Poterlowicz Krzysztof, Yarker Joanne L, Malashchuk Igor, Lajoie Brian R, Mardaryev Andrei N, Gdula Michal R, Sharov Andrey A, Kohwi-Shigematsu Terumi, Botchkarev Vladimir A, Fessing Michael Y
Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom.
Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
PLoS Genet. 2017 Sep 1;13(9):e1006966. doi: 10.1371/journal.pgen.1006966. eCollection 2017 Sep.
Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription.
哺乳动物基因组包含几十个大型（>0.5 Mbp）的谱系特异性基因座，这些基因座含有功能相关的基因。然而，这些基因座中的空间染色质折叠、增强子-启动子网络的组织及其与拓扑相关结构域（TADs）的相关性仍知之甚少。TADs是基因组折叠的主要单位，代表了DNA区域，在该区域内DNA在TAD边界两侧的相互作用频率较高和较低。在这里，我们使用染色质构象捕获碳拷贝（5C）技术来表征3.1 Mb表皮分化复合体（EDC）基因座中的空间染色质相互作用网络，该基因座包含61个功能相关的基因，这些基因在表皮终末角质形成细胞分化过程中表现出谱系特异性激活。经3D-FISH验证的5C数据表明，EDC基因座被组织成几个TADs，根据其转录活性和基因丰富或基因贫乏状态显示出不同的谱系特异性染色质相互作用网络。5C结果与全基因组增强子特异性组蛋白修饰（H3K4me1和H3K27ac）研究的相关性表明，角质形成细胞中EDC基因座处涉及基因丰富TADs的大多数空间染色质相互作用包括TAD内和TAD间相互作用网络，连接基因启动子和增强子。与EDC基因座大多转录不活跃的胸腺细胞相比，这些相互作用被发现是角质形成细胞特异性的。在角质形成细胞中，基因丰富的转录活跃TADs中的启动子-增强子锚定区域富含染色质结构蛋白CTCF、Rad21和染色质重塑因子Brg1的结合。与基因丰富的TADs相反，基因贫乏的TADs彼此之间表现出优先的空间接触，不包含活性增强子，并且在角质形成细胞中CTCF、Rad21和Brg1的结合减少。因此，皮肤上皮细胞中多TAD EDC基因座处基因启动子和增强子之间的空间相互作用是细胞类型特异性的，涉及TAD内以及不同基因丰富TADs之间的广泛接触，形成了谱系特异性转录的框架。
