Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.

Swetansu K. Hota,Yiwen Zhu,Reuben Thomas,Benoit G. Bruneau,Len A. Pennacchio,Erik Verschueren,Aaron M. Blotnick,Nevan J. Krogan,Xin Sun,Jeffrey R. Johnson

doi:10.1242/dev.174086

Abstract

ABSTRACTChromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM-associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunopurification with mass spectrometry, we have determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, identifying several cell-type specific subunits. We focused on the CP- and cardiomyocyte (CM)-enriched subunits BAF60c (SMARCD3) and BAF170 (SMARCC2). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, and in CMs their loss results in broadly deregulated cardiac gene expression. BRG1, BAF60c and BAF170 modulate chromatin accessibility, to promote accessibility at activated genes while closing chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition, and BAF170 loss leads to retention of BRG1 at CP-specific sites. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby participates in directing temporal gene expression programs in cardiogenesis.

Highlights

INRODUCTION Cell differentiation and organogenesis are regulated by the precise transcriptional output of a coordinated gene regulatory network (Davidson, 2010)
We identify several BRM-associated factor (BAF) complex subunits as enriched in cardiac precursors (CPs) and CMs, and along with brahmarelated gene 1 (BRG1) chose to focus on BAF60c and BAF170
We find that BRG1 initiates cardiac gene expression programs in precursor cells, a role shared by BAF60c and BAF170, which maintain the cardiac program to facilitate CM differentiation

Summary

Introduction

INRODUCTION Cell differentiation and organogenesis are regulated by the precise transcriptional output of a coordinated gene regulatory network (Davidson, 2010). The BRG1/ BRM-associated factor (BAF) chromatin remodeling complexes are composed of the mutually exclusive brahma (BRM) or brahmarelated gene 1 (BRG1; known as SMARCA4) ATPAses, along with several other structural subunits and their isoforms. These form diverse BAF complexes that serve specific functions in widely different cell types and developmental processes (Ho and Crabtree, 2010; Hota and Bruneau, 2016; Wang et al, 1996). Brg (Smarca4) is haploinsufficient in the mouse heart, and genetically interacts with genes encoding DNA-binding transcription factors associated with CHDs, indicating a potentially general role for BAF complexes in these common birth defects (Takeuchi et al, 2011). These results reveal the instructive nature that a specific combination of BAF subunits attains to dictate functional outcomes during lineage commitment and differentiation

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