H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

Methylated H3K4 (H3K4me) is highly conserved and has been widely considered to be involved in transcriptional control. However, this once popular model was recently challenged by multiple groups, because blocking this modification does not appreciably affect transcription. Thus, the function of the H3K4me remains unclear. To investigate how H3K4 methylation influences the processes of transcription and replication under HU-stress, we used chromatin immunoprecipitation-sequencing (ChIP-seq) to identify genomic sites of active transcription marked by Rpb3, a subunit of RNA Polymerase II, and sites of replication pausing marked by DNA Pol2, a subunit of DNA Polymerase e. Our data lead us to the surprising conclusion that H3K4me pauses the progression of replication forks, and we propose that high levels of H3K4me deposited by high transcriptional activity result in a large cushioning effect on fork progression to protect against transcription-replication collisions (TRCs), which cause genome instability. 16 Samples of RPB3 or DNA pol2 ChIP-Seq for S.cerevisiae in wild type and relevant mutant conditions.

H3K4甲基化修饰（Methylated H3K4, H3K4me）具有高度保守性，长期被学界广泛认为参与转录调控。然而，这一曾被广泛接受的模型近期遭到多个研究团队的质疑——因为阻断该修饰并未对转录产生显著影响，因此H3K4me的具体生物学功能仍未明确。为探究HU应激条件下H3K4甲基化如何影响转录与复制过程，我们采用染色质免疫共沉淀测序（chromatin immunoprecipitation-sequencing, ChIP-seq）技术，鉴定由RNA聚合酶II亚基Rpb3标记的活跃转录基因组位点，以及由DNA聚合酶ε亚基DNA Pol2标记的复制停滞位点。我们的研究数据得出了令人意外的结论：H3K4me会阻滞复制叉的行进，并由此提出假说：高转录活性所沉积的高水平H3K4me，可对复制叉行进产生显著缓冲效应，从而抵御引发基因组不稳定的转录-复制冲突（transcription-replication collisions, TRCs）。本数据集包含16份酿酒酵母（S.cerevisiae）在野生型及相关突变体条件下的RPB3或DNA pol2的ChIP-seq样本。