Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets

• Published in: PLoS genetics Vol. 17; no. 6; p. e1009574
• Main Authors: Hass, Matthew R., Brissette, Daniel, Parameswaran, Sreeja, Pujato, Mario, Donmez, Omer, Kottyan, Leah C., Weirauch, Matthew T., Kopan, Raphael
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10.06.2021; Public Library of Science (PLoS)
• Subjects: Analysis; Animals; Binding sites; Biology and Life Sciences; Cbfa-1 protein; Chromatin; Chromatin - metabolism; Clustered Regularly Interspaced Short Palindromic Repeats; Core Binding Factor Alpha 2 Subunit - genetics; Core Binding Factor Alpha 2 Subunit - physiology; CRISPR; Down-Regulation; Gene expression; Gene loci; Genetic aspects; Genetic engineering; Genomes; Identification and classification; Mesenchyme; Mice; Mice, Knockout; Ontology; Physiological aspects; Proteins; Repressor Proteins - metabolism; Roles; Runx1 protein; Transcription factors; Transcription Factors - metabolism; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1009574

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 mouse metanephric mesenchyme-derived mK4 cells results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci enriched for Runx sites in mK4 cells lose chromatin accessibility in Runx1 knockout cells, despite remaining Runx2-bound. 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, and CRISPR mediated deletion of Zeb1 and Zeb2 phenocopies the gained expression and chromatin accessibility changes seen in Runx1KO due in part to subsequent activation of factors like Grhl2. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that Zeb proteins are required and sufficient to maintain Runx1-dependent genome-scale repression.