Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development

Abstract

The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.

Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis

“…In particular, which subunits within plant SWI/SNF complexes are responsible for their interaction with target chromatin and the mechanisms by which these interactions occur are largely unknown. Some subunits of SWI/SNF complexes in yeast and animals contain single or multiple bromodomains, which are evolutionarily conserved epigenetic reader domains capable of recognizing and binding to acetylated lysine on histones (Dhalluin C et al, 1999;Filippakopoulos and Knapp, 2014;Filippakopoulos et al, 2012;Fujisawa and Filippakopoulos, 2017;Ho et al, 2019;Rao et al, 2014). The Arabidopsis genome encodes 29 bromodomain-containing proteins (Pandey et al, 2002).…”

Interplay of BAF and MLL4 promotes cell type-specific enhancer activation

“…Mammalian SWI/SNF complexes exist in three different isoforms with distinct subunit compositions: BRG1/BRM-associated factor (BAF), polybromo-associated BAF (PBAF), and noncanonical GLTSCR1L-containing BAF (GBAF, also known as ncBAF) 5,6 . All three complexes contain an ATPase catalytic subunit, either SMARCA4 (BRG1) or SMARCA2 (BRM), and an initial core, composed of SMARCC1 (BAF155), SMARCC2 (BAF170), and SMARCD1/D2/D3 (BAF60A/B/C) 5,7 . The BAF complex contains SMARCB1 (SNF5, INI1, or BAF47), SMARCE1 (BAF57), and SS18 and BAF-specific subunits ARID1A/B (BAF250A/B) and DPF1/2/3 ( Fig.…”

“…Like BAF, PBAF complex also consists of the initial core, SMARCB1 and SMARCE1 as well as PBAF-specific subunits PHF10, ARID2 (BAF200), BRD7, and PBRM1. The recently characterized GBAF is a smaller complex containing SMARCA4 or SMARCA2, the initial core, SS18, and GBAF-specific subunits GLTSCR1/L and BRD9 [5][6][7] . These three distinct complexes exhibit different genomic localization patterns.…”

Temporal mechanisms of myogenic specification in human induced pluripotent stem cells

“…BRG1/BRM associated factor (BAF)/polybromo associated BAF (pBAF) and NuRD (nucleosome remodeling and deacetylase) are chromatin-modifying complexes that operate largely at the nucleosome level ( 26 , 27 ). Several components of the BAF family complexes showed a cell line–dependent expression, including adenosine 5′-triphosphate (ATP)–dependent enzyme SMARCA2 and targeting components BCL7A and BCL11A ( Fig.…”