Molecular basis of CD4 repression by the Swi/Snf‐like BAF chromatin remodeling complex

Abstract

The Brg1/Brm-associated factor (BAF) chromatin remodeling complex directly binds the CD4 silencer and is essential for CD4 repression during T-cell development, because deletion of the ATPase subunit Brg1 or a dominant negative mutant of BAF57 each impairs CD4 repression in early thymocytes. Paradoxically, BAF57 is dispensable for remodeling nucleosomes in vitro or for binding of the BAF complex to the CD4 silencer in vivo. Thus, it is unclear whether BAF57-dependent CD4 repression involves chromatin remodeling and, if so, how the remodeling translates into CD4 repression. Here we show that nucleosomes at the CD4 silencer occupy multiple translational frames. BAF57 dominant negative mutant does not alter these frames, but reduces the accessibility of the entire silencer without affecting the flanking regions, concomitant with localized accumulation of linker histone H1 and eviction of Runx1, a key repressor of CD4 transcription that directly binds the CD4 silencer. Our data indicate that precise nucleosome positioning is not critical for the CD4 silencer function and that BAF57 participates in remodeling H1-containing chromatin at the CD4 silencer, which enables Runx1 to access the silencer and repress CD4. In addition to BAF57, multiple other subunits in the BAF complex are also dispensable for chromatin remodelling in vitro. Our data suggest that these subunits could also help remodel chromatin at a step after the recruitment of the BAF complex to target genes.Key words: BAF57 . CD4 . Chromatin Supporting Information available online IntroductionChromatin remodeling complexes are capable of using energy derived from ATP hydrolysis to physically disrupt DNA-histone contacts and facilitate the binding of transcription factors to nucleosomal DNA (for recent reviews, see [1,2]). There are multiple types of chromatin remodeling complexes in mammals, the best known being the Swi/Snf-like Brg1/Brm-associated factor (BAF) complexes that play diverse but tissue-specific roles in gene regulation [3][4][5]. The BAF complex consists of about 8-15 subunits including the catalytic ATPase subunit Brg1 or its homolog Brm. Surprisingly, the majority of these 15 subunits are dispensable for chromatin remodeling in vitro. The first clue came from the observation that the N-terminal HMG domain of BAF57, 580an HMG-box protein, is dispensable for the BAF complex to remodel mononucleosomes in vitro [6]. Subsequently, it was found that only four of the BAF subunits (Brg1, BAF45, BAF155 and BAF170) are sufficient to reconstitute a core complex possessing full remodeling activity on mononucleosomes and nucleosomal arrays [7]. The in vivo roles of the remaining 11 ''dispensable'' BAF subunits remain unclear, except that some of these subunits are thought to function by helping recruit the BAF complex to target genes via interactions with sequence-specific transcription factors or chromatin, thus indirectly contributing to chromatin remodeling. For example, BAF250 contains an ARID DNA-binding domain and a C-terminal domain capable of in...

Chromatin remodeling complex NURF regulates thymocyte maturation

“…More importantly, we found that Srf binding to Egr1, as revealed by ChIP, is dependent on Bptf. A similar requirement for SWI/SNF in the binding of RunX1 to the CD4 silencer in chromatin has been shown (Wan et al 2009). It is possible that initial Srf binding to partially accessible SREs, the DNA-binding elements for Srf, recruits NURF to reposition nucleosomes, thereby allowing increased accessibility of SREs to additional Srf.…”

“…We also examined the CD4 silencer, a regulatory element that requires Brg1 to regulate its chromatin structure and function during thymocyte development, and found no Bptf-dependent effects on its chromatin structure (Supplemental Fig. 6E; Wan et al 2009). Taken together, the results indicate that Bptf is a selective regulator of chromatin structure as early as the DN stages, Cold…”

ATP-dependent chromatin remodeling during mammalian development

“…CD4 repression depends on a 434 bp transcriptional silencer region, and both BRG1 and BAF57 increase chromatin accessibility by reducing H1 linker histone content and facilitating the binding of RUNX1, a transcriptional repressor, to this silencer region (Wan et al, 2009). BRG1 is also involved in CD4 activation and regulatory T-cell activation, which partially require its chromatin-remodeling ability and physical interactions between BRG1 and the Cd4 locus (Chaiyachati et al, 2013;Jani et al, 2008).…”

The Epigenetic Landscape of Lineage Choice: Lessons From the Heritability of Cd4 and Cd8 Expression

“…Genetic studies have demonstrated that BAF57 and BRG subunits of the SWI/SNF-like chromatin remodeling complexes are critical for Cd4 silencing in DN cells (Chi et al, 2003;Chi et al, 2002). Interestingly, dominant negative BAF57 expression or T cell specific Brg deletion results in decreased chromatin accessibility and Runx1 binding at S4 accompanied by CD4 de-repression in DN cells (Wan et al, 2009), indicating that SWI/SNF contributes to reversible silencing by remodeling chromatin to allow for Runx1 recruitment. In contrast to SWI/SNF, the NuRD chromatin remodeling complex has been implicated in reversing Cd4 silencing.…”