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srnaMapper: an optimal mapping tool for sRNA-Seq reads [article]

Matthias Zytnicki, Christine Gaspin
2021 bioRxiv   pre-print
Motivation: Sequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among other. The first step to make use of these reads is to map them to a genome. Existing mapping tools have been developed for the long RNAs in mind, and, so far, no tool has been conceived for short RNAs. However, short RNAs have several distinctive features which make them different from messenger RNAs: they are shorter (not greater than 200bp),
more » ... they often redundant, they can be produced by duplicated loci, and they may be edited at their ends. Results: In this work, we present a new tool, srnaMapper, that maps these reads with all these objectives in mind. We show on two data sets that srnaMapper is more efficient considering computation time and edition error handling: it quickly retrieves all the hits, with arbitrary number of errors. Availability: srnaMapper source code is available at
doi:10.1101/2021.01.12.426326 fatcat:tkh4zn3bmnbbvp3e2hqk4ull6u

mmannot: How to improve small–RNA annotation?

Matthias Zytnicki, Christine Gaspin, Francesca Rizzo
2020 PLoS ONE  
Writing -review & editing: Matthias Zytnicki, Christine Gaspin.  ...  (GZ) Author Contributions Conceptualization: Matthias Zytnicki, Christine Gaspin. Software: Matthias Zytnicki. Fig 2 . 2 Comparison of the different strategies on the A. thaliana data sets.  ... 
doi:10.1371/journal.pone.0231738 pmid:32463818 fatcat:cv6eno53ivhzfnyvnccwjcsl2q

DARN! A Weighted Constraint Solver for RNA Motif Localization

Matthias Zytnicki, Christine Gaspin, Thomas Schiex
2008 Constraints  
Following recent discoveries about the important roles of non-coding RNAs (ncRNAs) in the cellular machinery, there is now great interest in identifying new occurrences of ncRNAs in available genomic sequences. In this paper, we show how the problem of finding new occurrences of characterized ncRNAs can be modeled as the problem of finding all locally-optimal solutions of a weighted constraint network using dedicated weighted global constraints, encapsulating pattern-matching algorithms and
more » ... structures. This is embodied in DARN!, a software tool for ncRNA localization, which, compared to existing pattern-matching based tools, offers additional expressivity (such as enabling RNA-RNA interactions to be described) and improved specificity (through the exploitation of scores and local optimality) without compromises in CPU efficiency. This is demonstrated on the actual search for tRNAs and H/ACA sRNA on different genomes.
doi:10.1007/s10601-007-9033-9 fatcat:vqpi2n2grnc6hlu34jjj7glmcq

LeARN: a platform for detecting, clustering and annotating non-coding RNAs

Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
2008 BMC Bioinformatics  
doi:10.1186/1471-2105-9-21 pmid:18194551 pmcid:PMC2241582 fatcat:kzi7rsqk3zeh3lprth2yihw74u

Jflow: a workflow management system for web applications

Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Ibouniyamine Nabihoudine, Céline Noirot, Marie-Stéphane Trotard, Christine Gaspin, Christophe Klopp
2015 Bioinformatics  
Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a
more » ... Python library providing all requested features to setup, run and monitor workflows.
doi:10.1093/bioinformatics/btv589 pmid:26454273 pmcid:PMC5859998 fatcat:v67562cyr5cdpdr4bbxm4hjssu

Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function

Christine Gaspin, Jean-François Rami, Bernard Lescure
2010 BMC Plant Biology  
BMC Plant Biology 2010, 10:283 Page 3 of 12 Gaspin et al. BMC Plant Biology 2010, 10:283 Page 5 of 12  ...  23 21 17 1 O. sativa Intronic snoRNA clusters 25 22 22 1 Intronic orphan snoRNAs 7 5 3 0 Intergenic snoRNA clusters 42 20 19 1 Intergenic orphan snoring 47 13 8 0 Gaspin  ... 
doi:10.1186/1471-2229-10-283 pmid:21171996 pmcid:PMC3022908 fatcat:nzja44coorer7fjdhyhgpoaefq

Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001

Isabelle Caldelari, Béatrice Chane-Woon-Ming, Céline Noirot, Karen Moreau, Pascale Romby, Christine Gaspin, Stefano Marzi
2017 Genome Announcements  
Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a positive activator of SigB).
doi:10.1128/genomea.00783-17 pmid:28798184 pmcid:PMC5552993 fatcat:s3kkj3hv5bgprfhpp624x5ov5y

Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing

Amelie Juanchich, Philippe Bardou, Olivier Rué, Jean-Charles Gabillard, Christine Gaspin, Julien Bobe, Yann Guiguen
2016 BMC Genomics  
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues
more » ... next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs. Results: A total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species. Conclusion: This study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.
doi:10.1186/s12864-016-2505-9 pmid:26931235 pmcid:PMC4774146 fatcat:xurgaqn6jfevve2wzn4e3ogin4

