Abstract

Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

中文翻译：

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2021年3DIV更新：3D基因组和3D癌症基因组的全面资源

摘要

三维（3D）基因组组织与各种生物过程和疾病中的基因调控紧密结合。在癌症中，各种类型的大规模基因组重排可破坏3D基因组，导致致癌基因表达。但是，解开3D癌症基因组的致病性仍然是一个挑战，因为由于缺少专门用于无序的高阶染色质结构的适当工具，进一步限制了仔细检查。在这里，我们通过统一处理约2300亿个原始Hi-C读码，将我们的内容扩展到3D癌症基因组，从而更新了3D基因组交互查看器和名为3DIV的数据库。3DIV的更新如下：（i）收集401个样本，包括220个癌细胞系/肿瘤Hi-C数据，153个正常细胞系/组织Hi-C数据，和28个启动子捕获Hi-C数据，（ii）3D癌症基因组的实时交互操作以模拟结构变异的影响，以及（iii）通过用户定义的染色体顺序重建Hi-C接触图以研究3D复杂基因组重排的基因组。总之，更新的3DIV将是探索正常3D基因组和癌症3D基因组的基因调控作用的最全面资源。“ 3DIV”可从http://3div.kr免费获得。更新的3DIV将是探索正常3D基因组和癌症3D基因组的基因调控作用的最全面资源。“ 3DIV”可从http://3div.kr免费获得。更新的3DIV将是探索正常3D基因组和癌症3D基因组的基因调控作用的最全面资源。“ 3DIV”可从http://3div.kr免费获得。