Formation of new chromatin domains determines pathogenicity of genomic duplications
Formation of new chromatin domains determines pathogenicity of genomic duplications
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DOI：
10.1038/nature19800
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发表时间：
2016-10-13
期刊：
影响因子：
64.8
通讯作者：
Mundlos, Stefan
中科院分区：
文献类型：
--
作者：
Franke, Martin;Ibrahim, Daniel M.;Mundlos, Stefan
染色体构象捕获方法已经鉴定了被称为拓扑相关结构域（TADs）的高阶染色质相互作用的亚染色体结构，其通过边界区域彼此分离（1，2）。通过将基因组细分为离散的调控单元，TADs限制增强子与其靶基因建立的接触（3-5）。然而，基因组划分为TADs的机制仍然知之甚少。在这里，我们通过染色体构象捕获（捕获Hi-C和4C-seq方法）表明，患者细胞和转基因小鼠中的基因组重复可以导致新染色质结构域（neo-TADs）的形成，并且这个过程决定了它们的分子病理学。小鼠Sox 9基因组内非编码DNA的复制导致了人类雌性向雄性的性别逆转（6），显示出Sox 9基因组内复制区域的接触增加，但整个Sox 9基因组结构没有变化。相反，重叠重复延伸到下一个边界进入相邻的染色质结构域（间染色质结构域），导致形成一个新的染色质结构域（新染色质结构域），该结构域与基因组的其余部分分离。由于这种绝缘，内重复没有表型效应。然而，下一个侧翼基因，Kcnj 2，在neo-tumor中的掺入导致Kcnj 2与Sox 9调控区的重复部分的异位接触，Kcnj 2的连续错误表达，和肢体畸形表型。我们的研究结果提供的证据表明，TADs是具有高度内部稳定性的基因组调控单位，可以通过结构基因组变异进行雕刻。这个过程对于解释拷贝数变异很重要，因为这些变异在遗传疾病和癌症的诊断测试中是常规检测的。这一发现也与进化背景有关，因为拷贝数差异被认为在基因组复杂性的进化中起着至关重要的作用。
Chromosome conformation capture methods have identified subchromosomal structures of higher-order chromatin interactions called topologically associated domains (TADs) that are separated from each other by boundary regions(1,2). By subdividing the genome into discrete regulatory units, TADs restrict the contacts that enhancers establish with their target genes(3-5). However, the mechanisms that underlie partitioning of the genome into TADs remain poorly understood. Here we show by chromosome conformation capture (capture Hi-C and 4C-seq methods) that genomic duplications in patient cells and genetically modified mice can result in the formation of new chromatin domains (neo-TADs) and that this process determines their molecular pathology. Duplications of non-coding DNA within the mouse Sox9 TAD (intra-TAD) that cause female to male sex reversal in humans(6), showed increased contact of the duplicated regions within the TAD, but no change in the overall TAD structure. In contrast, overlapping duplications that extended over the next boundary into the neighbouring TAD (inter-TAD), resulted in the formation of a new chromatin domain (neo-TAD) that was isolated from the rest of the genome. As a consequence of this insulation, inter-TAD duplications had no phenotypic effect. However, incorporation of the next flanking gene, Kcnj2, in the neo-TAD resulted in ectopic contacts of Kcnj2 with the duplicated part of the Sox9 regulatory region, consecutive misexpression of Kcnj2, and a limb malformation phenotype. Our findings provide evidence that TADs are genomic regulatory units with a high degree of internal stability that can be sculptured by structural genomic variations. This process is important for the interpretation of copy number variations, as these variations are routinely detected in diagnostic tests for genetic disease and cancer. This finding also has relevance in an evolutionary setting because copy-number differences are thought to have a crucial role in the evolution of genome complexity.