Whole-genome DNA methylation maps for human and chimpanzee peripheral blood leukocytes (PBLs).. Whole-genome DNA methylation maps for human and chimpanzee peripheral blood leukocytes (PBLs).

It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. To study differences in DNA methylation between humans and chimanzees, we collected methylated DNAs from age- and gender-matched PBL samples of the two species, and deeply sequenced. The map counts were then converted to MEDIPS scores in 100-bp bins, which are related to absolute methylation levels. Overall design: Genomic DNA samples of PBLs from 4 individuals for each species were pooled, and the pooled samples were flagmented into 200-600 bp by sonication. Methylated DNA fragments were collected by using the His-tagged MBD1. The sequence libraries were constructed for total and MBD1-collected DNA fragments by using paired-end sequencing kit (Illumina). The library was deeply sequenced on Illumina Genome Analyzer II with 75-bp paired-end sequencing. These reads were aligned to the human (hg19) or chimpanzee (panTro3) genomes using Bowtie. The aligned results were further processed using MEDIPS, which gave methylation scores in 100-bp windows.

学界普遍认为，表观遗传变化是近缘物种间表型进化分化的内在基础。为研究人类与黑猩猩（chimpanzee）之间的DNA甲基化差异，我们从两个物种的年龄、性别匹配的外周血淋巴细胞（peripheral blood lymphocytes, PBL）样本中获取甲基化DNA，并进行深度测序。随后将比对计数结果转换为100bp窗口内的MEDIPS得分，该得分与绝对甲基化水平相关。
实验整体设计如下：将每个物种4名个体的外周血淋巴细胞基因组DNA样本混合，通过超声破碎将混合样本打断为200-600bp的片段；利用带有His标签的MBD1蛋白富集甲基化DNA片段；使用Illumina配对末端测序建库试剂盒，分别为总DNA片段和MBD1富集的DNA片段构建测序文库；将构建好的文库在Illumina Genome Analyzer II测序平台上进行75bp配对末端深度测序。使用Bowtie软件将测序读段比对至人类（hg19）或黑猩猩（panTro3）参考基因组，随后使用MEDIPS软件对比对结果进行进一步处理，得到100bp窗口内的甲基化得分。