DNA Methylome in Human Peripheral Blood Monocytes

Purpose: We characterized genome-wide DNA methylation profiles (methylome) in purified peripheral blood monocytes (PBMs) from 18 healthy postmenopausal Caucasian females aged 50-56 years.Methods: DNA methylome of Human Peripheral Blood Monocytes were generated by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq), using Illumina GAIIx. The sequence reads that passed quality filters were analyzed using MEDIPS package. Targeted methylation validation analysis was performed by using MassARRAY EpiTYPER assays. Genome-wide gene expression profiles have been obtained for 7 of the 18 subjects by using Affymetrix 1.0 Human Exon ST arrays following the manufacturer's recommended protocols.Results: Using MeDIP-seq,a total of approximately 283 million reads were uniquely aligned to human genome (Build NCBI37, HG19), resulting in average ~16 million uniquely aligned high quality reads per sample. Distinct patterns were revealed at different genomic features. For instance, promoters were commonly (~58%) found to be unmethylated; whereas protein coding regions were largely (~84%) methylated. We found that approximately 24% CpG islands (CGIs) were highly methylated in PBMs. Further characterization of CGIs with respect to their relative locations to RefSeq genes revealed that the highly methylated CGIs were largely enriched (~89%) in CGIs located in gene bodies and intergenic regions. By integration of the methylome data with genome-wide PBM gene expression data, we found negative correlation between promoter methylation levels and gene transcription levels when comparing groups of genes with different expression levels, and this relationship was consistently observed across promoters with high to low CpG densities. Furthermore, we observed a modest but significant excess (permutation p<0.0001) of genes showing negative correlation between inter-individual promoter methylation and transcription levels, particularly for genes associated with CpG-rich promoters. Across the 18 individual PBM methylomes, we also identified genomic regions that were constitutively highly methylated in PBMs as well as regions showing large inter-individual variability.Conclusions: This study represents a comprehensive analysis of the PBM methylome and our data provides a valuable resource for future epigenomic and multi-omic studies exploring biological and disease-related regulatory mechanisms in PBMs.

研究目的：我们针对18名年龄介于50至56岁的绝经后健康高加索女性，对其纯化外周血单核细胞（peripheral blood monocytes, PBMs）的全基因组DNA甲基化谱（methylome）开展了表征分析。
研究方法：采用Illumina GAIIx测序平台，通过甲基化DNA免疫共沉淀结合高通量测序（methylated DNA immunoprecipitation combined with high-throughput sequencing, MeDIP-seq）构建人外周血单核细胞的DNA甲基组。对通过质量过滤的序列读段使用MEDIPS软件包进行数据分析。采用MassARRAY EpiTYPER检测技术开展靶向甲基化验证分析。按照厂商推荐的实验流程，使用Affymetrix 1.0 Human Exon ST芯片对18名受试者中的7名完成了全基因组基因表达谱检测。
研究结果：通过MeDIP-seq技术，总计约2.83亿条序列读段被唯一比对至人类基因组（构建版本NCBI37，即HG19），每个样本平均获得约1600万条唯一比对的高质量读段。不同基因组特征区域呈现出独特的甲基化模式：例如，约58%的启动子区域通常呈非甲基化状态；而约84%的蛋白编码区域则处于甲基化状态。我们发现，在外周血单核细胞中，约24%的CpG岛（CpG islands, CGIs）呈现高度甲基化。进一步结合CGIs与RefSeq基因的相对位置进行分析发现，高度甲基化的CGIs主要富集（约89%）于基因本体及基因间区域。将甲基组数据与全基因组外周血单核细胞基因表达数据整合后，我们观察到：在对比不同表达水平的基因分组时，启动子甲基化水平与基因转录水平呈负相关，且这一关系在CpG密度从高到低的各类启动子中均一致存在。此外，我们发现存在数量适度但具有统计学显著性的基因（置换检验p<0.0001），其个体间启动子甲基化水平与转录水平呈负相关，这一现象在CpG富集型启动子关联基因中尤为显著。在18份个体外周血单核细胞甲基组数据中，我们还鉴定出了在外周血单核细胞中持续高度甲基化的基因组区域，以及个体间差异较大的基因组区域。
研究结论：本研究对人外周血单核细胞甲基组开展了全面分析，所获数据可为未来探索外周血单核细胞中生物学及疾病相关调控机制的表观基因组学与多组学研究提供宝贵的资源。

搜集汇总

背景与挑战

背景概述

该数据集提供了18名健康绝经后高加索女性外周血单核细胞的全基因组DNA甲基化谱，采用MeDIP-seq技术生成，平均每个样本产生约1600万条高质量测序读数。研究发现启动子区域普遍未甲基化，而蛋白质编码区域高度甲基化，并揭示了启动子甲基化与基因转录水平之间的负相关关系，为表观基因组和多组学研究提供了重要资源。