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

Matthew R Hass,Daniel Brissette,Raphael Kopan,Omer Donmez,Sreeja Parameswaran,Matthew T Weirauch,Mario Pujato,Leah C Kottyan,John M Greally

doi:10.1371/journal.pgen.1009574

Matthew R Hass, Daniel Brissette + Show 7 more

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https://doi.org/10.1371/journal.pgen.1009574

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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 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.

Highlights

Mammalian genomes encode over 1,000 Transcription factors (TFs) which precisely control gene expression through complex combinatorial interactions and transcriptional cascades [1], executing the first step in translating genomic DNA sequence into function
Closed areas contained Runx1 binding sites and were enriched near genes whose expression depended on Runx1
This occurred despite continued binding of Runx2 to the same regions of DNA, which suggests that Runx2 is insufficient to maintain open chromatin and expression of Runx1 target genes in this cellular context

Summary

Introduction

Mammalian genomes encode over 1,000 Transcription factors (TFs) which precisely control gene expression through complex combinatorial interactions and transcriptional cascades [1], executing the first step in translating genomic DNA sequence into function. To achieve this precision, TFs use a wide range of mechanisms, including initiating the activation or repression of gene expression directly or through the recruitment of co-factors, initiating new chromatin looping interactions between enhancers and target promoters, and altering the chromatin landscape through the repositioning of nucleosomes [2]. How Runx proteins influence gene regulatory networks in different cellular contexts remains to be elucidated

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