Zhang Hongliang, Sun Yilun, Saha Sourav, Saha Liton Kumar, Pongor Lorinc S, Dhall Anjali, Pommier Yves
Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
bioRxiv. 2024 Jun 21:2024.06.17.599352. doi: 10.1101/2024.06.17.599352.
Both transcription and replication can take place simultaneously on the same DNA template, potentially leading to transcription-replication conflicts (TRCs) and topological problems. Here we asked which topoisomerase(s) is/are the best candidate(s) for sensing TRC. Genome-wide topoisomerase binding sites were mapped in parallel for all the nuclear topoisomerases (TOP1, TOP2A, TOP2B, TOP3A and TOP3B). To increase the signal to noise ratio (SNR), we used ectopic expression of those topoisomerases in H293 cells followed by a modified CUT&Tag method. Although each topoisomerase showed distinct binding patterns, all topoisomerase binding signals positively correlated with gene transcription. TOP3A binding signals were suppressed by DNA replication inhibition. This was also observed but to a lesser extent for TOP2A and TOP2B. Hence, we propose the involvement of TOP3A in sensing both head-on TRCs (HO-TRCs) and co-directional TRCs (CD-TRCs). In which case, the TOP3A signals appear concentrated within the promoters and first 20 kb regions of the 5' -end of genes, suggesting the prevalence of TRCs and the recruitment of TOP3A in the 5'-regions of transcribed and replicated genes.
转录和复制都可以在同一个DNA模板上同时进行，这可能会导致转录-复制冲突（TRC）和拓扑学问题。在这里，我们研究了哪种拓扑异构酶是感知TRC的最佳候选者。我们并行绘制了所有核拓扑异构酶（TOP1、TOP2A、TOP2B、TOP3A和TOP3B）全基因组范围的拓扑异构酶结合位点。为了提高信噪比（SNR），我们在H293细胞中异位表达这些拓扑异构酶，随后采用改良的CUT&Tag方法。尽管每种拓扑异构酶都表现出不同的结合模式，但所有拓扑异构酶的结合信号都与基因转录呈正相关。DNA复制抑制会抑制TOP3A的结合信号。在TOP2A和TOP2B中也观察到了这种情况，但程度较轻。因此，我们提出TOP3A参与感知迎面而来的TRC（HO-TRC）和同向TRC（CD-TRC）。在这种情况下，TOP3A信号似乎集中在基因5'端的启动子和前20 kb区域内，这表明TRC的普遍性以及TOP3A在转录和复制基因的5'区域中的募集。
