Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

Epigenetics : Official Journal of the DNA Methylation Society
Lingzhao FangGeorge Liu

Abstract

Sperm DNA methylation is crucial for fertility and viability of offspring but epigenome evolution in mammals is largely understudied. By comparing sperm DNA methylomes and large-scale genome-wide association study (GWAS) signals between human and cattle, we aimed to examine the DNA methylome evolution and its associations with complex phenotypes in mammals. Our analysis revealed that genes with conserved non-methylated promoters (e.g., ANKS1A and WNT7A) among human and cattle were involved in common system and embryo development, and enriched for GWAS signals of body conformation traits in both species, while genes with conserved hypermethylated promoters (e.g., TCAP and CD80) were engaged in immune responses and highlighted by immune-related traits. On the other hand, genes with human-specific hypomethylated promoters (e.g., FOXP2 and HYDIN) were engaged in neuron system development and enriched for GWAS signals of brain-related traits, while genes with cattle-specific hypomethylated promoters (e.g., LDHB and DGAT2) mainly participated in lipid storage and metabolism. We validated our findings using sperm-retained nucleosome, preimplantation transcriptome, and adult tissue transcriptome data, as well as sequence evolutionary f...Continue Reading

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Citations

Dec 4, 2020·International Journal of Molecular Sciences·Pevindu AbeysingheMurray D Mitchell
Jan 6, 2021·Journal of Applied Genetics·Jana HaluškováJana Staničová
Nov 14, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xiao WangHaja N Kadarmideen
Jul 13, 2021·Frontiers in Veterinary Science·Memmet ÖzbekErdogan Memili

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Datasets Mentioned

BETA
GSE119263
GSE106538
GSE49624

Methods Mentioned

BETA
WGBS

Software Mentioned

R package clusterProfiler
Ploycomb
Bismark
FastQC
bowtie2

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