Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication

Scientific Reports
Qinghe LiNing Li

Abstract

It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Using meDIP-chip we mapped the promoter methylomes for 23,316 genes in muscle tissues of ancestral and domestic chickens. We systematically examined the variation of promoter DNA methylation in terms of different breeds, differentially expressed genes, SNPs and genes undergo genetic selection sweeps. While considerable changes in DNA sequence and gene expression programs were prevalent, we found that the inter-strain DNA methylation patterns were highly conserved in promoter region between the wild and domestic chicken breeds. Our data suggests a global preservation of DNA methylation between the wild and domestic chicken breeds in either a genome-wide or locus-specific scale in chick muscle tissues.

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Citations

Apr 11, 2018·BMC Genomics·L Curry WoodsJiuzhou Song
Mar 23, 2017·Molecular Genetics and Genomics : MGG·Zsofia BanlakiZsolt Ronai
Sep 16, 2017·Nature Communications·Shinji MaegawaJean-Pierre J Issa
Jan 20, 2021·Communications Biology·Günter RaddatzFrank Lyko
Jun 18, 2021·Frontiers in Veterinary Science·Yiming YanQingmei Xie

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Methods Mentioned

BETA
immunoprecipitation
pull down
bis-seq
RNA-seq
meDIP-chip
methylation profiling
PCR
electrophoresis

Software Mentioned

Bioconductor
limma
Ensemble
Ensembl
Ringo
ArrayStar
MeDIP
MEDME
MEDMD

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