; Martínez-Lage, Andrés; Marz, Manja
Systematic analysis and evolution of 5S ribosomal DNA in metazoans Journal Article
In: Heredity, vol. 111, pp. 410–421, 2013.
Abstract | Links | BibTeX | Tags: DNA / genomics, evolution, ncRNAs, RNA structure
@article{Vierna:13,
title = {Systematic analysis and evolution of 5S ribosomal DNA in metazoans},
author = {Joaquin Vierna and Stefanie Wehner and Christian {Höner zu Siederdissen} and Andrés Martínez-Lage and Manja Marz},
doi = {10.1038/hdy.2013.63},
year = {2013},
date = {2013-07-10},
urldate = {2013-07-10},
journal = {Heredity},
volume = {111},
pages = {410--421},
abstract = {Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12,766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.},
keywords = {DNA / genomics, evolution, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12,766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.
Backofen, Rolf; Fricke, Markus; Marz, Manja; Qin, Jing; Stadler, Peter F
Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures Proceedings Article
In: International Workshop on Algorithms in Bioinformatics, pp. 112–125, 2013, (published in Algorithms Mol Biol: https://dx.doi.org/10.1186/1748-7188-9-19).
BibTeX | Tags: RNA / transcriptomics, RNA structure, software
@inproceedings{Backofen:13,
title = {Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures},
author = {Rolf Backofen and Markus Fricke and Manja Marz and Jing Qin and Peter F Stadler},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
booktitle = {International Workshop on Algorithms in Bioinformatics},
pages = {112--125},
note = {published in Algorithms Mol Biol: https://dx.doi.org/10.1186/1748-7188-9-19},
keywords = {RNA / transcriptomics, RNA structure, software},
pubstate = {published},
tppubtype = {inproceedings}
}
Wieseke, Nicolas; Lechner, Marcus; Ludwig, Marcus; Marz, Manja
POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria Proceedings Article
In: Cai, Zhipeng; Eulenstein, Oliver; Janies, Daniel; Schwartz, Daniel (Ed.): Proceedings of the 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC, USA, May 20-22, 2013., pp. pp 249-260, Springer, 2013.
Abstract | Links | BibTeX | Tags: alignment, bacteria, phylogenetics, RNA structure, software
@inproceedings{Wieseke:13,
title = {POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria},
author = {Nicolas Wieseke and Marcus Lechner and Marcus Ludwig and Manja Marz},
editor = {Zhipeng Cai and Oliver Eulenstein and Daniel Janies and Daniel Schwartz},
url = {http://www.rna.uni-jena.de/supplements/pomago},
doi = {10.1007/978-3-642-38036-5_25},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
booktitle = {Proceedings of the 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC, USA, May 20-22, 2013.},
volume = {7875},
number = {1},
pages = {pp 249-260},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
abstract = {Multiple Genome-wide Alignments are a first crucial step to compare genomes. Gain and loss of genes, duplications and genomic rearrangements are challenging problems that aggravate with increasing phylogenetic distances. We describe a multiple genome-wide alignment tool for bacteria, called POMAGO, which is based on orthologous genes and their syntenic information determined by Proteinortho.This strategy enables POMAGO to efficiently define anchor points even across wide phylogenetic distances and outperform existing approaches in this field of application. The given set of orthologous genes is enhanced by several cleaning and completion steps, including the addition of previously undetected orthologous genes. Protein-coding genes are aligned on nucleotide and protein level, whereas intergenic regions are aligned on nucleotide level only. We tested and compared our program at three very different sets of bacteria that exhibit different degrees of phylogenetic distances: 1) 15 closely related, well examined and described E. coli species, 2) six more divergent Aquificales, as putative basal bacteria, and 3) a set of eight extreme divergent species, distributed among the whole phylogenetic tree of bacteria. POMAGO is written in a modular way which allows extending or even exchanging algorithms in different stages of the alignment process. Intergenic regions might for instance be aligned using an RNA secondary structure aware algorithm rather than to rely on sequence data alone. The software is freely available from
},
keywords = {alignment, bacteria, phylogenetics, RNA structure, software},
pubstate = {published},
tppubtype = {inproceedings}
}
