Transcriptome-wide investigation of genomic imprinting in chicken

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and di...

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Main Authors:	Frésard, Laure, Leroux, Sophie, Servin, Bertrand, Gourichon, David, Dehais, Patrice, Cristobal, Magali San, Marsaud, Nathalie, Vignoles, Florence, Bed'hom, Bertrand, Coville, Jean-Luc, Hormozdiari, Farhad, Beaumont, Catherine, Zerjal, Tatiana, Vignal, Alain, Morisson, Mireille, Lagarrigue, Sandrine, Pitel, Frédérique
Format:	Online
Language:	English
Published:	Oxford University Press 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973300/

id	pubmed-3973300
recordtype	oai_dc
spelling	pubmed-39733002014-04-04 Transcriptome-wide investigation of genomic imprinting in chicken Frésard, Laure Leroux, Sophie Servin, Bertrand Gourichon, David Dehais, Patrice Cristobal, Magali San Marsaud, Nathalie Vignoles, Florence Bed'hom, Bertrand Coville, Jean-Luc Hormozdiari, Farhad Beaumont, Catherine Zerjal, Tatiana Vignal, Alain Morisson, Mireille Lagarrigue, Sandrine Pitel, Frédérique Genomics Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken. Oxford University Press 2014-04 2014-01-21 /pmc/articles/PMC3973300/ /pubmed/24452801 http://dx.doi.org/10.1093/nar/gkt1390 Text en © The Author(s) 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Frésard, Laure Leroux, Sophie Servin, Bertrand Gourichon, David Dehais, Patrice Cristobal, Magali San Marsaud, Nathalie Vignoles, Florence Bed'hom, Bertrand Coville, Jean-Luc Hormozdiari, Farhad Beaumont, Catherine Zerjal, Tatiana Vignal, Alain Morisson, Mireille Lagarrigue, Sandrine Pitel, Frédérique
spellingShingle	Frésard, Laure Leroux, Sophie Servin, Bertrand Gourichon, David Dehais, Patrice Cristobal, Magali San Marsaud, Nathalie Vignoles, Florence Bed'hom, Bertrand Coville, Jean-Luc Hormozdiari, Farhad Beaumont, Catherine Zerjal, Tatiana Vignal, Alain Morisson, Mireille Lagarrigue, Sandrine Pitel, Frédérique Transcriptome-wide investigation of genomic imprinting in chicken
author_facet	Frésard, Laure Leroux, Sophie Servin, Bertrand Gourichon, David Dehais, Patrice Cristobal, Magali San Marsaud, Nathalie Vignoles, Florence Bed'hom, Bertrand Coville, Jean-Luc Hormozdiari, Farhad Beaumont, Catherine Zerjal, Tatiana Vignal, Alain Morisson, Mireille Lagarrigue, Sandrine Pitel, Frédérique
author_sort	Frésard, Laure
title	Transcriptome-wide investigation of genomic imprinting in chicken
title_short	Transcriptome-wide investigation of genomic imprinting in chicken
title_full	Transcriptome-wide investigation of genomic imprinting in chicken
title_fullStr	Transcriptome-wide investigation of genomic imprinting in chicken
title_full_unstemmed	Transcriptome-wide investigation of genomic imprinting in chicken
title_sort	transcriptome-wide investigation of genomic imprinting in chicken
description	Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
publisher	Oxford University Press
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973300/
_version_	1612073343417057280

Transcriptome-wide investigation of genomic imprinting in chicken

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