Abstract
Abstract Background: DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results: Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486×coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. Conclusion: In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.
Highlights
DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others
Pearson correlation analysis showed that methylation levels within Methylation haplotype block (MHB) were less correlated among individuals (0.52 ~ 0.86) compared to those of various genomic elements (Additional file 1: Figure S1b), which was concordant with the previous observation that MHBs were variable among individuals and highly enriched in variably methylated regions (VMRs) [15]
The MHBs were highly enriched in CpG islands, 5’UTRs, exons and promoters (1000 times of permutation test using RegioneR [24], P < 0.001), indicating that they may play important roles in transcriptional regulation (Fig. 2d)
Summary
DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. DNA methylation in sperm has been shown to be involved in many biological processes, including X chromosome inactivation in females, Liu et al BMC Genomics (2019) 20:888 for understanding the relationships between sperm DNA methylation and complex traits in mammals, in males. VMRs within co-methylated networks in fibroblasts were enriched for four clusters of HOX genes Both genetic factors and environmental exposures like diet, stress, toxic exposure and exercise contribute to epigenetic variation [17,18,19]. While VMRs were studied in human and model organisms, to our knowledge, no studies have been published to investigate interindividual variation of DNA methylation in cattle, in sperm, which is of importance in dairy cattle due to the wide use of artificial insemination technology
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