| Title: |
Integrated analysis of methylome and transcriptome highlights limited impact of DNA methylation on age-related gene regulation in laying hens |
| Authors: |
Cossard, Guillaume; Hubert, Alexandre; Degalez, Fabien; Allain, Coralie; Burlot, Thierry; Eynard, Sonia; Gòdia, Marta; Emily, Mathieu; Lagoutte, Laetitia; Lebez, Bénédicte; Madsen, Ole; Rau, Andrea; Rousse, Stacy; Seraphin, Remi; Zerjal, Tatiana; Pitel, Frederique; Lagarrigue, Sandrine |
| Contributors: |
Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage Rennes (PEGASE); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro); NOVOGEN; Groupe Grimaud; Génétique Physiologie et Systèmes d'Elevage (GenPhySE); École nationale vétérinaire de Toulouse (ENVT); Institut National Polytechnique (Toulouse) (Toulouse INP); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Institut National Polytechnique (Toulouse) (Toulouse INP); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-École nationale supérieure agronomique de Toulouse (ENSAT, INP-ENSAT, AgroToulouse, INP-AgroToulouse); Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Communauté d'universités et établissements de Toulouse (Comue de Toulouse)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (EI Purpan); Communauté d'universités et établissements de Toulouse (Comue de Toulouse); Wageningen University and Research Wageningen (WUR); Institut de Recherche Mathématique de Rennes (IRMAR); Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes); Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers; Génétique Animale et Biologie Intégrative (GABI); AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); ANR-20-CE20-0029,EFFICACE,Analyse du contrôle génétique de différents caractères sur de longues carrières de production, chez la poule pondeuse(2020); European Project: 101000236,H2020-SFS-2018-2020,H2020-SFS-2020-2,GEroNIMO(2021) |
| Source: |
PAG33 ; https://hal.inrae.fr/hal-05560755 ; PAG33, Jan 2026, San diego (Californie), France. , https://plan.core-apps.com/pag33/abstract/415187ea4e428372ccc62388543d5c98, 2026 ; https://intlpag.org/PAG33/ |
| Publisher Information: |
CCSD |
| Publication Year: |
2026 |
| Collection: |
Université Toulouse III - Paul Sabatier: HAL-UPS |
| Subject Terms: |
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics |
| Subject Geographic: |
San diego (Californie); France |
| Description: |
International audience ; Understanding how organisms respond to environmental challenges requires an integrat-ed view of gene expression and regulation. While transcriptome profiling captures dynamic shifts in gene expression, it does not reveal the underlying regulatory mechanisms. DNA meth-ylation, a key epigenetic modification sensitive to environmental factors, provides complemen-tary information on regulatory changes. Integrating methylome and transcriptome data from the same tissue enables a deeper understanding of how environmental stressors may shape gene regulation and phenotype. In a previous transcriptome study of the liver’s response to ageing in laying hens, we identified 634 and 941 differentially expressed (DE) protein-coding genes (PCG) that were respectively under- or over-expressed in 90-week-old laying hens (n=225) compared to 70-week-old (n=241). Here, we extend these results to examine the complex interplay between the transcrip-tome and the methylome, using Reduced Representation Bisulfite Sequencing (RRBS) obtained on a subset of 347 hens (n=174 at 90wk, n=173 at 70wk) from the first study. Among the 9.2M CpG sites identified with a minimum coverage of 10 reads, we selected those that fulfilled the following criteria: no overlap with known genomic variants (2M), at least 10 reads in 80% of samples (475,178), and methylation rate standard deviation >0.05, yielding 139,362 high-quality CpG sites located within 4,569 PCG including the 2kb promoter. A modest but significant global increase in DNA methylation with age was observed, with 906 differential-ly methylated CpG (DMC) sites, of which 557 were hypermethylated and 349 hypomethylated at 90wkcompared to 70wk, respectively corresponding to 89 and 57 genes.We then investigated relationships between methylation and expression using four com-plementary approaches: (i) overlap of DE genes with DMC-associated genes, (ii) multivariate linear models (Expr~site1+site2+…), (iii) unsupervised multi-omics factor analysis (MOFA2), (iv) weighted gene ... |
| Document Type: |
conference object; still image |
| Language: |
English |
| Relation: |
info:eu-repo/grantAgreement//101000236/EU/GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics/GEroNIMO |
| Availability: |
https://hal.inrae.fr/hal-05560755; https://hal.inrae.fr/hal-05560755v1/document; https://hal.inrae.fr/hal-05560755v1/file/PAG_Methyl_Trancriptome.pdf |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.1093DACD |
| Database: |
BASE |