Multiple Genome-wide Alignments are a first crucial step to compare genomes. Gain and loss of genes, duplications and genomic rearrangements are challenging problems that aggravate with increasing phylogenetic distances. We describe a multiple genome-wide alignment tool for bacteria, called POMAGO, which is based on orthologous genes and their syntenic information determined by Proteinortho.This strategy enables POMAGO to efficiently define anchor points even across wide phylogenetic distances and outperform existing approaches in this field of application. The given set of orthologous genes is enhanced by several cleaning and completion steps, including the addition of previously undetected orthologous genes. Protein-coding genes are aligned on nucleotide and protein level, whereas intergenic regions are aligned on nucleotide level only. We tested and compared our program at three very different sets of bacteria that exhibit different degrees of phylogenetic distances: 1) 15 closely related, well examined and described E. coli species, 2) six more divergent Aquificales, as putative basal bacteria, and 3) a set of eight extreme divergent species, distributed among the whole phylogenetic tree of bacteria. POMAGO is written in a modular way which allows extending or even exchanging algorithms in different stages of the alignment process. Intergenic regions might for instance be aligned using an RNA secondary structure aware algorithm rather than to rely on sequence data alone. The software is freely available from
2011
Marz, Manja; Gruber, Andreas R.; zu Siederdissen, Christian Höner; Amman, Fabian; Badelt, Stefan; Bartschat, Sebastian; Bernhart, Stephan H.; Beyer, Wolfgang; Kehr, Stephanie; Lorenz, Ronny; Tanzer, Andrea; Yusuf, Dilmurat; Tafer, Hakim; Hofacker, Ivo L.; Stadler, Peter F.
Animal snoRNAs and scaRNAs with exceptional structures Journal Article
In: RNA Biol, vol. 8, pp. 938–946, 2011.
Abstract | Links | BibTeX | Tags: alignment, ncRNAs, RNA / transcriptomics, RNA structure
@article{Marz:11,
title = {Animal snoRNAs and scaRNAs with exceptional structures},
author = {Manja Marz and Andreas R. Gruber and Christian {Höner zu Siederdissen} and Fabian Amman and Stefan Badelt and Sebastian Bartschat and Stephan H. Bernhart and Wolfgang Beyer and Stephanie Kehr and Ronny Lorenz and Andrea Tanzer and Dilmurat Yusuf and Hakim Tafer and Ivo L. Hofacker and Peter F. Stadler},
doi = {10.4161/rna.8.6.16603},
year = {2011},
date = {2011-11-01},
urldate = {2011-11-01},
journal = {RNA Biol},
volume = {8},
pages = {938--946},
abstract = {The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.},
keywords = {alignment, ncRNAs, RNA / transcriptomics, RNA structure},
pubstate = {published},
tppubtype = {article}
}
The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.
Marz, Manja; Stadler, Peter F
RNA interactions Book Section
In: RNA Infrastructure and Networks, vol. 722, pp. 20–38, Springer, New York, NY, 2011.
Abstract | Links | BibTeX | Tags: ncRNAs, RNA structure
@incollection{Marz:11a,
title = {RNA interactions},
author = {Manja Marz and Peter F Stadler},
doi = {10.1007/978-1-4614-0332-6_2},
year = {2011},
date = {2011-01-01},
urldate = {2011-01-01},
booktitle = {RNA Infrastructure and Networks},
volume = {722},
pages = {20--38},
publisher = {Springer, New York, NY},
series = {Advances in Experimental Medicine and Biology},
abstract = {Noncoding RNAs form an indispensible component of the cellular information processing networks, a role that crucially depends on the specificity of their interactions among each other as well as with DNA and protein. Patterns of intramolecular and intermolecular base pairs govern most RNA interactions. Specific base pairs dominate the structure formation of nucleic acids. Only little details distinguish intramolecular secondary structures from those cofolding molecules. RNA-protein interactions, on the other hand, are strongly dependent on the RNA structure as well since the sequence content of helical regions is largely unreadable, so that sequence specificity is mostly restricted to unpaired loop regions. Conservation of both sequence and structure thus this can give indications of the functioning of the diversity of ncRNAs.},
keywords = {ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {incollection}
}
Noncoding RNAs form an indispensible component of the cellular information processing networks, a role that crucially depends on the specificity of their interactions among each other as well as with DNA and protein. Patterns of intramolecular and intermolecular base pairs govern most RNA interactions. Specific base pairs dominate the structure formation of nucleic acids. Only little details distinguish intramolecular secondary structures from those cofolding molecules. RNA-protein interactions, on the other hand, are strongly dependent on the RNA structure as well since the sequence content of helical regions is largely unreadable, so that sequence specificity is mostly restricted to unpaired loop regions. Conservation of both sequence and structure thus this can give indications of the functioning of the diversity of ncRNAs.
