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.
Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian
RNAcentral: A vision for an international database of RNA sequences Journal Article
In: RNA, vol. 17, pp. 1941–1946, 2011.
Abstract | Links | BibTeX | Tags: database, ncRNAs, RNA / transcriptomics
@article{Bateman:11,
title = {RNAcentral: A vision for an international database of RNA sequences},
author = {Alex Bateman and Shipra Agrawal and Ewan Birney and Elspeth A. Bruford and Janusz M. Bujnicki and Guy Cochrane and James R. Cole and Marcel E. Dinger and Anton J. Enright and Paul P. Gardner and Daniel Gautheret and Sam Griffiths-Jones and Jen Harrow and Javier Herrero and Ian H. Holmes and Hsien-Da Huang and Krystyna A. Kelly and Paul Kersey and Ana Kozomara and Todd M. Lowe and Manja Marz and Simon Moxon and Kim D. Pruitt and Tore Samuelsson and Peter F. Stadler and Albert J. Vilella and Jan-Hinnerk Vogel and Kelly P. Williams and Mathew W. Wright and Christian Zwieb},
doi = {10.1261/rna.2750811},
year = {2011},
date = {2011-09-22},
urldate = {2011-09-22},
journal = {RNA},
volume = {17},
pages = {1941--1946},
abstract = {During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.},
keywords = {database, ncRNAs, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.
Lechner, Marcus; Findeiss, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F; Prohaska, Sonja J
Proteinortho: detection of (co-)orthologs in large-scale analysis Journal Article
In: BMC Bioinf, vol. 12, pp. 124, 2011.
Abstract | Links | BibTeX | Tags: alignment, bacteria, phylogenetics, proteins, software
@article{Lechner:11,
title = {Proteinortho: detection of (co-)orthologs in large-scale analysis},
author = {Marcus Lechner and Sven Findeiss and Lydia Steiner and Manja Marz and Peter F Stadler and Sonja J Prohaska},
url = {http://bioinf.pharmazie.uni-marburg.de/supplements/proteinortho/},
doi = {10.1186/1471-2105-12-124},
year = {2011},
date = {2011-04-28},
urldate = {2011-04-28},
journal = {BMC Bioinf},
volume = {12},
pages = {124},
abstract = {Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.},
keywords = {alignment, bacteria, phylogenetics, proteins, software},
pubstate = {published},
tppubtype = {article}
}
Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.
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.
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.
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/.
Dalloul, Rami A.; Long, Julie A.; Zimin, Aleksey V.; Aslam, Luqman; Beal, Kathryn; Blomberg, Le Ann; Bouffard, Pascal; Burt, David W.; Crasta, Oswald; Crooijmans, Richard P. M. A.; Cooper, Kristal; Coulombe, Roger A.; De, Supriyo; Delany, Mary E.; Dodgson, Jerry B.; Dong, Jennifer J.; Evans, Clive; Frederickson, Karin M.; Flicek, Paul; Florea, Liliana; Folkerts, Otto; Groenen, Martien A. M.; Harkins, Tim T.; Herrero, Javier; Hoffmann, Steve; Megens, Hendrik-Jan; Jiang, Andrew; Jong, Pieter; Kaiser, Pete; Kim, Heebal; Kim, Kyu-Won; Kim, Sungwon; Langenberger, David; Lee, Mi-Kyung; Lee, Taeheon; Mane, Shrinivasrao; Marcais, Guillaume; Marz, Manja; McElroy, Audrey P.; Modise, Thero; Nefedov, Mikhail; Notredame, Cédric; Paton, Ian R.; Payne, William S.; Pertea, Geo; Prickett, Dennis; Puiu, Daniela; Qioa, Dan; Raineri, Emanuele; Ruffier, Magali; Salzberg, Steven L.; Schatz, Michael C.; Scheuring, Chantel; Schmidt, Carl J.; Schroeder, Steven; Searle, Stephen M. J.; Smith, Edward J.; Smith, Jacqueline; Sonstegard, Tad S.; Stadler, Peter F.; Tafer, Hakim; Tu, Zhijian Jake; Tassell, Curtis P. Van; Vilella, Albert J.; Williams, Kelly P.; Yorke, James A.; Zhang, Liqing; Zhang, Hong-Bin; Zhang, Xiaojun; Zhang, Yang; Reed, Kent M.
