Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

View ORCID ProfileYaqun Liu, Xia Wu, Yves D’aubenton-Carafa, View ORCID ProfileClaude Thermes, View ORCID ProfileChun-Long Chen
doi: https://doi.org/10.1101/2022.01.12.476022
Yaqun Liu
1Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, 75005, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yaqun Liu
Xia Wu
1Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, 75005, France
3Current address: Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yves D’aubenton-Carafa
2Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Claude Thermes
2Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Claude Thermes
Chun-Long Chen
1Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, 75005, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chun-Long Chen
  • For correspondence: chunlong.chen@curie.fr
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

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.fr

Category Genome analysis

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/CL-CHEN-Lab/OK-Seq

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted January 13, 2022.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
OKseqHMM: a genome-wide replication fork directionality analysis toolkit
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
OKseqHMM: a genome-wide replication fork directionality analysis toolkit
Yaqun Liu, Xia Wu, Yves D’aubenton-Carafa, Claude Thermes, Chun-Long Chen
bioRxiv 2022.01.12.476022; doi: https://doi.org/10.1101/2022.01.12.476022
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
OKseqHMM: a genome-wide replication fork directionality analysis toolkit
Yaqun Liu, Xia Wu, Yves D’aubenton-Carafa, Claude Thermes, Chun-Long Chen
bioRxiv 2022.01.12.476022; doi: https://doi.org/10.1101/2022.01.12.476022

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4246)
  • Biochemistry (9173)
  • Bioengineering (6806)
  • Bioinformatics (24064)
  • Biophysics (12158)
  • Cancer Biology (9565)
  • Cell Biology (13825)
  • Clinical Trials (138)
  • Developmental Biology (7660)
  • Ecology (11737)
  • Epidemiology (2066)
  • Evolutionary Biology (15544)
  • Genetics (10672)
  • Genomics (14362)
  • Immunology (9515)
  • Microbiology (22910)
  • Molecular Biology (9131)
  • Neuroscience (49156)
  • Paleontology (358)
  • Pathology (1487)
  • Pharmacology and Toxicology (2584)
  • Physiology (3851)
  • Plant Biology (8351)
  • Scientific Communication and Education (1473)
  • Synthetic Biology (2301)
  • Systems Biology (6206)
  • Zoology (1303)