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

Henri Grosjean, Christine Gaspin, Christian Marck, Wayne A Decatur, Valérie de Crécy-Lagard
2008 BMC Genomics  
Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or
more » ... of the modifications genes. Results: By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion: The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation. Post-transcriptional modification of RNA Modification pattern of tRNAs Thanks to the "tour de force" of Gupta [28, 29] , a list of almost all of the modified nucleosides present in the different tRNAs of Haloferax volcanii, a typical mesophilic halophile, is available. Figure 1A shows their distribution (identity and location) in the general 2D-cloverleaf structure of tRNA, while Figure 1B shows their positions in a schematic 3D-architecture model. The modifications that are unique to archaeal tRNAs are shown in gray. For example G + -15 (for Archaeosine), C*-34 (for a lysidine-type of nucleoside) and m 1 Ψ-54 are unique to all archaeal tRNAs analyzed so far, both by their chemical structure and their positions in the nucleic acid, while others such as m 2 2 G-10, Ψ-22, Ψ-52, C m -56 and m 1 I-57 (I for inosine) are unique only because of their position, rather than their chemical structure (see in [1, 4] , reviewed in [23]). Since
doi:10.1186/1471-2164-9-470 pmid:18844986 pmcid:PMC2584109 fatcat:c4cvuabszfaffagutq2dmjo644

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart, David Fenyo
2017 mSystems  
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that
more » ... tes different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach.
doi:10.1128/msystems.00186-16 pmid:28317029 pmcid:PMC5350546 fatcat:nxkbkxedvreqrkkagovmh5jqoy

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks

Patricia Thébault, Romain Bourqui, William Benchimol, Christine Gaspin, Pascal Sirand-Pugnet, Raluca Uricaru, Isabelle Dutour
2014 Briefings in Bioinformatics  
The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are
more » ... l for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA-mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA-mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks.
doi:10.1093/bib/bbu045 pmid:25477348 pmcid:PMC4570199 fatcat:g4rxhjivpjgrjghna2tdx34ooy

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria

Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
2017 BMC Genomics  
Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. Results: We designed a robust
more » ... nd generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. Conclusions: Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria.
doi:10.1186/s12864-017-4242-0 pmid:29145803 pmcid:PMC5689173 fatcat:kqvh44lpcngf3fwkmjzcyfh57y

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot
2015 BMC Bioinformatics  
CG (Gaspin) provided the knowledge for miRNA biology. SH, CG (Gautier), CG (Gaspin), and MFS together conceived the project, analysed the results and wrote the manuscript.  ... 
doi:10.1186/s12859-015-0594-0 pmid:26022464 pmcid:PMC4448272 fatcat:vf4rmuka4faangigsrimhrpnbq

Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval
2011 BMC Genomics  
Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs. Results: Using a combination of in silico and experimental approaches, we identified and characterized novel P. abyssi ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in
more » ... he late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel P. abyssi ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four P. abyssi CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized. Conclusions: This work proposes a revised annotation of CRISPR loci in P. abyssi and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.
doi:10.1186/1471-2164-12-312 pmid:21668986 pmcid:PMC3124441 fatcat:27bcsuffqrgfzasek5gzuobnze

Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates

Thomas Esquerré, Annick Moisan, Hélène Chiapello, Liisa Arike, Raivo Vilu, Christine Gaspin, Muriel Cocaign-Bousquet, Laurence Girbal
2015 BMC Genomics  
Changes to mRNA lifetime adjust mRNA concentration, facilitating the adaptation of growth rate to changes in growth conditions. However, the mechanisms regulating mRNA lifetime are poorly understood at the genome-wide scale and have not been investigated in bacteria growing at different rates. Results: We used linear covariance models and the best model selected according to the Akaike information criterion to identify and rank intrinsic and extrinsic general transcript parameters correlated
more » ... h mRNA lifetime, using mRNA half-life datasets for E. coli, obtained at four growth rates. The principal parameter correlated with mRNA stability was mRNA concentration, the mRNAs most concentrated in the cells being the least stable. However, sequence-related features (codon adaptation index (CAI), ORF length, GC content, polycistronic mRNA), gene function and essentiality also affected mRNA lifetime at all growth rates. We also identified sequence motifs within the 5′UTRs potentially related to mRNA stability. Growth rate-dependent effects were confined to particular functional categories (e.g. carbohydrate and nucleotide metabolism). Finally, mRNA stability was less strongly correlated with the amount of protein produced than mRNA concentration and CAI. Conclusions: This study provides the most complete genome-wide analysis to date of the general factors correlated with mRNA lifetime in E. coli. We have generalized for the entire population of transcripts or excluded determinants previously defined as regulators of stability for some particular mRNAs and identified new, unexpected general indicators. These results will pave the way for discussions of the underlying mechanisms and their interaction with the growth physiology of bacteria.
doi:10.1186/s12864-015-1482-8 pmid:25887031 pmcid:PMC4421995 fatcat:dvsunph4hvenbocxyumtgm6c2q
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