Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.
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进化断点的紧密 3D 接近性支持了空间同线性的概念。
DOI：
10.1186/1471-2164-12-303
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发表时间：
2011-06-10
期刊：
影响因子：
4.4
通讯作者：
Sagot MF
中科院分区：
文献类型：
--
作者：
Véron AS;Lemaitre C;Gautier C;Lacroix V;Sagot MF
染色体的折叠和混合有可能使基因组上很远的位点彼此靠近，甚至在不同的染色体上。另一方面，基因组重排在位点邻近性的重组中也起着重要作用。在体细胞重排的情况下，是否同一基因座参与了这两种机制的研究，但从未从进化的角度出发。在本文中，我们分析了两个数据集之间的相关性：(i)使用Hi-C协议在人类细胞中获得的全基因组染色质接触数据；（ii）自人类和小鼠谱系分裂以来，由于进化重排而产生的一系列断点区域。令人惊讶的是，我们发现在人类基因组中相距遥远但在小鼠基因组中相邻的两个位点在人类细胞核中被观察到的接近程度明显高于预期。重要的是，我们表明这一结果适用于位于同一染色体上的位点，而不管它们之间的基因组距离如何，并且信号在基因丰富和开放染色质区域更强。这些发现有力地表明，染色体的部分三维组织可能在非常大的进化距离上是保守的。为了描述这种现象，我们建议使用空间合成的概念，将基因组合成的概念推广到3D情况。
Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same loci are involved in both mechanisms has been studied in the case of somatic rearrangements, but never from an evolutionary standpoint. In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages. Surprisingly, we found that two loci distant in the human genome but adjacent in the mouse genome are significantly more often observed in close proximity in the human nucleus than expected. Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions. These findings strongly suggest that part of the 3D organisation of chromosomes may be conserved across very large evolutionary distances. To characterise this phenomenon, we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case.
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影响因子：
56.9
作者：
Murphy, WJ;Larkin, DM;Lewin, HA
通讯作者：
Lewin, HA
影响因子：
5.3
作者：
Goetze, Sandra;Mateos-Langerak, Julio;van Driel, Roel
通讯作者：
van Driel, Roel
影响因子：
3.4
作者：
Hinsch, Hanno;Hannenhalli, Sridhar
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Hannenhalli, Sridhar
影响因子：
9.8
作者：
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通讯作者：
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编码UCSC基因组浏览器中的全基因组数据。
影响因子：
14.9
作者：
Rosenbloom KR;Dreszer TR;Pheasant M;Barber GP;Meyer LR;Pohl A;Raney BJ;Wang T;Hinrichs AS;Zweig AS;Fujita PA;Learned K;Rhead B;Smith KE;Kuhn RM;Karolchik D;Haussler D;Kent WJ
通讯作者：
Kent WJ