Topologically associating domains are stable units of replication-timing regulation.
Topologically associating domains are stable units of replication-timing regulation.
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DOI：
10.1038/nature13986
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发表时间：
2014-11-20
期刊：
影响因子：
64.8
通讯作者：
Gilbert, David M.
中科院分区：
文献类型：
--
作者：
Pope, Benjamin D.;Ryba, Tyrone;Dileep, Vishnu;Yue, Feng;Wu, Weisheng;Denas, Olgert;Vera, Daniel L.;Wang, Yanli;Hansen, R. Scott;Canfield, Theresa K.;Thurman, Robert E.;Cheng, Yong;Guelsoy, Guenhan;Dennis, Jonathan H.;Snyder, Michael P.;Stamatoyannopoulos, John A.;Taylor, James;Hardison, Ross C.;Kahveci, Tamer;Ren, Bing;Gilbert, David M.
小鼠和人类细胞中DNA复制时间的研究揭示了复制结构域（同时复制的基因组结构域）与拓扑相关结构域的相关性;这些结果使细胞类型特异性亚核区室化与发育稳定的染色体结构域相一致，并为大规模染色体结构和功能提供了统一的模型。本文的在线版本（doi：10.1038/nature 13986）包含补充材料，可供授权用户使用。作为小鼠ENCODE项目的一部分，大卫吉尔伯特和同事们研究了小鼠和人类中复制时间与高级染色质结构域之间的关系。他们发现，复制域的边界-基因组内同时复制的域-与拓扑相关域具有接近一对一的相关性。这些和其他结果调和细胞类型特异性亚核区室化与发育稳定的染色体结构域，并提供了一个统一的模型，大规模的染色体结构和功能。本文的在线版本（doi：10.1038/nature 13986）包含补充材料，可供授权用户使用。真核细胞染色体复制的时间顺序称为复制定时程序。在哺乳动物中，复制时间是细胞类型特异性的，在发育过程中至少有一半的基因组切换复制时间，主要是以400-800个复制结构域（“复制结构域”）为单位，其位置在不同的细胞类型中保留，在物种之间保守，并且似乎限制了染色体重排的长期影响。早期和晚期复制分别与通过高分辨率染色体构象捕获（Hi-C）鉴定的开放和封闭的三维染色质区室相关，并且在较小程度上，晚期复制与核纤层相关结构域（LAD）相关。最近的Hi-C作图揭示了染色质区室内的亚结构，称为拓扑关联结构域（TADs），其在细胞类型之间的位置在很大程度上是保守的，并且大小与复制结构域相似。然而，TADs可以进一步细分为更小的域，挑战任何特定尺度下结构的重要性。此外，试图调和TADs和LAD复制定时数据没有发现一个共同的，潜在的域结构。在这里，我们本地化的复制域的边界复制定时转换的早期复制边界，并映射其位置在18个人类和13个小鼠细胞类型。我们证明，总的来说，复制域边界共享一个接近一对一的相关性与TADs的边界，而在一个细胞类型，相邻的TADs，在相似的时间复制模糊复制域边界，主要占以前报道的缺乏对齐。此外，细胞类型特异性的复制时间的TADs分区的基因组成两个大规模的亚核隔室揭示，复制时间的转换是无法区分的晚期复制区域的染色质组成和层协会和会计的相关性降低的复制时间的LAD和异染色质。我们的研究结果调和了细胞类型特异性亚核区室化和复制时间与发育稳定的结构域，并为大规模染色体结构和功能提供了一个统一的模型。本文的在线版本（doi：10.1038/nature 13986）包含补充材料，可供授权用户使用。
A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a correlation with topologically associating domains; these results reconcile cell-type-specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large scale chromosome structure and function. The online version of this article (doi:10.1038/nature13986) contains supplementary material, which is available to authorized users. As part of the mouse ENCODE project, David Gilbert and colleagues study the relationship between replication timing and higher order chromatin domains in mouse and human. They find that boundaries of replication domains — domains within the genome which replicate at the same time — share a near one-to-one correlation with topology associated domains. These and other results reconcile cell-type specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large-scale chromosome structure and function. The online version of this article (doi:10.1038/nature13986) contains supplementary material, which is available to authorized users. Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400–800 kilobases (‘replication domains’), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function. The online version of this article (doi:10.1038/nature13986) contains supplementary material, which is available to authorized users.
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DOI：
10.1186/1748-7188-9-14
发表时间：
2014
期刊：
Algorithms for molecular biology : AMB
影响因子：
--
作者：
Filippova D;Patro R;Duggal G;Kingsford C
通讯作者：
Kingsford C
影响因子：
16
作者：
McGuffee, Sean R.;Smith, Duncan J.;Whitehouse, Iestyn
通讯作者：
Whitehouse, Iestyn
影响因子：
64.5
作者：
Phillips-Cremins JE;Sauria ME;Sanyal A;Gerasimova TI;Lajoie BR;Bell JS;Ong CT;Hookway TA;Guo C;Sun Y;Bland MJ;Wagstaff W;Dalton S;McDevitt TC;Sen R;Dekker J;Taylor J;Corces VG
通讯作者：
Corces VG
影响因子：
16
作者：
Chandra, Tamir;Kirschner, Kristina;Thuret, Jean-Yves;Pope, Benjamin D.;Ryba, Tyrone;Newman, Scott;Ahmed, Kashif;Samarajiwa, Shamith A.;Salama, Rafik;Carroll, Thomas;Stark, Rory;Janky, Rekin's;Narita, Masako;Xue, Lixiang;Chicas, Agustin;Nunez, Sabrina;Janknecht, Ralf;Hayashi-Takanaka, Yoko;Wilson, Michael D.;Marshall, Aileen;Odom, Duncan T.;Babu, M. Madan;Bazett-Jones, David P.;Tavare, Simon;Edwards, Paul A. W.;Lowe, Scott W.;Kimura, Hiroshi;Gilbert, David M.;Narita, Masashi
通讯作者：
Narita, Masashi
影响因子：
4.3
作者：
Baker A;Audit B;Chen CL;Moindrot B;Leleu A;Guilbaud G;Rappailles A;Vaillant C;Goldar A;Mongelard F;d'Aubenton-Carafa Y;Hyrien O;Thermes C;Arneodo A
通讯作者：
Arneodo A