OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Yaqun Liu (1) , Xia Wu (1) , Yves D’aubenton-Carafa , Claude Thermes (2) , Chun-Long Chen (1)

1 DIG CANCER - Dynamique de l'information génétique : bases fondamentales et cancer
2 I2BC - Institut de Biologie Intégrative de la Cellule

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 headon 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.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Molecular biology; Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]; Life Sciences [q-bio]; Cellular Biology; Subcellular Processes [q-bio.SC]; Life Sciences [q-bio]; Cancer; Life Sciences [q-bio]; Genetics; Human genetics

Yaqun Liu, Xia Wu, Yves D’aubenton-Carafa, Claude Thermes, Chun-Long Chen. OKseqHMM: a genome-wide replication fork directionality analysis toolkit. 2022. ⟨hal-03840939⟩