Show simple item record

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMEGUERDITCHIAN, Caroline
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorERGUN, Ayse
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDECROOCQ, Véronique
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLEFEBVRE, Marie
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBUI, Quynh-Trang
dc.date.issued2021-07-06
dc.identifier.issn2780-0539
dc.descriptionRecommendationEmmanuelle Lerat (2021) A new tool to cross and analyze TE and gene annotations. Peer Community inGenomics, 100010. 10.24072/pci.genomics.100010Transposable elements (TEs) are important components of genomes. Indeed, they are now recognized as having a major role in gene and genome evolution (Biémont 2010). In particular, several examples have shown that the presence of TEs near genes may influence their functioning, either by recruiting particular epigenetic modifications (Guio et al. 2018) or by directly providing new regulatory sequences allowing new expression patterns (Chung et al. 2007; Sundaram et al. 2014). Therefore, the study of the interaction between TEs and their host genome requires tools to easily cross-annotate both types of entities. In particular, one needs to be able to identify all TEs located in the close vicinity of genes or inside them. Such task may not always be obvious for many biologists, as it requires informatics knowledge to develop their own script codes.In their work, Meguerdichian et al. (2021) propose a command-line pipeline that takes as input the annotations of both genes and TEs for a given genome, then detects and reports the positional relationships between each TE insertion and their closest genes. The results are processed into an R script to provide tables displaying some statistics and graphs to visualize these relationships. This tool has the potential to be very useful for performing preliminary analyses before studying the impact of TEs on gene functioning, especially for biologists. Indeed, it makes it possible to identify genes close to TE insertions. These identified genes could then be specifically considered in order to study in more detail the link between the presence of TEs and their functioning. For example, the identification of TEs close to genes may allow to determine their potential role on gene expression.
dc.description.abstractEnUnderstanding the relationship between transposable elements (TEs) and their closest positional genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural organization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline.
dc.language.isoen
dc.publisherPeer Community In
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enTransposable element
dc.subject.enGene
dc.subject.enGenome
dc.subject.enBioinformatics
dc.subject.enPipeline
dc.title.enA pipeline to detect the relationship between transposable elements and adjacent genes in host genomes
dc.typeDocument de travail - Pré-publication
dc.identifier.doi10.1101/2021.02.25.432867
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
bordeaux.journalPeer Community In Genomics
hal.identifierhal-03325096
hal.version1
hal.popularnon
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03325096v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Peer%20Community%20In%20Genomics&rft.date=2021-07-06&rft.eissn=2780-0539&rft.issn=2780-0539&rft.au=MEGUERDITCHIAN,%20Caroline&ERGUN,%20Ayse&DECROOCQ,%20V%C3%A9ronique&LEFEBVRE,%20Marie&BUI,%20Quynh-Trang&rft.genre=preprint


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record