Li, Andrew X; Marz, Manja; Qin, Jing; Reidys, Christian M
RNA-RNA interaction prediction based on multiple sequence alignments Journal Article
In: Bioinformatics, vol. 27, pp. 456–463, 2011.
Abstract | Links | BibTeX | Tags: alignment, evolution, RNA structure, RNA-RNA interactions
@article{Li:11,
title = {RNA-RNA interaction prediction based on multiple sequence alignments},
author = {Andrew X Li and Manja Marz and Jing Qin and Christian M Reidys},
url = {http://www.combinatorics.cn/cbpc/ripalign.html},
doi = {10.1093/bioinformatics/btq659},
year = {2011},
date = {2011-01-01},
urldate = {2011-01-01},
journal = {Bioinformatics},
volume = {27},
pages = {456--463},
abstract = {Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, O(N(6)) time and O(N(4)) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both: thermodynamic stability as well as sequence/structure covariation. We present the a priori folding algorithm ripalign, whose input consists of two (given) multiple sequence alignments (MSA). ripalign outputs (i) the partition function, (ii) base pairing probabilities, (iii) hybrid probabilities and (iv) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm rip, ripalign requires negligible additional memory resource but offers much better sensitivity and specificity, once alignments of suitable quality are given. ripalign additionally allows to incorporate structure constraints as input parameters. The algorithm described here is implemented in C as part of the rip package.},
keywords = {alignment, evolution, RNA structure, RNA-RNA interactions},
pubstate = {published},
tppubtype = {article}
}
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, O(N(6)) time and O(N(4)) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both: thermodynamic stability as well as sequence/structure covariation. We present the a priori folding algorithm ripalign, whose input consists of two (given) multiple sequence alignments (MSA). ripalign outputs (i) the partition function, (ii) base pairing probabilities, (iii) hybrid probabilities and (iv) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm rip, ripalign requires negligible additional memory resource but offers much better sensitivity and specificity, once alignments of suitable quality are given. ripalign additionally allows to incorporate structure constraints as input parameters. The algorithm described here is implemented in C as part of the rip package.
2010
Marz, Manja; Vanzo, Nathalie; Stadler, Peter F
Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history Journal Article
In: J Bioinform Comput Biol, vol. 8, no. 1, pp. 1–17, 2010.
Abstract | Links | BibTeX | Tags: evolution, RNA structure, splicing
@article{Marz:10,
title = {Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history},
author = {Manja Marz and Nathalie Vanzo and Peter F Stadler},
doi = {10.1142/S0219720010004525},
year = {2010},
date = {2010-09-14},
urldate = {2010-01-01},
journal = {J Bioinform Comput Biol},
volume = {8},
number = {1},
pages = {1--17},
abstract = {The structures attained by RNA molecules depend not only on their sequence but also on environmental parameters such as their temperature. So far, this effect has been largely neglected in bioinformatics studies. Here, we show that structural comparisons can be facilitated and more coherent structural models can be obtained when differences in environmental parameters are taken into account. We re-evaluate the secondary structures of the spliced leader (SL) RNAs from the seven eukaryotic phyla in which SL RNA trans-splicing has been described. Adjusting structure prediction to the natural growth temperatures and considering energetically similar secondary structures, we observe striking similarities among Euglenida, Kinetoplastida, Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and Tunicata that cannot be explained easily by the independent innovation of SL RNAs in each of these phyla. Supplementary Table is available at http://www.worldscinet.com/jbcb/.},
keywords = {evolution, RNA structure, splicing},
pubstate = {published},
tppubtype = {article}
}
The structures attained by RNA molecules depend not only on their sequence but also on environmental parameters such as their temperature. So far, this effect has been largely neglected in bioinformatics studies. Here, we show that structural comparisons can be facilitated and more coherent structural models can be obtained when differences in environmental parameters are taken into account. We re-evaluate the secondary structures of the spliced leader (SL) RNAs from the seven eukaryotic phyla in which SL RNA trans-splicing has been described. Adjusting structure prediction to the natural growth temperatures and considering energetically similar secondary structures, we observe striking similarities among Euglenida, Kinetoplastida, Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and Tunicata that cannot be explained easily by the independent innovation of SL RNAs in each of these phyla. Supplementary Table is available at http://www.worldscinet.com/jbcb/.
