Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing

被引:0
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作者
Xia Wu
Yaqun Liu
Yves d’Aubenton-Carafa
Claude Thermes
Olivier Hyrien
Chun-Long Chen
Nataliya Petryk
机构
[1] Sun Yat-sen University,Zhongshan School of Medicine
[2] Université PSL,Institut Curie
[3] Sorbonne Université,Institute for Integrative Biology of the Cell (I2BC)
[4] CNRS UMR3244,Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, Inserm
[5] Dynamics of Genetic Information,Institut Gustave Roussy
[6] Université Paris-Saclay,undefined
[7] CEA,undefined
[8] CNRS,undefined
[9] Université PSL,undefined
[10] Epigenetics & Cell Fate CNRS UMR7216 Université Paris-Cité,undefined
[11] Université Paris-Saclay CNRS UMR9019,undefined
[12] Genome Stability and Cancers,undefined
来源
Nature Protocols | 2023年 / 18卷
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摘要
Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki fragment sequencing (OK-seq), a quantitative approach based on the isolation and strand-specific sequencing of Okazaki fragments, the lagging strand replication intermediates. OK-seq quantitates the proportion of leftward- and rightward-oriented forks at every genomic locus and reveals the location and efficiency of replication initiation and termination events. Here we provide the detailed experimental procedures for performing OK-seq in unperturbed cultured human cells and budding yeast and the bioinformatics pipelines for data processing and computation of replication fork directionality. Furthermore, we present the analytical approach based on a hidden Markov model, which allows automated detection of ascending, descending and flat replication fork directionality segments revealing the zones of replication initiation, termination and unidirectional fork movement across the entire genome. These tools are essential for the accurate interpretation of human and yeast replication programs. The experiments and the data processing can be accomplished within six days. Besides revealing the genome replication program in fine detail, OK-seq has been instrumental in numerous studies unravelling mechanisms of genome stability, epigenome maintenance and genome evolution.
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页码:1260 / 1295
页数:35
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