A Candidate X-linked Mental Retardation Gene Is a Component of a New Family of Histone Deacetylase-containing Complexes

Abstract

Eukaryotic genes are under the control of regulatory complexes acting through chromatin structure to control gene expression. Here we report the identification of a family of multiprotein corepressor complexes that function through modifying chromatin structure to keep genes silent. The polypeptide composition of these complexes has in common a core of two subunits, HDAC1,2 and BHC110, an FAD-binding protein. A candidate X-linked mental retardation gene and the transcription initiation factor II-I (TFII-I) are components of a novel member of this family of complexes. Other subunits of these complexes include polypeptides associated with cancer causing chromosomal translocations. These findings not only delineate a novel class of multiprotein complexes involved in transcriptional repression but also reveal an unanticipated role for TFII-I in transcriptional repression.The 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 a 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). One way to modulate nucleosomal structure is through enzymatic modification of histones by acetylation, phosphorylation, or methylation.A number of transcriptional regulatory complexes have been identified that contain histone acetylation or deacetylation activities. It was previously shown that the hyperacetylated chromatin correlates with active genes whereas the repressed genes exhibit a pattern of hypoacetylation (2, 3). This contention was strengthened by the discovery of the association of a number of transcriptional corepressors with histone deacetylation activity. The HDACs 1 identified in mammalian cells can be divided into three classes. Homologs of the yeast protein Rpd3 are members of the Class I HDACs (4, 5). Included in this class are HDAC1, HDAC2, HDAC3, and HDAC8. Members of the Class II HDACs include HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10. These HDACs appear to be more similar to yeast protein Hda1 (6 -9). A third class of HDACs exists, which unlike the other classes of HDACs, requires an NAD cofactor for activity. The members of this class are homologs of the yeast Sir2 protein (10 -12).Previous biochemical analysis revealed the association of transcriptional corepressor Sin3 with a multiprotein complex containing histone deacetylase activity (13)(14)(15). This complex was shown to contain HDAC1,2 and act as a transcriptional corepressor for a number of DNA-binding repressors including Mad, the nuclear hormone receptors, and the RE1-binding silencer protein, REST (also called NRSF) (14, 16 -19). In addition, a number of groups reported the isolation and characterization of a complex termed NuRD (also NURD and NRD) that not only contains histone deacetylases 1 and 2 but also a DNA...

Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes

“…This domain is named for its presence in the proteins Swi3, Rsc8, and Moira, which are homologous members in the SWI͞SNF-family of ATP-dependent chromatin remodeling complexes SWI͞SNF, RSC, and BRM, respectively. However, the SWIRM domain is also present in many other chromatin regulatory proteins such as the Gcn5 histone acetyltransferase subunit Ada2, and the recently identified histone demethylase BHC110͞LSD1 (14,15). Additionally, this domain is found in other proteins associated with ubiquitin-mediated protein degradation (13).…”

Isolation and characterization of histone H3 lysine 4 demethylase-containing complexes

“…Importantly, we were able to assess not only histone demethylation activity but also HDAC activity under the same assay conditions (Lee et al, 2005;Lee et al, 2006). It should be noted that this complex contains two enzymatic subunits: the histone demethylase BHC110 and the histone deacetylases HDAC1/2 (Hakimi et al, 2003). The reaction mixture was analyzed by SDS-PAGE, followed by Western blotting.…”

“…BHC was isolated as a multiprotein complex containing histone deacetylase 1 and 2 (Hakimi et al, 2002;Marmorstein et al, 2001), and has been shown to mediate silencing of neuron-specific genes by REST (RE1-silencing transcription factor) in differentiated non-neuronal cells (Hakimi et al, 2002). Subsequently, we isolated this complex using a two-step purification involving P11 column fractionation followed by an affinity chromatography using antibodies to BHC110 (Hakimi et al, 2003). More recently, we developed an epitope-tagged stable cell line expressing Flag-BHC110 that allowed the isolation of BHC110-containing complexes through a single-step affinity-purification (Lee et al, 2005).…”

Signal-induced functions of the transcription factor TFII-I

“…First, it allows cfos expression to be silenced in the absence of signaling, which is a necessary requirement for quiescence. In this regard, it has been shown that TFII-I might serve to negatively regulate cfos gene expression, although the precise mechanism or the usage of specific isoforms was not addressed (38). Second, it perhaps ensures specificity such that the same promoter site can be utilized for signal-induced transcriptional activation mediated by TFII-IΔ.…”

“…However, the precise mechanism by which these dynamics are achieved upon mitogenic signaling remains unknown. The alteration in promoter occupancy by the two isoforms of TFII-I, together with their respective interactions with MAPK and HDACs (37)(38)(39)(40), perhaps provides a reasonable mechanism to explain the unusual dynamics of c-fos regulation. Moreover, TFII-I is also shown to be associated with histone demethylase co-repressor complex, LSD1/BHC110 (38).…”