E-Mail: marie.lataretu@uni-jena.de
Room: 08S01
Phone: +49-3641-9-46482
Publications
2020
Lataretu, Marie; Hölzer, Martin
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow Journal Article
In: Genes, vol. 11, no. 12, pp. 1487, 2020.
@article{Lataretu:20,
title = {RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow},
author = {Marie Lataretu and Martin Hölzer},
url = {https://github.com/hoelzer-lab/rnaflow},
doi = {10.3390/genes11121487},
year = {2020},
date = {2020-12-10},
urldate = {2020-01-01},
journal = {Genes},
volume = {11},
number = {12},
pages = {1487},
publisher = {MDPI AG},
abstract = {RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.
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.
@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 = {},
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.
Hölzer, Martin; Barf, Lisa-Marie; Lamkiewicz, Kevin; Vorimore, Fabien; Lataretu, Marie; Favaroni, Alison; Schnee, Christiane; Laroucau, Karine; Marz, Manja; Sachse, Konrad
Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species Journal Article
In: Pathogens, vol. 9, no. 11, pp. 899, 2020.
@article{Hölzer:20,
title = {Comparative Genome Analysis of 33 \textit{Chlamydia} Strains Reveals Characteristic Features of \textit{Chlamydia Psittaci} and Closely Related Species},
author = {Martin Hölzer and Lisa-Marie Barf and Kevin Lamkiewicz and Fabien Vorimore and Marie Lataretu and Alison Favaroni and Christiane Schnee and Karine Laroucau and Manja Marz and Konrad Sachse},
url = {github.com/hoelzer-lab/ribap},
doi = {10.3390/pathogens9110899},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Pathogens},
volume = {9},
number = {11},
pages = {899},
publisher = {MDPI AG},
abstract = {To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.
2019
Mostajo, Nelly F.; Lataretu, Marie; Krautwurst, Sebastian; Mock, Florian; Desirò, Daniel; Lamkiewicz, Kevin; Collatz, Maximilian; Schoen, Andreas; Weber, Friedemann; Marz, Manja; Hölzer, Martin
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes Journal Article
In: NAR Genomics Bioinf, vol. 2, no. 1, pp. lqz006, 2019.
@article{Mostajo:20,
title = {A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes},
author = {Nelly F. Mostajo and Marie Lataretu and Sebastian Krautwurst and Florian Mock and Daniel Desirò and Kevin Lamkiewicz and Maximilian Collatz and Andreas Schoen and Friedemann Weber and Manja Marz and Martin Hölzer},
url = {https://www.rna.uni-jena.de/supplements/bats/index.html},
doi = {10.1093/nargab/lqz006},
year = {2019},
date = {2019-09-30},
urldate = {2019-09-30},
journal = {NAR Genomics Bioinf},
volume = {2},
number = {1},
pages = {lqz006},
abstract = {Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.