Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: transcription

The early embryonic divisions of many organisms, including fish, flies and frogs are characterised by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much longer due to both a reduction in the total number of initiation events and the imposition of a temporal order of origin activation. The physiological importance of changes in the rate and timing of replication initiation in S-phase remains unclear. Here we assess the importance of the temporal control of replication initiation using a conditional system in budding yeast to drive the early replication of all origins in a single cell cycle. We show that global early replication disrupts the expression of over a quarter of all genes. By deleting individual origins we show that delaying replication is sufficient to restore normal gene expression, directly establishing replication timing control in this regulation. Global early replication disrupts nucleosome positioning and transcription factor binding during S-phase, suggesting that the rate of S-phase is important to regulate the chromatin landscape. Together these data provide new insight into the role of a temporal order of origin firing for coordinating replication, gene expression and chromatin establishment as occurs in the early embryo.包括鱼类、果蝇与青蛙在内的诸多生物，其早期胚胎分裂均以极短的S期（S-phase）为特征，该特征源于极高的复制起始（replication initiation）速率。在体细胞（somatic cells）中，S期则显著更长，这既源于总复制起始事件数量的减少，也源于复制起始位点激活（origin activation）存在严格的时序秩序。目前，S期内复制起始速率与起始时机改变的生理学重要性仍不明确。本研究借助酿酒酵母（budding yeast）中的条件性系统（conditional system），驱动所有复制起始位点在单个细胞周期内提前完成复制，以此评估复制起始时序调控的重要性。我们发现，全局提前复制会扰乱超过四分之一的全部基因的表达。通过单独删除复制起始位点，我们证实延迟复制足以恢复正常的基因表达，直接确立了复制时序调控在该基因表达调控中的核心作用。全局提前复制会在S期内扰乱核小体定位（nucleosome positioning）与转录因子结合（transcription factor binding），这表明S期的进程速率对调控染色质景观（chromatin landscape）具有关键作用。综上，本研究数据为复制起始位点激活（origin firing）的时序秩序在协调复制、基因表达与染色质构建过程中的作用提供了新的见解，而这类调控过程正如早期胚胎中所发生的那样。