PT  - JOURNAL ARTICLE
AU  - Liu, Yaqun
AU  - Wu, Xia
AU  - D’aubenton-Carafa, Yves
AU  - Thermes, Claude
AU  - Chen, Chun-Long
TI  - OKseqHMM: a genome-wide replication fork directionality analysis toolkit
AID  - 10.1101/2022.01.12.476022
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.12.476022
4099  - http://biorxiv.org/content/early/2022/01/13/2022.01.12.476022.short
4100  - http://biorxiv.org/content/early/2022/01/13/2022.01.12.476022.full
AB  - Motivation During each cell division, tens of thousands of DNA replication origins are coordinately activated to ensure the complete duplication of the entire human genome. However, the progression of replication forks can be challenged by numerous factors. One such factor is transcription-replication conflicts (TRC), which can either be co-directional or head-on with the latter being revealed as more dangerous for genome integrity.Results In order to study the direction of replication fork movement and TRC, we developed a bioinformatics tool, called OKseqHMM, to directly measure the genome-wide replication fork directionality (RFD) as well as replication initiation and termination from data obtained by Okazaki fragment sequencing (OK-Seq) and related techniques.Availability and Implementation We have gathered and analyzed OK-seq data from a large number of organisms including yeast, mouse and human, to generate high-quality RFD profiles and determine initiation zones and termination zones by using Hidden Markov Model (HMM) algorithm (all tools and data are available at https://github.com/CL-CHEN-Lab/OK-Seq). In addition, we have extended our analysis to data obtained by related techniques, such as eSPAN and TrAEL-seq, which also contain RFD information. Our works, therefore, provide an important tool and resource for the community to further study TRC and genome instability, in a wide range of cell line models and growth conditions, which is of prime importance for human health.Contact Chun-Long Chen (Institut Curie), chunlong.chen{at}curie.frCategory Genome analysisCompeting Interest StatementThe authors have declared no competing interest.