表观遗传修饰的调控作用日益受到人们的重视。然而，我们对进化过程中表观遗传修饰如何影响表型仍然知之甚少，尤其是表观遗传分歧在人脑进化中扮演何种角色正逐渐成为一个关乎神经精神疾病和人类意识的基础问题，而人脑在近期经历了一次无与伦比的进化革新。为了进一步了解人脑特异性的表观遗传变化，我们实验室与乔治亚理工学院的Soojin V. Yi 实验室合作，对人脑和黑猩猩脑之间的差异甲基化区域 （DMR） 进行了鉴别和进一步的分析。我们首先比较了人类和黑猩猩的全基因组亚硫酸氢盐测序图谱（甲基化组），然后再通过对比猕猴的脑甲基化组以对这些DMR在系统发育过程中的的变异进行了分析。我们还采集了六个灵长类物种的脑样本从而对这些DMR区域进行了DNA甲基化测序验证以及DNA序列测定，结果显示我们的策略可以解释物种间基因组和表观遗传变异。我们所鉴别出的DMR显著地富集于之前的研究所鉴别出的人类特异性H3K4me3修饰信号区，这表明各种表观遗传标记之间的进化改变是协调的。我们在没有任何先验信息的情况下进行全基因组扫描，发现近一半的DMR位于距已知转录起始位点3kb范围内，并且这些DMR与多种组织，尤其是脑组织中的启动子和增强子的染色质信号有联系。此外，很多距离基因很远的DMR也呈现出明显的而且几乎只存在于脑组织中的活性启动子的染色质信号，这表明这些区域可能是目前尚未注释的人脑特异性的活性转录区域。此外，这些DMR也显示出参与活性染色质环，以及参与转录因子结合的证据，尤其是在神经发育过程中有关键作用的转录因子。以上这些结果表明大量进化表观遗传修饰与人脑特异性转录调控有关。以本次研究为例表明，比较表观遗传学分析对人脑发育和病理生理学提供了独特和关键的视角。此外，在上述所鉴别出的人类特异性DMR中，一个位于小头症相关基因EOMES上游的候选DMR（我们命名为met2）引起了我们的关注，因met2区域的组蛋白修饰信号预示其可能为增强子。因此我们提出这样一个问题——met2的甲基化差异是否会影响EOMES基因的表达，从而对人类脑容量的增大有所贡献？因此我们进行了报告基因实验以验证met2是否为增强子，以及如果met2是增强子，甲基化差异是否会显著影响其增强子活性。目前实验正在进行，预计在论文答辩之前可以完成全部实验。; The regulatory significance of epigenetic modifications is increasingly appreciated. However, how epigenetic modifications impact phenotypes in evolution remain poorly understood. In particular, the role of epigenetic divergence on the evolution of human brains, which underwent an unparalleled degree of recent evolutionary innovation, is emerging as a fundamental question with deep implications for neuropsychiatric diseases and human cognition. To gain further insights into human brain specific epigenetic changes, our laboratory cooperated with Soojin V. Yi ’ s laboratory in Georgia Institute of Technology to explore this problem. here we report the discovery and analyses of differentially methylated genomic regions （DMRs） in human brains compared to the brains of our closest extant relative, chimpanzees. We began by comparing whole genome bisulfite sequencing methylation maps （methylomes） of humans and chimpanzees. We further examined deeper phylogenetic variation of these DMRs by incorporating brain methylomes of rhesus macaques. Targeted genome and DNA methylation sequencing of brain samples across six primate species shows that our discovery pipeline strategy can account for genomic and epigenomic variation within species. The DMRs are significantly enriched in previously identified human-specific signatures of H3K4me3 modification, revealing coordinated epigenetic evolutionary changes. Nearly half of the putative DMRs, identified from genome-wide scans without any a priori information, locate within 3kb of known transcription start sites, and associate with promoter and enhancer chromatin signatures in many tissues, primarily in brain samples. Moreover, a substantial number of distal intergenic DMRs also exhibit conspicuous chromatin signatures of active promoters almost exclusively in brain samples, suggesting that they mark currently unannotated loci of active human brain-specific transcription. DMRs also show evidence for participation in active chromatin loops and transcription factor binding, in particular those with critical roles in neurodevelopment. Together these results support substantial evolutionary epigenetic modifications implicated in human brain specific transcription regulation. Comparative epigenomic analyses such as the current study provide unique and critical insights into brain development and pathophysiology. In addition, one of the Candidate DMRs has brought our attention.This DMR （named met2）is located in upstream of gene EOMES involved Microcephaly,and it may be a enhancer according to it’s histone modification.So we raise a question : may the methylation difference of met2 lead EOMES to express differently and futher contribute to the increase of human brain volume ? Therfore, we did reporter gene assays to test whether met2 has the activity of enhancer, and if so, whether methylation difference can change its activity significantly.Now the experiment is ongoing and we expect it will be finished before my graduate paper defense.
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