Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France.
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
Nucleic Acids Res. 2023 Feb 28;51(4):e22. doi: 10.1093/nar/gkac1239.
During each cell division, tens of thousands of DNA replication origins are co-ordinately activated to ensure the complete duplication of the human genome. However, replication fork progression can be challenged by many factors, including co-directional and head-on transcription-replication conflicts (TRC). Head-on TRCs are more dangerous for genome integrity. To study the direction of replication fork movement and TRCs, we developed a bioinformatics toolkit called OKseqHMM (https://github.com/CL-CHEN-Lab/OK-Seq, https://doi.org/10.5281/zenodo.7428883). Then, we used OKseqHMM to analyse a large number of datasets obtained by Okazaki fragment sequencing to directly measure the genome-wide replication fork directionality (RFD) and to accurately predict replication initiation and termination at a fine resolution in organisms including yeast, mouse and human. We also successfully applied our analysis to other genome-wide sequencing techniques that also contain RFD information (e.g. eSPAN, TrAEL-seq). Our toolkit can be used to predict replication initiation and fork progression direction genome-wide in a wide range of cell models and growth conditions. Comparing the replication and transcription directions allows identifying loci at risk of TRCs, particularly head-on TRCs, and investigating their role in genome instability by checking DNA damage data, which is of prime importance for human health.
在每个细胞分裂过程中，数以万计的 DNA 复制起点被协调激活，以确保人类基因组的完全复制。然而，复制叉的推进可能会受到许多因素的挑战，包括同向和迎面转录-复制冲突 (TRC)。迎面 TRC 对基因组完整性的威胁更大。为了研究复制叉运动和 TRC 的方向，我们开发了一种名为 OKseqHMM 的生物信息学工具包（https://github.com/CL-CHEN-Lab/OK-Seq，https://doi.org/10.5281/zenodo.7428883）。然后，我们使用 OKseqHMM 分析了大量通过 Okazaki 片段测序获得的数据集，以直接测量全基因组复制叉方向性 (RFD)，并以精细分辨率准确预测酵母、小鼠和人类等生物中的复制起始和终止。我们还成功地将我们的分析应用于其他包含 RFD 信息的全基因组测序技术（例如 eSPAN、TrAEL-seq）。我们的工具包可用于在广泛的细胞模型和生长条件下预测全基因组的复制起始和叉推进方向。比较复制和转录方向可以识别易发生 TRC 的位点，特别是迎面 TRC，并通过检查 DNA 损伤数据来研究它们在基因组不稳定性中的作用，这对人类健康至关重要。
