Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
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DOI：
10.1038/nature20158
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发表时间：
2016-12-08
期刊：
影响因子：
64.8
通讯作者：
Tanay, Amos
中科院分区：
文献类型：
--
作者：
Olivares-Chauvet, Pedro;Mukamel, Zohar;Tanay, Amos
染色体被折叠成高度紧凑的结构，以适应细胞核内的物理约束，并调节对基因组信息的访问（1，2）。最近，成对接触的全局映射显示，环锚定拓扑结构域（TADs）在细胞类型和物种之间高度保守（3-8）。成对环（9-14）是否协同形成更高级的结构仍不清楚。在这里，我们开发了一种构象捕获测定法，使用染色体步移（C步移）将多个基因组位点连接在一起，形成人类和小鼠细胞中的邻近链，来研究高阶组织。这种方法捕获不同尺度的染色体结构。染色体间接触仅占染色体对的7-10%，并且受到界面TAD的限制。大约有一半的C步停留在一条染色体内，其中几乎一半限制在染色体内空间。耦合2-4个TAD的C-步线表明转录活性的早期复制基因座之间的随机关联。对锚定在高表达基因上的数千个3步的靶向分析支持活性基因座上的成对而非枢纽样染色体拓扑结构。多梳抑制的Hox结构域显示通过相同的方法来富集协同枢纽。总之，这些数据表明，染色体领土，TADs，和intra-tumor循环主要是由嵌套的，可能是动态的，成对的接触。
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information(1,2). Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species(3-8). Whether pairwise loops(9-14) synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells. This approach captures chromosomal structure at varying scales. Inter-chromosomal contacts constitute only 7-10% of the pairs and are restricted by interfacing TADs. About half of the C-walks stay within one chromosome, and almost half of those are restricted to intra-TAD spaces. C-walks that couple 2-4 TADs indicate stochastic associations between transcriptionally active, early replicating loci. Targeted analysis of thousands of 3-walks anchored at highly expressed genes support pairwise, rather than hub-like, chromosomal topology at active loci. Polycomb-repressed Hox domains are shown by the same approach to enrich for synergistic hubs. Together, the data indicate that chromosomal territories, TADs, and intra-TAD loops are primarily driven by nested, possibly dynamic, pairwise contacts.