In Vitro Targeting Reveals Intrinsic Histone Tail Specificity of the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressor Complexes

Vermeulen, Michiel; Carrozza, Michael J.; Lasonder, Edwin; Workman, Jerry L.; Logie, Colin; Stunnenberg, Hendrik G.

doi:10.1128/mcb.24.6.2364-2372.2004

Cited by 44 publications

(49 citation statements)

References 45 publications

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“…To assess whether the purified complexes were enzymatically active, we performed deacetylation assays on nucleosomal templates acetylated by the SAGA and NuA4 complex (38). Both MBD2 and MBD3 protein complexes displayed robust trichostatin A-sensitive deacetylation activity towards histone H3 and histone H4 (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Purification of MBD3 from this cell line resulted in the purification of a Mi-2/NuRD complex lacking MBD2, indicating that in HeLa cells MBD2 and MBD3 are also mutually exclusive (unpublished data). (38). The amount of H3 or H4 acetylation was determined by Western blotting using antibodies against diacetylated histone H3 Lys-9,14 or tetraacetylated H4, respectively.…”

Section: Resultsmentioning

confidence: 99%

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MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties

Guezennec

Vermeulen

Brinkman

et al. 2006

Molecular and Cellular Biology

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303

297

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The human genome contains a number of methyl CpG binding proteins that translate DNA methylation into a physiological response. To gain insight into the function of MBD2 and MBD3, we first applied protein tagging and mass spectrometry. We show that MBD2 and MBD3 assemble into mutually exclusive distinct Mi-2/ NuRD-like complexes, called MBD2/NuRD and MBD3/NuRD. We identified DOC-1, a putative tumor suppressor, as a novel core subunit of MBD2/NuRD as well as MBD3/NuRD. PRMT5 and its cofactor MEP50 were identified as specific MBD2/NuRD interactors. PRMT5 stably and specifically associates with and methylates the RG-rich N terminus of MBD2. Chromatin immunoprecipitation experiments revealed that PRMT5 and MBD2 are recruited to CpG islands in a methylation-dependent manner in vivo and that H4R3, a substrate of PRMT, is methylated at these loci. Our data show that MBD2/NuRD and MBD3/NuRD are distinct protein complexes with different biochemical and functional properties.Methylation of CpG dinucleotides in regulatory regions of genes is an important mark for epigenetic regulation of transcription (2). Since DNA methylation is passed on to daughter cells during cell division, these methyl CpG marks can be maintained during development and provide epigenetic memory (31). A number of proteins have been identified in the human genome that can specifically bind to methylated CpG residues via a methyl CpG binding domain (MBD) (15, 39). Recruitment of these proteins to promoters containing methylated CpG-rich stretches-CpG islands-is thought to result in modulation of chromatin structure and repression of transcription. The human genome encodes five MBD proteins: 14,23). Apart from MBD3, these proteins have been shown to have specific methyl CpG binding activity. Recently a novel protein, Kaiso, was identified as a methyl CpG binding protein even though this protein lacks a classical MBD but appears to bind specifically to methylated DNA via a zinc finger domain (30).Several MBD proteins have been reported to interact with histone deacetylases (HDACs) as well as histone methyltransferases. MeCP2 has been described to interact with the Sin3/ HDAC corepressor complex (18) and Brahma (13), as well as with the histone H3 lysine-9 methyltransferase Suvar 3-9 (12), although these interactions may not be stable since MeCP2 is mostly present inside the cell as a monomer (12,18,19,26). MBD2 and MBD3 have been identified as core subunits of the Mi-2/NuRD complex (9, 27), whereas Kaiso is part of the HDAC-containing N-CoR complex that plays an important role in transcription regulation by nuclear hormone receptors (27,42,44). Collectively, these findings suggest a functional link between DNA methylation, histone deacetylation, and histone methylation and indicate that these epigenetic events functionally cooperate to regulate transcription and cellular memory.MBD2 and MBD3 have both been described as subunits of the Mi-2/NuRD complex. It has been proposed that MBD2, which exhibits methyl CpG binding activity, serves to recruit the MBD3...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties

Guezennec

Vermeulen

Brinkman

et al. 2006

Molecular and Cellular Biology

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303

297

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“…When targeted to preacetylated nucleosomal templates, Sin3/HDAC was found to deacetylate both H3 and H4, whereas the N-CoR/SMRT-HDAC3 complex displayed preferential activity toward H3 (Vermeulen et al, 2004). This result is somewhat surprising, considering the data discussed above (Johnson et al, 2002;Hartman et al, 2005).…”

Section: Substrate Specificitymentioning

confidence: 96%

“…Using an in vitro reconstituted chromatin template, Vermeulen et al (2004) tested histone deacetylation specificity of SMRT/N-CoR complexes. When targeted to preacetylated nucleosomal templates, Sin3/HDAC was found to deacetylate both H3 and H4, whereas the N-CoR/SMRT-HDAC3 complex displayed preferential activity toward H3 (Vermeulen et al, 2004).…”

