He Ximiao, Chatterjee Raghunath, Tillo Desiree, Smith Andrew, FitzGerald Peter, Vinson Charles
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.
Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India.
Epigenetics Chromatin. 2014 Dec 2;7(1):34. doi: 10.1186/1756-8935-7-34. eCollection 2014.
The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with transcriptional repression, is the most highly studied chemical modification of DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated regions (HMRs) often occur in CG islands (CGIs), however, they also occur outside of CGIs and function as cell-type specific enhancers. During the process of differentiation, reorganization of chromatin and nucleosome arrangement at regulatory regions is thought to occur in order for the establishment of cell-type specific transcriptional programs. However, the specifics regarding the organization of nucleosomes at HMRs and the potential mechanisms regulating nucleosome occupancy in these regions are unknown. Here, we have investigated nucleosome organization around hypomethylated regions (HMRs) identified in two mouse primary cells.
Microccocal nuclease (MNase) digested mononucleosomes from primary cultures of new-born female mouse dermal fibroblasts and keratinocytes were mapped and compared to the HMRs obtained from single base-pair resolution methylomes. In both cell types, we find that nucleosomes are enriched at HMR boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region. Nucleosomes are enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types suggesting that nucleosome organization surrounding HMR boundaries is independent of methylation status. In addition, we find potential transcription factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries.
Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome. Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.
表观遗传修饰与染色质结构之间的相互作用是我们理解基因组功能不可或缺的部分。CG二核苷酸处的胞嘧啶甲基化（5mC），传统上与转录抑制相关，是研究最为深入的DNA化学修饰，在基因组中超过70%的CG二核苷酸处发生。低甲基化区域（HMRs）常出现在CG岛（CGIs）中，然而，它们也出现在CGIs之外，并作为细胞类型特异性增强子发挥作用。在分化过程中，为了建立细胞类型特异性转录程序，调控区域的染色质和核小体排列被认为会发生重组。然而，关于HMRs处核小体的组织特异性以及调节这些区域核小体占据的潜在机制尚不清楚。在这里，我们研究了在两种小鼠原代细胞中鉴定出的低甲基化区域（HMRs）周围的核小体组织情况。
微球菌核酸酶（MNase）消化新生雌性小鼠皮肤成纤维细胞和角质形成细胞原代培养物中的单核小体，并进行定位，然后与从单碱基对分辨率甲基化组获得的HMRs进行比较。在两种细胞类型中，我们发现核小体在HMR边界处富集。与CGIs中HMR边界处发现的核小体不同，CGIs之外的HMRs经计算被认为优先被核小体结合，且相位核小体延伸到甲基化区域。在两种细胞类型中，核小体都在组织特异性HMRs（TS - HMRs）边界处富集，这表明HMR边界周围的核小体组织与甲基化状态无关。此外，我们发现在非CGI TS - HMR边界中富集了潜在的转录因子（TF）结合位点（E - 盒基序）。
我们的结果表明，固有核小体占据分数（INOS）与非CGI TS - HMRs周围的核小体组织呈正相关，这表明DNA序列在基因组中HMRs的建立中发挥作用。由于核小体影响涉及基因组的所有过程，我们的结果提供了表观遗传修饰、染色质结构和调控功能之间的联系。
