Integrative DNA Methylation and Gene Expression Analyses Identify DNA Packaging and Epigenetic Regulatory Genes Associated with Low Motility Sperm

BackgroundIn previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. Methods and ResultsSperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,578 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P = 0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (QHDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). There was a trend among altered expression of these epigenetic regulatory genes and RPMM DNA methylation class. ConclusionsUsing integrative genome-wide approaches we identified CpG methylation profiles and mRNA alterations associated with low sperm motility.研究背景：既往采用候选基因策略的相关研究表明，少精子症（oligospermia）与精子mRNA含量改变以及印记基因、非印记基因的DNA甲基化异常存在关联。本研究针对精子DNA甲基化与mRNA含量开展全基因组分析，以检验其与精子功能的相关性。方法与结果：从就诊于三级男性生殖健康专科门诊的21名男性受试者中分离获得精子DNA与mRNA，其精液参数存在一定差异。采用Illumina Infinium芯片对27578个CpG位点进行DNA甲基化检测。对甲基化数据进行无监督聚类后，可依据21份精子样本的活力值对其进行区分。对甲基化数据开展递归分割混合建模（recursively partitioned mixture modeling, RPMM），得到4种不同的甲基化分型，该分型与精子活力显著相关（P=0.01）。基于精子活力开展微阵列分析线性模型（linear models of microarray analysis, LIMMA）分析，共鉴定出9189个甲基化水平显著改变的CpG位点，其中包括QHDAC1（NCBI编号3065）、SIRT3（NCBI编号23410）及DNMT3A（NCBI编号1788）。上述表观遗传调控基因的表达变化与RPMM所得DNA甲基化分型存在关联趋势。结论：本研究通过整合性全基因组分析方法，鉴定出与精子低活力相关的CpG甲基化分型与mRNA表达改变。