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

Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets

Matthew R. Hass, Daniel Brisette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
doi: https://doi.org/10.1101/2020.09.25.313767
Matthew R. Hass
1Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel Brisette
1Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sreeja Parameswaran
2Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mario Pujato
2Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Omer Donmez
2Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leah C. Kottyan
2Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
3Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew T. Weirauch
1Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
2Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
3Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
4Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: Raphael.Kopan@cchmc.org Matthew.Weirauch@cchmc.org
Raphael Kopan
1Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
3Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: Raphael.Kopan@cchmc.org Matthew.Weirauch@cchmc.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Runt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion of Runx1 in an embryonic kidney-derived cell (mK4) results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci are enriched for Runx sites, remain bound by Runx2, but lose chromatin accessibility and expression in Runx1 knockout cells. Unexpectedly, regions near upregulated genes are depleted of Runx sites and are instead enriched for Zeb transcription factor binding sites. Re-expressing Zeb2 in Runx1 knockout cells restores suppression. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that genome-scale derepression is an indirect consequence of losing Runx1-dependent Zeb expression.

Competing Interest Statement

The authors have declared no competing interest.

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 September 26, 2020.
Download PDF
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.
Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets
(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
Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets
Matthew R. Hass, Daniel Brisette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
bioRxiv 2020.09.25.313767; doi: https://doi.org/10.1101/2020.09.25.313767
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets
Matthew R. Hass, Daniel Brisette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
bioRxiv 2020.09.25.313767; doi: https://doi.org/10.1101/2020.09.25.313767

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

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2430)
  • Biochemistry (4789)
  • Bioengineering (3330)
  • Bioinformatics (14673)
  • Biophysics (6635)
  • Cancer Biology (5168)
  • Cell Biology (7424)
  • Clinical Trials (138)
  • Developmental Biology (4362)
  • Ecology (6873)
  • Epidemiology (2057)
  • Evolutionary Biology (9914)
  • Genetics (7345)
  • Genomics (9522)
  • Immunology (4552)
  • Microbiology (12674)
  • Molecular Biology (4942)
  • Neuroscience (28320)
  • Paleontology (199)
  • Pathology (808)
  • Pharmacology and Toxicology (1391)
  • Physiology (2024)
  • Plant Biology (4495)
  • Scientific Communication and Education (977)
  • Synthetic Biology (1299)
  • Systems Biology (3913)
  • Zoology (725)