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis Journal Article
In: PLoS Biol, vol. 8, 2010.
Abstract | Links | BibTeX | Tags: alignment, annotation, assembly, DNA / genomics, ncRNAs
@article{Dalloul:10,
title = {Multi-platform next-generation sequencing of the domestic turkey (\textit{Meleagris gallopavo}): genome assembly and analysis},
author = {Rami A. Dalloul and Julie A. Long and Aleksey V. Zimin and Luqman Aslam and Kathryn Beal and Le Ann Blomberg and Pascal Bouffard and David W. Burt and Oswald Crasta and Richard P. M. A. Crooijmans and Kristal Cooper and Roger A. Coulombe and Supriyo De and Mary E. Delany and Jerry B. Dodgson and Jennifer J. Dong and Clive Evans and Karin M. Frederickson and Paul Flicek and Liliana Florea and Otto Folkerts and Martien A. M. Groenen and Tim T. Harkins and Javier Herrero and Steve Hoffmann and Hendrik-Jan Megens and Andrew Jiang and Pieter Jong and Pete Kaiser and Heebal Kim and Kyu-Won Kim and Sungwon Kim and David Langenberger and Mi-Kyung Lee and Taeheon Lee and Shrinivasrao Mane and Guillaume Marcais and Manja Marz and Audrey P. McElroy and Thero Modise and Mikhail Nefedov and Cédric Notredame and Ian R. Paton and William S. Payne and Geo Pertea and Dennis Prickett and Daniela Puiu and Dan Qioa and Emanuele Raineri and Magali Ruffier and Steven L. Salzberg and Michael C. Schatz and Chantel Scheuring and Carl J. Schmidt and Steven Schroeder and Stephen M. J. Searle and Edward J. Smith and Jacqueline Smith and Tad S. Sonstegard and Peter F. Stadler and Hakim Tafer and Zhijian Jake Tu and Curtis P. Van Tassell and Albert J. Vilella and Kelly P. Williams and James A. Yorke and Liqing Zhang and Hong-Bin Zhang and Xiaojun Zhang and Yang Zhang and Kent M. Reed},
doi = {10.1371/journal.pbio.1000475},
year = {2010},
date = {2010-09-07},
urldate = {2010-09-07},
journal = {PLoS Biol},
volume = {8},
abstract = {A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.},
keywords = {alignment, annotation, assembly, DNA / genomics, ncRNAs},
pubstate = {published},
tppubtype = {article}
}
A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
Yusuf, Dilmurat; Marz, Manja; Stadler, Peter F; Hofacker, Ivo L
Bcheck: a wrapper tool for detecting RNase P RNA genes Journal Article
In: BMC Genomics, vol. 11, pp. 432, 2010.
Abstract | Links | BibTeX | Tags: annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software
@article{Yusuf:10,
title = {Bcheck: a wrapper tool for detecting RNase P RNA genes},
author = {Dilmurat Yusuf and Manja Marz and Peter F Stadler and Ivo L Hofacker},
url = {http://rna.tbi.univie.ac.at/bcheck},
doi = {10.1186/1471-2164-11-432},
year = {2010},
date = {2010-07-13},
urldate = {2010-07-13},
journal = {BMC Genomics},
volume = {11},
pages = {432},
abstract = {Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.},
keywords = {annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software},
pubstate = {published},
tppubtype = {article}
}
Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.
Donath, Alexander; Findeiß, Sven; Hertel, Jana; Marz, Manja; Otto, Wolfgang; Schulz, Christine; Stadler, Peter F.; Wirth, Stefan
Noncoding RNA Book Section
In: Evolutionary Genomics and Systems Biology, pp. 251-293, John Wiley & Sons, Ltd, 2010, ISBN: 9780470570418.