2009
Marz, Manja; Stadler, Peter F
Comparative analysis of eukaryotic U3 snoRNA Journal Article
In: RNA Biol, vol. 6, pp. 503–507, 2009.
Abstract | Links | BibTeX | Tags: ncRNAs, RNA structure
@article{Marz:09a,
title = {Comparative analysis of eukaryotic U3 snoRNA},
author = {Manja Marz and Peter F Stadler},
doi = {10.4161/rna.6.5.9607},
year = {2009},
date = {2009-11-01},
urldate = {2009-11-01},
journal = {RNA Biol},
volume = {6},
pages = {503--507},
abstract = {The U3 snoRNA is an exceptional box C/D snoRNA, which is involved in pre-rRNA processing without directing chemical modifications. We report here on a comprehensive computational survey resulting in U3 sequences for more than 90 additional eukaryotes. This extended data basis is used to improve the secondary structure models. The detailed investigation of the structural variation of U3 snoRNAs turns out to be much more extensive than previously thought. Many fungal U3 genes, in addition, contain introns. U3 promoters are snRNA-like but show substantial variations even between related species.},
keywords = {ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
The U3 snoRNA is an exceptional box C/D snoRNA, which is involved in pre-rRNA processing without directing chemical modifications. We report here on a comprehensive computational survey resulting in U3 sequences for more than 90 additional eukaryotes. This extended data basis is used to improve the secondary structure models. The detailed investigation of the structural variation of U3 snoRNAs turns out to be much more extensive than previously thought. Many fungal U3 genes, in addition, contain introns. U3 promoters are snRNA-like but show substantial variations even between related species.
Copeland, Claudia S.; Marz, Manja; Rose, Dominic; Hertel, Jana; Brindley, Paul J.; Santana, Clara Bermudez; Kehr, Stephanie; Attolini, Camille Stephan-Otto; Stadler, Peter F.
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum Journal Article
In: BMC Genomics, vol. 10, pp. 464, 2009.
Abstract | Links | BibTeX | Tags: annotation, ncRNAs, RNA structure
@article{Copeland:09,
title = {Homology-based annotation of non-coding RNAs in the genomes of \textit{Schistosoma mansoni} and \textit{Schistosoma japonicum}},
author = {Claudia S. Copeland and Manja Marz and Dominic Rose and Jana Hertel and Paul J. Brindley and Clara Bermudez Santana and Stephanie Kehr and Camille Stephan-Otto Attolini and Peter F. Stadler},
doi = {10.1186/1471-2164-10-464},
year = {2009},
date = {2009-10-08},
urldate = {2009-10-08},
journal = {BMC Genomics},
volume = {10},
pages = {464},
abstract = {Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.},
keywords = {annotation, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.
Marz, Manja; Donath, Alexander; Verstraete, Nina; Nguyen, Van Trung; Stadler, Peter F; Bensaude, Olivier
Evolution of 7SK RNA and its protein partners in metazoa Journal Article
In: Mol Biol Evol, vol. 26, no. 12, pp. 2821–2830, 2009.
