人类基因组高分辨率三维结构分析

THE RESEARCH OF HUMAN 3D GENOME ORGANIZATION IN HIGHER-RESOLUTION

李家硕

11849444

硕士

生物学

黄鸿达

2020-06-05

2020-07-09

哈尔滨工业大学

深圳

在细胞核内的三维空间中，染色质以精确的空间折叠，形成了不同尺度层次的 三维基因组空间结构，使得互不相邻的两个基因组位点得以相互接触，从而实现了 DNA 调控元件对相关基因的表达调控。目前的染色质三维空间结构研究均集中在 较大尺度结构变化上，如染色质区室(A/B compartments)，拓扑相关结构域(the topologically associating domains, TADs)以及染色质环状结构(loop domain)等， 而对于拓扑相关结构域内部细微的染色质三维空间结构的研究尚未被报道。本课 题利用基于 In situ Hi-C 技术开发的 SAFE Hi-C(simplified amplification-free and economically efficient Hi-C)技术，以人类癌细胞 K562 为实验材料，并结合相关生 物信息学方法，在高分辨率下鉴定人类三维基因组细微结构。本课题成功构建出高 质量 SAFE Hi-C 文库，并与已发表的 In situ Hi-C 数据相比，二者比对率大致相同,均为 91%以上，Hi-C contacts 分别为 82.38%，69.65%，染色体内相互作用数分别 为 81.08%，65.06%。通过观察染色体相互作用图谱，染色体互作频率衰减曲线以 及计算全基因组范围内的 Border Index，发现 SAFE Hi-C 数据可能含有丰富的染色 质空间相互作用信息。其次，本课题利用 Arrowhead 算法分别在 SAFE Hi-C 数据 和 In situ Hi-C 数据中鉴定出拓扑相关结构域，并发现 CTCF，RNA polymerase II， H3K27ac 等蛋白高度富集于 SAFE Hi-C 和 In situ Hi-C 各自特异性以及共同的拓扑 相关结构域边界区域。此外，通过计算 SAFE Hi-C 数据和 In situ Hi-C 数据的 Border Index，本课题成功在全基因组范围内筛选了各自的 border 结构，发现 CTCF，RNA polymeraseII，H3K27ac等转录因子以及相关组蛋白修饰在两类border区域的富集 情况大致相同。通过将 SAFE Hi-C 和 In situ Hi-C 的 border 结构的 Border Index 相 除，进一步分析了二者染色质空间相互作用差异情况，发现 SAFE Hi-C 的 border 区域的 Border Index 整体上高于 In situ Hi-C 的 border 区域的 Border Index，而且 CTCF，RNA polymerase II，H3K27ac 等蛋白在不同的比值范围的 border 区域有着不同的富集程度。总之，本课题为进一步分析鉴定人类三维基因组精细结构打下了坚实的基础。关键词:基因表达调控;三维基因组;SAFE Hi-C 技术;人类三维基因组精细结构

In the three-dimensional space of the nucleus, there are many chromatins spatial structures at different scales and levels that are be folded accurately by some chromatins to help the DNA regulatory elements realize the spaciotemporal specific expression regulation of related genes. Currently, the researches about the three-dimensional structure of chromatins has focused on large-scale structural changes, such as A / B compartments, the topologically associating domains (TADs) and chromatin loop domains, but the researches on the more detailed chromatin spatial structures within TADs has not been reported. This project is designed to identify the more detailed three- dimensional structure of chromatins in human genome at high resolution by using relevant bioinformatics methods and SAFE Hi-C (simplified amplification-free and economically efficient Hi-C) technology that is based on the In situ Hi-C technology. And the K562 human cell line is the experimental materials. This project successfully constructed a high-quality SAFE Hi-C library. Compared with the published In situ Hi-C data, we found that the alignment of SAFE Hi-C and In situ Hi-C data are similar, both are over 91%, and the Hi-C contacts are 82.38% and 69.65%, intrachromosomal interactions are 81.08%, 65.06%, respectively. The chromatin interaction map, decay curve and border index suggest that SAFE Hi-C data has more proximal chromatin interaction information. Secondly, we used Arrowhead algorithm to identify the TADs in SAFE Hi-C data and In situ Hi-C data, respectively, and found that proteins such as CTCF, RNA polymerase II, H3K27ac and others are highly enriched in most TADs boundary ,including SAFE Hi-C specific TADs boundary, In situ Hi-C data specific TADs boundary and common TADs boundary; In addition, by calculating the Border Index of SAFE Hi-C data and In situ Hi-C data, we successfully screened their borders , and found that the enrichment of CTCF, RNA polymerase II, H3K27ac and other proteins in the two types of borders has no differences. By dividing the Border Index of SAFE Hi- C and In situ Hi-C, the different chromatin spatial interaction between them is further analyzed, and it is found that the border of SAFE Hi-C is higher than that of In situ Hi-C on the whole, and the proteins such as CTCF, RNA polymerase II, H3K27ac had different enrichment degrees in the border regions of different ratios. Keywords: gene expression regulation, three-dimensional genome, SAFE Hi-C technology, human three-dimensional genome fine structure

基因表达调控 三维基因组 SAFE Hi-C 技术 人类三维基因组精细结构

gene expression regulation three-dimensional genome SAFE Hi-C technology human three-dimensional genome fine structure

中文

联合培养

南方科技大学

李家硕. 人类基因组高分辨率三维结构分析[D]. 深圳. 哈尔滨工业大学,2020.