Abstract | Links | BibTeX | Tags: ncRNAs
@incollection{nokey,
title = {Noncoding RNA},
author = {Alexander Donath and Sven Findeiß and Jana Hertel and Manja Marz and Wolfgang Otto and Christine Schulz and Peter F. Stadler and Stefan Wirth},
doi = {10.1002/9780470570418.ch14},
isbn = {9780470570418},
year = {2010},
date = {2010-03-01},
booktitle = {Evolutionary Genomics and Systems Biology},
pages = {251-293},
publisher = {John Wiley & Sons, Ltd},
chapter = {14},
abstract = {Summary This chapter contains sections titled: Introduction Ancient RNAs Domain-Specific RNAs Conserved ncRNAs with Limited Distribution ncRNAs from Repeats and Pseudogenes mRNA-like ncRNAs RNAs with Dual Functions Concluding Remarks Acknowledgments References},
keywords = {ncRNAs},
pubstate = {published},
tppubtype = {incollection}
}
Summary This chapter contains sections titled: Introduction Ancient RNAs Domain-Specific RNAs Conserved ncRNAs with Limited Distribution ncRNAs from Repeats and Pseudogenes mRNA-like ncRNAs RNAs with Dual Functions Concluding Remarks Acknowledgments References
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.
Hertel, Jana; Jong, Danielle; Marz, Manja; Rose, Dominic; Tafer, Hakim; Tanzer, Andrea; Schierwater, Bernd; Stadler, Peter F
Non-coding RNA annotation of the genome of Ŧrichoplax adhaerens Journal Article
In: Nucleic Acids Res, vol. 37, no. 5, pp. 1602–1615, 2009.
Abstract | Links | BibTeX | Tags: annotation, ncRNAs
@article{Hertel:09,
title = {Non-coding RNA annotation of the genome of \textit{Ŧrichoplax adhaerens}},
author = {Jana Hertel and Danielle Jong and Manja Marz and Dominic Rose and Hakim Tafer and Andrea Tanzer and Bernd Schierwater and Peter F Stadler},
doi = {10.1093/nar/gkn1084},
year = {2009},
date = {2009-01-26},
urldate = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {5},
pages = {1602--1615},
abstract = {A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.},
keywords = {annotation, ncRNAs},
pubstate = {published},
tppubtype = {article}
}
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.
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.
Ingalls, Todd; Martius, Georg; Marz, Manja; Prohaska, Sonja J.
Converting DNA to music: ComposAlign Proceedings Article
In: Proceedings of the German Conference on Bioinformatics (GCB 2009), pp. 93-104, 2009.
Abstract | Links | BibTeX | Tags: alignment
@inproceedings{Ingalls:09,
title = {Converting DNA to music: ComposAlign},
author = {Todd Ingalls and Georg Martius and Manja Marz and Sonja J. Prohaska},
url = {https://dl.gi.de/handle/20.500.12116/20313},
year = {2009},
date = {2009-01-01},
urldate = {2009-01-01},
booktitle = {Proceedings of the German Conference on Bioinformatics (GCB 2009)},
volume = {P-157},
pages = {93-104},
series = {GI Lecture Notes in Informatics},
abstract = {Alignments are part of the most important data type in the field of comparative genomics. They can be abstracted to a character matrix derived from aligned sequences. A variety of biological questions forces the researcher to inspect these alignments. Our tool, called COMPOSALIGN, was developed to sonify large scale genomic data. The resulting musical composition is based on COMMON MUSIC and allows the mapping of genes to motifs and species to instruments. It enables the researcher to listen to the musical representation of the genome-wide alignment and contrasts a bioinformatician's sight-oriented work at the computer.},
keywords = {alignment},
pubstate = {published},
tppubtype = {inproceedings}
}
Alignments are part of the most important data type in the field of comparative genomics. They can be abstracted to a character matrix derived from aligned sequences. A variety of biological questions forces the researcher to inspect these alignments. Our tool, called COMPOSALIGN, was developed to sonify large scale genomic data. The resulting musical composition is based on COMMON MUSIC and allows the mapping of genes to motifs and species to instruments. It enables the researcher to listen to the musical representation of the genome-wide alignment and contrasts a bioinformatician's sight-oriented work at the computer.
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.
Gruber, Andreas R; Koper-Emde, Dorota; Marz, Manja; Tafer, Hakim; Bernhart, Stephan; Obernosterer, Gregor; Mosig, Axel; Hofacker, Ivo L; Stadler, Peter F; Benecke, Bernd-Joachim
Invertebrate 7SK snRNAs Journal Article
In: J Mol Evol, vol. 66, pp. 107–115, 2008.
