Dataset Information

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.

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 (± 10?kb) 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.

SUBMITTER: Liu S

PROVIDER: S-EPMC6873545 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.

Liu Shuli S Fang Lingzhao L Zhou Yang Y Santos Daniel J A DJA Xiang Ruidong R Daetwyler Hans D HD Chamberlain Amanda J AJ Cole John B JB Li Cong-Jun CJ Yu Ying Y Ma Li L Zhang Shengli S Liu George E GE

BMC genomics 20191121 1

<h4>Background</h4>DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others.<h4>Results</h4>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 regio ...[more]

PMID: 31752687

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Project description:Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also for understanding how the environment affects variability, and for incorporation into statistical analyses. The inter-individual variation in DNA methylation patterns in female cattle and the effect that a prenatal stressor has on such variability have yet to be quantified. Thus, the objective of this study was to utilize methylation data from mature Brahman females to quantify the inter-individual variation in DNA methylation. Pregnant Brahman cows were transported for 2 h durations at days 60 ± 5; 80 ± 5; 100 ± 5; 120 ± 5; and 140 ± 5 of gestation. A non-transport group was maintained as a control. Leukocytes, amygdala, and anterior pituitary glands were harvested from eight cows born from the non-transport group (Control) and six from the transport group (PNS) at 5 years of age. The DNA harvested from the anterior pituitary contained the greatest variability in DNA methylation of cytosine-phosphate-guanine (mCpG) sites from both the PNS and Control groups, and the amygdala had the least. Numerous variable mCpG sites were associated with retrotransposable elements and highly repetitive regions of the genome. Some of the genomic features that had high variation in DNA methylation are involved in immune responses, signaling, responses to stimuli, and metabolic processes. The small overlap of highly variable CpG sites and features between tissues and leukocytes supports the role of variable DNA methylation in regulating tissue-specific gene expression. Many of the CpG sites that exhibited high variability in DNA methylation were common between the PNS and Control groups within a tissue, but there was little overlap in genomic features with high variability. The interaction between the prenatal environment and the genome could be responsible for the differences in location of the variable DNA methylation.

Project description:BACKGROUND: Dental microwear analyses are commonly used to deduce the diet of extinct mammals. Conventional methods rely on the user identifying features within a 2D image. However, recent interdisciplinary research has lead to the development of an advanced methodology that is free of observer error, based on the automated quantification of 3D surfaces by combining confocal microscopy with scale-sensitive fractal analysis. This method has already proved to be very efficient in detecting dietary differences between species. Focusing on a finer, intra-specific scale of analysis, the aim of this study is to test this method's ability to track such differences between individuals from a single population. METHODOLOGY/PRINCIPAL FINDINGS: For the purposes of this study, the 3D molar microwear of 78 individuals from a well-known population of extant roe deer (Capreolus caprelous) is quantified. Multivariate statistical analyses indicate significant seasonal and sexual differences in individual dental microwear design. These are probably the consequence of seasonal variations in fruit, seed and leaf availability, as well as differences in feeding preference between males and females due to distinct energy requirements during periods of rutting, gestation or giving birth. Nevertheless, further investigations using two-block Partial Least-Squares analysis show no strong relationship between individual stomach contents and microwear texture. This is an expected result, assuming that stomach contents are composed of food items ingested during the last few hours whereas dental microwear texture records the physical properties of items eaten over periods of days or weeks. CONCLUSIONS/SIGNIFICANCE: Microwear 3D scale-sensitive fractal analysis does detect differences in diet ranging from the inter-feeding styles scale to the intra-population between-season and between-sex scales. It is therefore a possible tool, to be used with caution, in the further exploration of the feeding biology and ecology of extinct mammals.

Dataset Information

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.

Publications

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.

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