Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.
复制标题
DOI：
10.1371/journal.pcbi.1002322
复制
发表时间：
2011-12
影响因子：
4.3
通讯作者：
Hyrien O
中科院分区：
文献类型：
--
作者：
Guilbaud G;Rappailles A;Baker A;Chen CL;Arneodo A;Goldar A;d'Aubenton-Carafa Y;Thermes C;Audit B;Hyrien O
全基因组复制时间的研究表明，哺乳动物的染色体由大的无起源的过渡区分开的协调起源发射的兆碱基规模的结构域。在这里，我们报告了一个定量的全基因组分析的DNA复制动力学在几种人类细胞类型，这与这种观点相矛盾。DNA梳理在HeLa细胞分为四个时间间隔的S期显示，复制起点间隔在40 kb的间隔和消防的同步性增加，在S期和复制叉速度（平均0.7 kb/min，最大2.0 kb/min）保持恒定，并狭窄地分布在整个S期的小集群。然而，多尺度分析的全基因组复制时序分布显示了广泛的复制时序梯度的分布，几乎没有区域大于100 kb的复制速度小于2 kb/min。因此，HeLa细胞缺乏大区域的单向叉进展。时间过渡区的复制顺序激活的起源在S阶段和复制的时间梯度增加的速率设置的延迟和连续的起源之间的间隔，而不是由单叉的速度。HeLa细胞IGH基因座的DNA梳理直接证明了特定时间过渡区的内部起源的激活。对已发表的HeLa细胞中的起源图和已发表的其他几种细胞类型中的复制时间和DNA梳理数据的分析证实了这些发现，有趣的是胚胎干细胞的例外，其中单向分叉进展的区域似乎更丰富。这些结果可以解释，如果起源火彼此独立，但控制下的远程染色质结构，或者如果复制叉从早期起源的进展刺激启动附近的未复制的DNA。这些发现揭示了哺乳动物基因组的复制定时程序的新的光，并提供了一个通用的复制动力学模型。真核细胞染色体从多个复制起点复制，在S期的不同时间点火。确定起始位置和发射时间以及协调起始点以确保完整基因组复制的机制尚不清楚。以前的研究提出，起源是安排在时间上协调的群体或火灾相互独立的随机方式。在这里，我们进行了人类基因组复制动力学的定量分析，使用DNA梳理的组合，它揭示了局部模式的起源射击和复制叉进展的单个DNA分子，和大规模测序的新复制的DNA，它揭示了整个基因组的人口平均复制时序配置文件。我们发现，起源同步激活在大区域的统一复制时间，但更逐渐在时间过渡区和起源射击的速度增加复制的进展。大区域的单向叉进展在胚胎干细胞中是丰富的，但在分化细胞中是罕见的。我们提出了一个模型，在该模型中，复制叉从早期起源的进展刺激启动附近的未复制的DNA的方式，解释了形状的复制时序配置文件。这些结果提供了一个基本的洞察哺乳动物基因组复制的时间调节。
Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general model for their replication kinetics. Eukaryotic chromosomes replicate from multiple replication origins that fire at different times in S phase. The mechanisms that specify origin position and firing time and coordinate origins to ensure complete genome duplication are unclear. Previous studies proposed either that origins are arranged in temporally coordinated groups or fire independently of each other in a stochastic manner. Here, we have performed a quantitative analysis of human genome replication kinetics using a combination of DNA combing, which reveals local patterns of origin firing and replication fork progression on single DNA molecules, and massive sequencing of newly replicated DNA, which reveals the population-averaged replication timing profile of the entire genome. We show that origins are activated synchronously in large regions of uniform replication timing but more gradually in temporal transition regions and that the rate of origin firing increases as replication progresses. Large regions of unidirectional fork progression are abundant in embryonic stem cells but rare in differentiated cells. We propose a model in which replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA in a manner that explains the shape of the replication timing profile. These results provide a fundamental insight into the temporal regulation of mammalian genome replication.
登录
查看更多内容
影响因子：
3.7
作者：
Goldar A;Marsolier-Kergoat MC;Hyrien O
通讯作者：
Hyrien O
影响因子：
3.7
作者：
Goldar, Arach;Labit, Helene;Hyrien, Olivier
通讯作者：
Hyrien, Olivier
影响因子：
7.7
作者：
Dazy, Sebastien;Gandrillon, Olivier;Prioleau, Marie-Noelle
通讯作者：
Prioleau, Marie-Noelle
影响因子：
21.3
作者：
Dimitrova, DS;Gilbert, DM
通讯作者：
Gilbert, DM
影响因子：
10.5
作者：
Ge, Xin Quan;Jackson, Dean A;Blow, J Julian
通讯作者：
Blow, J Julian