Abstract | Links | BibTeX | Tags: evolution, ncRNAs
@article{Gruber:08,
title = {Invertebrate 7SK snRNAs},
author = {Andreas R Gruber and Dorota Koper-Emde and Manja Marz and Hakim Tafer and Stephan Bernhart and Gregor Obernosterer and Axel Mosig and Ivo L Hofacker and Peter F Stadler and Bernd-Joachim Benecke},
doi = {10.1007/s00239-007-9052-6},
year = {2008},
date = {2008-01-12},
urldate = {2008-01-12},
journal = {J Mol Evol},
volume = {66},
pages = {107--115},
abstract = {7SK RNA is a highly abundant noncoding RNA in mammalian cells whose function in transcriptional regulation has only recently been elucidated. Despite its highly conserved sequence throughout vertebrates, all attempts to discover 7SK RNA homologues in invertebrate species have failed so far. Here we report on a combined experimental and computational survey that succeeded in discovering 7SK RNAs in most of the major deuterostome clades and in two protostome phyla: mollusks and annelids. Despite major efforts, no candidates were found in any of the many available ecdysozoan genomes, however. The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3' and 5' stem-loop motifs, and provide evidence for a third, structurally well-conserved domain.},
keywords = {evolution, ncRNAs},
pubstate = {published},
tppubtype = {article}
}
7SK RNA is a highly abundant noncoding RNA in mammalian cells whose function in transcriptional regulation has only recently been elucidated. Despite its highly conserved sequence throughout vertebrates, all attempts to discover 7SK RNA homologues in invertebrate species have failed so far. Here we report on a combined experimental and computational survey that succeeded in discovering 7SK RNAs in most of the major deuterostome clades and in two protostome phyla: mollusks and annelids. Despite major efforts, no candidates were found in any of the many available ecdysozoan genomes, however. The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3' and 5' stem-loop motifs, and provide evidence for a third, structurally well-conserved domain.
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%).
2006
Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Fried, Claudia; Tanzer, Andrea; Flamm, Christoph; Hofacker, Ivo L.; Stadler, Peter F.; & 2005, Students Bioinformatics Computer Labs 2004
The expansion of the metazoan microRNA repertoire Journal Article
In: BMC Genomics, vol. 7, pp. 25, 2006.
Abstract | Links | BibTeX | Tags: ncRNAs, phylogenetics
@article{Hertel:06,
title = {The expansion of the metazoan microRNA repertoire},
author = {Jana Hertel and Manja Lindemeyer and Kristin Missal and Claudia Fried and Andrea Tanzer and Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler and Students Bioinformatics Computer Labs 2004 & 2005},
doi = {10.1186/1471-2164-7-25},
year = {2006},
date = {2006-02-15},
urldate = {2006-02-15},
journal = {BMC Genomics},
volume = {7},
pages = {25},
abstract = {MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozen ancient microRNA clusters. Our results suggest that microRNA innovation is an ongoing process. Major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals.},
keywords = {ncRNAs, phylogenetics},
pubstate = {published},
tppubtype = {article}
}
MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozen ancient microRNA clusters. Our results suggest that microRNA innovation is an ongoing process. Major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals.
0000
Monecke, Stefan; Braun, Sascha D.; Collatz, Maximillian; Diezel, Celia; Müller, Elke; Reinicke, Martin; Rosel, Adriana Cabal; Feßler, Andrea T.; Hanke, Dennis; Loncaric, Igor; Schwarz, Stefan; de Jäckel, Sonia Cortez; Ruppitsch, Werner; Widen, Dolores Gavier; Hotzel, Helmut; Ehricht, Ralf
Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl Journal Article
In: Microorganisms, vol. 12, 0000.
Abstract | Links | BibTeX | Tags: bacteria, DNA / genomics, evolution
@article{nokey_92,
title = {Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl},
author = { Stefan Monecke and Sascha D. Braun and Maximillian Collatz and Celia Diezel and Elke Müller and Martin Reinicke and Adriana Cabal Rosel and Andrea T. Feßler and Dennis Hanke and Igor Loncaric and Stefan Schwarz and Sonia Cortez de Jäckel and Werner Ruppitsch and Dolores Gavier Widen and Helmut Hotzel and Ralf Ehricht},
doi = {10.3390/microorganisms12010096},
journal = {Microorganisms},
volume = {12},
abstract = {Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain’s genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying “bird-specific” virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.},
keywords = {bacteria, DNA / genomics, evolution},
pubstate = {published},
tppubtype = {article}
}
Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain’s genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying “bird-specific” virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.