Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription.
Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription.
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DOI：
10.1101/gr.180497.114
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发表时间：
2015-03
期刊：
影响因子：
7
通讯作者：
Feng W
中科院分区：
文献类型：
--
作者：
Hoffman EA;McCulley A;Haarer B;Arnak R;Feng W
我们以前已经证明，在酿酒酵母复制，检查点失活通过mec 1突变导致染色体断裂的复制叉从几乎所有的起源后，短暂暴露于羟基脲（HU），核糖核苷酸还原酶的抑制剂。在这里，我们试图确定是否所有的复制叉含有单链DNA缺口产生双链断裂（DSB）的细胞试图从HU暴露恢复的概率相等。我们设计了一种新的方法，Break-seq，将我们先前描述的DSB标记与下一代测序相结合，以提高灵敏度和分辨率来绘制染色体断裂。我们发现，DSB优先发生在基因转录诱导的HU。值得注意的是，不同子集的HU诱导的基因产生的DSB在MEC 1和MEC 1细胞的复制叉穿越了更大的距离MEC 1细胞比在MEC 1细胞在HU的恢复。具体而言，虽然MEC 1细胞在应激反应转录因子中表现出染色体断裂，但MEC 1细胞主要在转运蛋白基因中遭受染色体断裂，其中许多是这些转录因子的底物。我们建议，胡诱导的染色体脆性出现在更高的频率附近的胡诱导的基因作为不稳定的复制叉遇到转录因子结合和/或转录的行为的结果。我们进一步提出，复制抑制剂可以诱导复制和转录之间的计划外相遇，并产生染色体脆性位点的不同模式。
We have previously demonstrated that in Saccharomyces cerevisiae replication, checkpoint inactivation via a mec1 mutation leads to chromosome breakage at replication forks initiated from virtually all origins after transient exposure to hydroxyurea (HU), an inhibitor of ribonucleotide reductase. Here we sought to determine whether all replication forks containing single-stranded DNA gaps have equal probability of producing double-strand breaks (DSBs) when cells attempt to recover from HU exposure. We devised a new methodology, Break-seq, that combines our previously described DSB labeling with next generation sequencing to map chromosome breaks with improved sensitivity and resolution. We show that DSBs preferentially occur at genes transcriptionally induced by HU. Notably, different subsets of the HU-induced genes produced DSBs in MEC1 and mec1 cells as replication forks traversed a greater distance in MEC1 cells than in mec1 cells during recovery from HU. Specifically, while MEC1 cells exhibited chromosome breakage at stress-response transcription factors, mec1 cells predominantly suffered chromosome breakage at transporter genes, many of which are the substrates of those transcription factors. We propose that HU-induced chromosome fragility arises at higher frequency near HU-induced genes as a result of destabilized replication forks encountering transcription factor binding and/or the act of transcription. We further propose that replication inhibitors can induce unscheduled encounters between replication and transcription and give rise to distinct patterns of chromosome fragile sites.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
21.3
作者：
Feng, Wenyi;Collingwood, David;Boeck, Max E;Fox, Lindsay A;Alvino, Gina M;Fangman, Walton L;Raghuraman, Mosur K;Brewer, Bonita J
通讯作者：
Brewer, Bonita J
影响因子：
3.1
作者：
Dubacq, C;Chevalier, A;Mann, C
通讯作者：
Mann, C
影响因子：
1
作者：
Konstantinou, Eleni;Pashalidis, Ioannis;Kontoghiorghes, George J.
通讯作者：
Kontoghiorghes, George J.
DOI：
10.1534/g3.111.000554
发表时间：
2011-10
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Feng W;Di Rienzi SC;Raghuraman MK;Brewer BJ
通讯作者：
Brewer BJ