A core–BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes

Abstract

BRAF35, a structural DNA-binding protein, initially was identified as a component of a large BRCA2-containing complex. Biochemical analysis revealed the presence of a smaller core-BRAF35 complex devoid of BRCA2. Here we report the isolation of a six-subunit core-BRAF35 complex with the capacity to deacetylate histones, termed the BRAF-histone deacetylase complex (BHC), from human cells. BHC contains polypeptides reminiscent of the chromatinremodeling complexes SWI͞SNF and NuRD (nucleosome remodeling and deacetylating). Similar to NuRD, BHC contains an Mi2-like subunit, BHC80, and a PHD zinc-finger subunit as well as histone deacetylases 1͞2 and an MTA-like subunit, the transcriptional corepressor CoREST. We show that BHC mediates repression of neuron-specific genes through the cis-regulatory element known as the repressor element 1 or neural restrictive silencer (RE1͞NRS).Chromatin-immunoprecipitation experiments demonstrate the recruitment of BHC by the neuronal repressor REST. Expression of BRAF35 containing a single point mutation in the HMG domain of the protein abrogated REST-mediated transcriptional repression. These results demonstrate a role for core-BRAF35-containing complex in the regulation of neuron-specific genes through modulation of the chromatin structure.T he genome of eukaryotes is packaged into chromatin, the fundamental unit of which is the nucleosome. The higher order chromatin structure is formed by arrangement of nucleosomes into an array. Such higher order chromatin structure presents a barrier to cellular processes such as transcription, DNA replication, and DNA repair. Therefore, controlling accessibility to the nucleosomal DNA provides an important regulatory point in these processes (1).Recent genetic and biochemical studies have culminated in the discovery of a host of multisubunit complexes that, in an ATP-dependent manner, are able to alter the structure of the nucleosome. The first of such multiprotein complexes, the SWI͞SNF complex, was discovered initially through genetic studies in yeast, and its catalytic subunit, SWI2͞SNF2, was identified as the DNA-dependent ATPase (2-4). A complex similar to that of the SWI͞SNF complex was identified recently in yeast (RSC), which unlike the SWI͞SNF complex is essential for growth (5). Complexes homologous in polypeptide composition and biochemical activity to that of SWI͞SNF have been identified in other organisms (6-10). More recently, a number of groups reported the isolation and characterization of a complex termed NuRD (nucleosome remodeling and deacetylating, also NURD and NRD), that not only contains a DNA-dependent ATPase subunit but also histone deacetylase (HDAC) 1͞2 (11-13).In addition to such chromatin-remodeling complexes a number of transcriptional regulatory complexes have been identified that contain histone acetylation or deacetylation activities. It was shown previously that the hyperacetylated chromatin correlates with active genes, whereas the repressed genes exhibit a pattern of hypoacetylation (14,15). This contention ...

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