Abstract | Links | BibTeX | Tags: evolution, ncRNAs, proteins, RNA structure
@article{Marz:09,
title = {Evolution of 7SK RNA and its protein partners in metazoa},
author = {Manja Marz and Alexander Donath and Nina Verstraete and Van Trung Nguyen and Peter F Stadler and Olivier Bensaude},
doi = {10.1093/molbev/msp198},
year = {2009},
date = {2009-09-04},
urldate = {2009-09-04},
journal = {Mol Biol Evol},
volume = {26},
number = {12},
pages = {2821--2830},
abstract = {7SK RNA is a key player in the regulation of polymerase II transcription. 7SK RNA was considered as a highly conserved vertebrate innovation. The discovery of poorly conserved homologs in several insects and lophotrochozoans, however, implies a much earlier evolutionary origin. The mechanism of 7SK function requires interaction with the proteins HEXIM and La-related protein 7. Here, we present a comprehensive computational analysis of these two proteins in metazoa, and we extend the collection of 7SK RNAs by several additional candidates. In particular, we describe 7SK homologs in Caenorhabditis species. Furthermore, we derive an improved secondary structure model of 7SK RNA, which shows that the structure is quite well-conserved across animal phyla despite the extreme divergence at sequence level.},
keywords = {evolution, ncRNAs, proteins, RNA structure},
pubstate = {published},
tppubtype = {article}
}
7SK RNA is a key player in the regulation of polymerase II transcription. 7SK RNA was considered as a highly conserved vertebrate innovation. The discovery of poorly conserved homologs in several insects and lophotrochozoans, however, implies a much earlier evolutionary origin. The mechanism of 7SK function requires interaction with the proteins HEXIM and La-related protein 7. Here, we present a comprehensive computational analysis of these two proteins in metazoa, and we extend the collection of 7SK RNAs by several additional candidates. In particular, we describe 7SK homologs in Caenorhabditis species. Furthermore, we derive an improved secondary structure model of 7SK RNA, which shows that the structure is quite well-conserved across animal phyla despite the extreme divergence at sequence level.
Hiller, Michael; Findeiss, Sven; Lein, Sandro; Marz, Manja; Nickel, Claudia; Rose, Dominic; Schulz, Christine; Backofen, Rolf; Prohaska, Sonja J; Reuter, Gunter; Stadler, Peter F
Conserved introns reveal novel transcripts in Drosophila melanogaster Journal Article
In: Genome Res, vol. 19, pp. 1289–1300, 2009.
Abstract | Links | BibTeX | Tags: insects, ncRNAs, RNA structure
@article{Hiller:09,
title = {Conserved introns reveal novel transcripts in \textit{Drosophila melanogaster}},
author = {Michael Hiller and Sven Findeiss and Sandro Lein and Manja Marz and Claudia Nickel and Dominic Rose and Christine Schulz and Rolf Backofen and Sonja J Prohaska and Gunter Reuter and Peter F Stadler},
doi = {10.1101/gr.090050.108},
year = {2009},
date = {2009-05-20},
urldate = {2009-05-20},
journal = {Genome Res},
volume = {19},
pages = {1289--1300},
abstract = {Noncoding RNAs that are-like mRNAs-spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is incomplete even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach searching for short conserved introns is capable of identifying conserved transcripts with a high specificity. Our approach requires neither an open reading frame nor substantial sequence or secondary structure conservation in the surrounding exons. Thus it identifies spliced transcripts in an unbiased way. After applying our approach to insect genomes, we predict 369 introns outside annotated coding transcripts, of which 131 are confirmed by expressed sequence tags (ESTs) and/or noncoding FlyBase transcripts. Of the remaining 238 novel introns, about half are associated with protein-coding genes-either extending coding or untranslated regions or likely belonging to unannotated coding genes. The remaining 129 introns belong to novel mlncRNAs that are largely unstructured. Using RT-PCR, we verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes. The expression level of all verified mlncRNA transcripts is low but varies during development, which suggests regulation. As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts.},
keywords = {insects, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Noncoding RNAs that are-like mRNAs-spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is incomplete even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach searching for short conserved introns is capable of identifying conserved transcripts with a high specificity. Our approach requires neither an open reading frame nor substantial sequence or secondary structure conservation in the surrounding exons. Thus it identifies spliced transcripts in an unbiased way. After applying our approach to insect genomes, we predict 369 introns outside annotated coding transcripts, of which 131 are confirmed by expressed sequence tags (ESTs) and/or noncoding FlyBase transcripts. Of the remaining 238 novel introns, about half are associated with protein-coding genes-either extending coding or untranslated regions or likely belonging to unannotated coding genes. The remaining 129 introns belong to novel mlncRNAs that are largely unstructured. Using RT-PCR, we verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes. The expression level of all verified mlncRNA transcripts is low but varies during development, which suggests regulation. As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts.