Section: Substrate Specificitymentioning

confidence: 99%

HDAC3: taking the SMRT-N-CoRrect road to repression

2007

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Known histone deacetylases (HDACs) are divided into different classes, and HDAC3 belongs to Class I. Through forming multiprotein complexes with the corepressors SMRT and N-CoR, HDAC3 regulates the transcription of a plethora of genes. A growing list of nonhistone substrates extends the role of HDAC3 beyond transcriptional repression. Here, we review data on the composition, regulation and mechanism of action of the SMRT/ N-CoR-HDAC3 complexes and provide several examples of nontranscriptional functions, to illustrate the wide variety of physiological processes affected by this deacetylase. Furthermore, we discuss the implication of HDAC3 in cancer, focusing on leukemia. We conclude with some thoughts about the potential therapeutic efficacies of HDAC3 activity modulation.

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“…Recent biochemical studies reveal that both SMRT and N-CoR exist in large protein complexes with an estimated size of 1.5 to 2 MDa and containing a set of core subunits, including histone deacetylase 3 (HDAC3), GPS2, TBL1 (transducin beta-like protein 1), and TBLR1 (TBL1-related protein) (16,23,36,37,41,44). Human TBL1 and TBLR1 are highly related WD-40 repeat proteins, sharing 89% sequence identity.…”

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confidence: 99%

Reading and Function of a Histone Code Involved in Targeting Corepressor Complexes for Repression

Yoon

Choi

Cole

et al. 2005

Molecular and Cellular Biology

100

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In eukaryotic cells, genetic information is organized in a highly conserved structural polymer, termed chromatin, which is composed of repeating subunits called nucleosomes. Emerging evidence suggests that covalent modifications of histones have pronounced roles in chromatin structure and function (3,34,48). For instance, acetylation and deacetylation of the lysine residues at the histone N-terminal tails correlate in general with transcriptional activation and repression, respectively (30). The recent identification of enzyme systems carrying out histone modifications, together with the discovery of binding proteins that "read" covalent marks on histones, has led to the proposal that the pattern of modifications acts as an information code that influences gene transcription (12,20,31,33,35).While it is evident that histone modifications can have profound effects on transcription, it is much less clear as to how different histone codes are recognized and utilized. Current studies appear to suggest that once a code is generated, it can serve as an independent signal that allows the recruitment of a downstream regulatory protein(s). For instance, the bromodomain of TAFII250 and the chromodomain of HP1 are capable of binding acetylated histone tails and the K9 methylated H3 tails in vitro, respectively (2, 19, 21). Furthermore, K9 methylation is required for heterochromatin association of HP1 in cells (28). As a histone code involved in transcriptional activation, a recent study showed that acetylation of H4 on lysines 8 and 12 is sufficient for recruitment of TFIID at least in vitro, presumably through the double bromodomains in TAFII250(1). However, exactly how these various codes are recognized and utilized in vivo is not clear.Identified initially as corepressors for nuclear receptors such as thyroid hormone receptors (TR) and retinoic acid receptors (6, 17), N-CoR and SMRT are related proteins and have also been implicated in repression by many other transcription factors, including Mad/Mxi, BCL6/LAZ3, ETO, and CBF {for a review, see reference 14). Recent biochemical studies reveal that both SMRT and N-CoR exist in large protein complexes with an estimated size of 1.5 to 2 MDa and containing a set of core subunits, including histone deacetylase 3 (HDAC3), GPS2, TBL1 (transducin beta-like protein 1), and TBLR1 (TBL1-related protein) (16,23,36,37,41,44). Human TBL1 and TBLR1 are highly related WD-40 repeat proteins, sharing 89% sequence identity. A redundant function of TBL1/TBLR1 in repression was revealed by a recent study using small interfering RNA (siRNA) to TBL1 and TBLR1 (41). Both TBL1 and TBLR1 can bind histones H2B and H4 in vitro (41), raising question as to whether these proteins are involved in potential histone code recognition during repression by SMRT/N-CoR complexes. The presence of TBL1 and TBLR1 in the HDAC3-containing SMRT/N-CoR complexes is reminiscent of the RbAp46 and RbAp48 (also highly related WD-40 repeat proteins) in the HDAC1/2-containing Sin3 and NURD complexes (40,45,46). In vitro r...

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In Vitro Targeting Reveals Intrinsic Histone Tail Specificity of the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressor Complexes

Cited by 44 publications

References 45 publications

MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties

MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties

HDAC3: taking the SMRT-N-CoRrect road to repression

Reading and Function of a Histone Code Involved in Targeting Corepressor Complexes for Repression

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