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Comparative analyses of sperm DNA methylomes among three commercial pig breeds reveal vital hypomethylated regions associated with spermatogenesis and embryonic development

ABSTRACT: Comparative analyses of sperm DNA methylomes among three commercial pig breeds reveal vital hypomethylated regions associated with spermatogenesis and embryonic development

PROVIDER: PRJNA746554 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15132625_1.fastq.gz	Fastqsanger.gz
	SRR15132625_2.fastq.gz	Fastqsanger.gz
	SRR15132626_1.fastq.gz	Fastqsanger.gz
	SRR15132626_2.fastq.gz	Fastqsanger.gz
	SRR15132627_1.fastq.gz	Fastqsanger.gz

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Comparative analyses of sperm DNA methylomes among three commercial pig breeds reveal vital hypomethylated regions associated with spermatogenesis and embryonic development

Project description:This study is the first to report a genome-wide comparative DNA methylation map of adult pig sperm in three commercial pig breeds using WGBS technology. Our results showed that DNA methylation was more conserved in the three commercial pig breeds. Moreover, our results indicated that breed-specific HMRs are related to phenotypic changes and economically complex traits for each breed. The conserved HMRs between pig sperm and testis close to or located in the promoter regions of important genes are mainly involved in DNA repair and spermatogenesis.

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Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development.

Project description:Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040-1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as NLGN1 (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.

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