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Multi-species annotation of transcriptome and chromatin structure in domesticated animals
BACKGROUND: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annot...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936065/ https://www.ncbi.nlm.nih.gov/pubmed/31884969 http://dx.doi.org/10.1186/s12915-019-0726-5 |
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author | Foissac, Sylvain Djebali, Sarah Munyard, Kylie Vialaneix, Nathalie Rau, Andrea Muret, Kevin Esquerré, Diane Zytnicki, Matthias Derrien, Thomas Bardou, Philippe Blanc, Fany Cabau, Cédric Crisci, Elisa Dhorne-Pollet, Sophie Drouet, Françoise Faraut, Thomas Gonzalez, Ignacio Goubil, Adeline Lacroix-Lamandé, Sonia Laurent, Fabrice Marthey, Sylvain Marti-Marimon, Maria Momal-Leisenring, Raphaelle Mompart, Florence Quéré, Pascale Robelin, David Cristobal, Magali San Tosser-Klopp, Gwenola Vincent-Naulleau, Silvia Fabre, Stéphane der Laan, Marie-Hélène Pinard-Van Klopp, Christophe Tixier-Boichard, Michèle Acloque, Hervé Lagarrigue, Sandrine Giuffra, Elisabetta |
author_facet | Foissac, Sylvain Djebali, Sarah Munyard, Kylie Vialaneix, Nathalie Rau, Andrea Muret, Kevin Esquerré, Diane Zytnicki, Matthias Derrien, Thomas Bardou, Philippe Blanc, Fany Cabau, Cédric Crisci, Elisa Dhorne-Pollet, Sophie Drouet, Françoise Faraut, Thomas Gonzalez, Ignacio Goubil, Adeline Lacroix-Lamandé, Sonia Laurent, Fabrice Marthey, Sylvain Marti-Marimon, Maria Momal-Leisenring, Raphaelle Mompart, Florence Quéré, Pascale Robelin, David Cristobal, Magali San Tosser-Klopp, Gwenola Vincent-Naulleau, Silvia Fabre, Stéphane der Laan, Marie-Hélène Pinard-Van Klopp, Christophe Tixier-Boichard, Michèle Acloque, Hervé Lagarrigue, Sandrine Giuffra, Elisabetta |
author_sort | Foissac, Sylvain |
collection | PubMed |
description | BACKGROUND: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RESULTS: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. CONCLUSIONS: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species. |
format | Online Article Text |
id | pubmed-6936065 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-69360652019-12-31 Multi-species annotation of transcriptome and chromatin structure in domesticated animals Foissac, Sylvain Djebali, Sarah Munyard, Kylie Vialaneix, Nathalie Rau, Andrea Muret, Kevin Esquerré, Diane Zytnicki, Matthias Derrien, Thomas Bardou, Philippe Blanc, Fany Cabau, Cédric Crisci, Elisa Dhorne-Pollet, Sophie Drouet, Françoise Faraut, Thomas Gonzalez, Ignacio Goubil, Adeline Lacroix-Lamandé, Sonia Laurent, Fabrice Marthey, Sylvain Marti-Marimon, Maria Momal-Leisenring, Raphaelle Mompart, Florence Quéré, Pascale Robelin, David Cristobal, Magali San Tosser-Klopp, Gwenola Vincent-Naulleau, Silvia Fabre, Stéphane der Laan, Marie-Hélène Pinard-Van Klopp, Christophe Tixier-Boichard, Michèle Acloque, Hervé Lagarrigue, Sandrine Giuffra, Elisabetta BMC Biol Research Article BACKGROUND: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RESULTS: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. CONCLUSIONS: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species. BioMed Central 2019-12-30 /pmc/articles/PMC6936065/ /pubmed/31884969 http://dx.doi.org/10.1186/s12915-019-0726-5 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Foissac, Sylvain Djebali, Sarah Munyard, Kylie Vialaneix, Nathalie Rau, Andrea Muret, Kevin Esquerré, Diane Zytnicki, Matthias Derrien, Thomas Bardou, Philippe Blanc, Fany Cabau, Cédric Crisci, Elisa Dhorne-Pollet, Sophie Drouet, Françoise Faraut, Thomas Gonzalez, Ignacio Goubil, Adeline Lacroix-Lamandé, Sonia Laurent, Fabrice Marthey, Sylvain Marti-Marimon, Maria Momal-Leisenring, Raphaelle Mompart, Florence Quéré, Pascale Robelin, David Cristobal, Magali San Tosser-Klopp, Gwenola Vincent-Naulleau, Silvia Fabre, Stéphane der Laan, Marie-Hélène Pinard-Van Klopp, Christophe Tixier-Boichard, Michèle Acloque, Hervé Lagarrigue, Sandrine Giuffra, Elisabetta Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title_full | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title_fullStr | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title_full_unstemmed | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title_short | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
title_sort | multi-species annotation of transcriptome and chromatin structure in domesticated animals |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936065/ https://www.ncbi.nlm.nih.gov/pubmed/31884969 http://dx.doi.org/10.1186/s12915-019-0726-5 |
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