Jones, Thomas A; Otto, Wolfgang; Marz, Manja; Eddy, Sean R; Stadler, Peter F
A survey of nematode SmY RNAs Journal Article
In: RNA Biol, vol. 6, pp. 5–8, 2009.
Abstract | Links | BibTeX | Tags: alignment, ncRNAs, RNA / transcriptomics, RNA structure, splicing
@article{Jones:09,
title = {A survey of nematode SmY RNAs},
author = {Thomas A Jones and Wolfgang Otto and Manja Marz and Sean R Eddy and Peter F Stadler},
doi = {10.4161/rna.6.1.7634},
year = {2009},
date = {2009-01-01},
urldate = {2009-01-01},
journal = {RNA Biol},
volume = {6},
pages = {5--8},
abstract = {SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.},
keywords = {alignment, ncRNAs, RNA / transcriptomics, RNA structure, splicing},
pubstate = {published},
tppubtype = {article}
}
SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.
2008
Marz, Manja; Kirsten, Toralf; Stadler, Peter F
Evolution of spliceosomal snRNA genes in metazoan animals Journal Article
In: J Mol Evol, vol. 67, pp. 594–607, 2008.
Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure, splicing
@article{Marz:08,
title = {Evolution of spliceosomal snRNA genes in metazoan animals},
author = {Manja Marz and Toralf Kirsten and Peter F Stadler},
doi = {10.1007/s00239-008-9149-6},
year = {2008},
date = {2008-11-22},
urldate = {2008-11-22},
journal = {J Mol Evol},
volume = {67},
pages = {594--607},
abstract = {While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.},
keywords = {evolution, insects, ncRNAs, RNA structure, splicing},
pubstate = {published},
tppubtype = {article}
}
While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.
Marz, Manja; Mosig, Axel; Stadler, Bärbel M R; Stadler, Peter F
U7 snRNAs: a computational survey Journal Article
In: Genomics Proteomics Bioinformatics, vol. 5, no. 3-4, pp. 187–195, 2008.
Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure
@article{Marz:07,
title = {U7 snRNAs: a computational survey},
author = {Manja Marz and Axel Mosig and Bärbel M R Stadler and Peter F Stadler},
doi = {10.1016/S1672-0229(08)60006-6},
year = {2008},
date = {2008-02-08},
urldate = {2008-02-08},
journal = {Genomics Proteomics Bioinformatics},
volume = {5},
number = {3-4},
pages = {187--195},
abstract = {U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.},
keywords = {evolution, insects, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.
2007
Washietl, Stefan; Pedersen, Jakob S; Korbel, Jan O; Stocsits, Claudia; Gruber, Andreas R; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Reiche, Kristin; Tanzer, Andrea; Ucla, Catherine; Wyss, Carine; Antonarakis, Stylianos E; Denoeud, France; Lagarde, Julien; Drenkow, Jorg; Kapranov, Philipp; Gingeras, Thomas R; Guigó, Roderic; Snyder, Michael; Gerstein, Mark B; Reymond, Alexandre; Hofacker, Ivo L; Stadler, Peter F
Structured RNAs in the ENCODE selected regions of the human genome Journal Article
In: Genome Res, vol. 17, pp. 852–864, 2007.
Abstract | Links | BibTeX | Tags: annotation, evolution, ncRNAs, RNA structure
@article{Washietl:07,
title = {Structured RNAs in the ENCODE selected regions of the human genome},
author = {Stefan Washietl and Jakob S Pedersen and Jan O Korbel and Claudia Stocsits and Andreas R Gruber and Jörg Hackermüller and Jana Hertel and Manja Lindemeyer and Kristin Reiche and Andrea Tanzer and Catherine Ucla and Carine Wyss and Stylianos E Antonarakis and France Denoeud and Julien Lagarde and Jorg Drenkow and Philipp Kapranov and Thomas R Gingeras and Roderic Guigó and Michael Snyder and Mark B Gerstein and Alexandre Reymond and Ivo L Hofacker and Peter F Stadler},
url = {https://www.tbi.univie.ac.at/papers/SUPPLEMENTS/ENCODE/},
doi = {10.1101/gr.5650707},
year = {2007},
date = {2007-01-01},
urldate = {2007-01-01},
journal = {Genome Res},
volume = {17},
pages = {852--864},
abstract = {Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).},
keywords = {annotation, evolution, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).