DNA replication initiation shapes the mutational landscape and expression of the human genome (RNA-Seq). DNA replication initiation shapes the mutational landscape and expression of the human genome (RNA-Seq)

The interplay between active biological processes and DNA repair is central to mutagenesis. We found that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with the formation of DNA breaks at the centre of the origins and local error-prone DNA synthesis in their immediate vicinity. To support our mutational signature analysis, we performed DSBs mapping (INDUCE-seq) in parallel with RNA-seq, ATAC-seq and TOP2A/B CUT&RUN assays and show that origin activation leads to the TOP2A/B-dependent accumulation of DSBs at origins found at TSS and splice sites of both expressed and non-expressed genes in human H9 embryonic stem cells. Overall design: Gene expression profiling analysis of RNA-seq data for H9 cells.

活性生物学过程与DNA修复之间的相互作用，是诱变发生的核心机制。本研究发现，普遍存在的DNA复制起始过程具有诱变效应，会在数千个早期且高效的复制起始位点留下特异性的突变足迹。观测到的突变模式与复制起始位点中心处的DNA双链断裂形成，以及其紧邻区域内的局部易错DNA合成过程高度吻合。为支撑本研究的突变特征分析，我们同步开展了DNA双链断裂（double-strand breaks, DSBs）定位实验（INDUCE-seq），并配套进行了RNA测序（RNA-seq）、转座酶可及性测序（ATAC-seq）以及TOP2A/B CUT&RUN检测；结果证实，在人类H9胚胎干细胞中，复制起始位点的激活会依赖TOP2A/B，在位于表达基因与非表达基因的转录起始位点（transcription start site, TSS）及剪接位点处的复制起始位点处，诱导DSBs的积累。整体实验设计：针对H9细胞的RNA-seq数据开展基因表达谱分析。