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Biochemistry of Multiprotein HDAC Complexes

  • Chapter
Histone Deacetylases

Part of the book series: Cancer Drug Discovery and Development ((CDD&D))

Abstract

Histone deacetylases perform an important role in the regulation of transcription by modifying the histone components of chromatin. This imparts specific restrictions to transcription and contributes to the proper coordination of gene expression. In order to perform these functions and to achieve proper modulation of their activity, HDACs associate with other proteins, and in some cases, even with themselves. The purification and analyses of these complexes during the last few years has changed our view of the functions of these enzymes, as well as how they are regulated and interconnect with other chromatin-related activities. We are starting to understand how a limited number of HDACs can perform such a variety of functions. Here we review all the known HDAC-containing complexes including classes I, II, and III and we summarize the implications of their composition to the function for HDACs in vivo.

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Abbreviations

Abf-1:

Activated B-cell factor-1

ACF1:

ATP-utilizing chromatin assembly and remodeling factor 1

ADA3:

Transcriptional adapter 3

ALL-1 (same as MLL, HRX, HTRX):

Acute lymphoblastic leukemia 1

AP-1:

Activator protein 1

APPL-1,-2:

Adaptor protein containing PH domain, PTB domain, and leucine zipper motif 1,2

ASAP:

Apoptosis- and splicing-associated protein

BAF57,-60a,-170:

BRG1-associated factor 57, 60a, 170

BCH110:

BRAF-HDAC component 110

Bcl6:

B-cell lymphoma 6

BRG1:

Brm/SWI2-related gene 1

BTB/POZ:

BR-C, ttk, and bab/poxvirus and zinc finger

CaMK:

Ca2+/calmodulin-dependent kinase cells

CoREST:

Corepressor of REST

Cpr1p:

Cyclophilin A peptidyl-prolyl isomerase

C-Ski:

Sloan-Kettering virus isolates

CtBP:

Carboxyl-terminal binding protein

CTCF:

CCCTC-binding factor

CTIP2:

Chicken ovalbumin upstream promoter transcription factor-interacting protein 2

DNMT1:

DNA (cytosine-5)-methyltransferases

Ebi:

Epidermal growth factor receptor regulator

Eto:

Eight twenty-one transcription factor

EuHMT:

Euchromatic histone-lysine N-methyltransferase

FAD+ :

Flavin adenine dinucleotide

FLO10:

Flocculation factor 10

FOXO:

Forkhead box

G9a:

Euchromatic histone-lysine N-methyltransferase

GSP2:

G protein pathway suppressor

HES:

Homeobox gene in ES

HML:

Silent mating type loci L

HMR:

Silent mating type loci R

Hos2p:

High osmolarity sensitivity two

HOXA9:

Homeobox protein A9

Hst1:

Homolog of Sir2p, 1

HTLV-1:

Type I human T-cell leukemia virus

Ini1:

Integrase interactor protein 1

IR10:

WD-repeat protein

ISWI:

Imitation-switch

KAP-1:

KRAB-interacting protein 1

KRAB:

Krüppel associated box

Ku70:

Lupus Ku autoantigen protein p70

Mad/Max:

MAX dimerization protein 1/MYC associated factor X

MAPK:

Mitogen activated protein kinases

MARK:

Microtubule affinity regulating kinase

MBD:

Methyl-CpG binding domain

MeCP2:

Methyl-CpG binding protein 2 gene

MEF2:

Myocyte enhancer factor 2

Mi2:

Dermatomyositis-specific autoantigen

MITR:

MEF2-interacting transcription repressor

MLL-1:

Myeloid/lymphoid leukemia 1

Mnt:

MYC antagonist

MTA2:

Metastasis-associated protein 2

Mxi1:

Max interactor 1

Myb:

Avian myeloblatosis virus oncogene

Nan1p:

Net1-associated nuclear protein

NCoR:

Nuclear receptor corepressor

Net1p:

Nucleolar silencing establishing factor and telophase regulator 1

NF-κB:

Nuclear factor κ-B

NLS:

Nuclear localization signal

Nop1:

Nuclear protein one

NoRC:

Nucleolar chromatin remodeling complex

NuRD:

Nucleosome remodeling and histone deacetylase

ORC1:

Origin replication complex 1

PCAF:

p300/CBP associated factor

PHD:

Plant homeodomain

PML:

Promyelocytic leukemia

PPAR-γ:

Peroxisome proliferator activated receptor, gamma

Pyr:

Pyrimidin-rich binding, SW1/SNF related complex

RAD21:

Radiation-sensitive mutant 21

Rap1:

Repressor/activator protein 1

RAR-α:

Retinoic acid receptor α

RAS:

Harvey sarcoma virus transforming gene

RbAp:

Retinoblastoma-associated protein

RBP-1:

Retinoblastoma binding protein 1

RENT:

Regulator of nucleolar silencing and telophase

REST/NRSF:

RE1-silencing transcription factor/Neuronal restricted silencing factor

RORγ:

Retinoid-related orphan receptor γ

Rpd3:

Reduced potassium dependency three

RunX2:

Runt-related transcription factor 2

SA1/SA2:

Stromal antigen 1/2

SANT:

SWI3, ADA2, NCoR, and TFIIIB B

Sap:

Sin3 associated protein

SBE:

Smad-binding element

SET:

SU(VAR)3-9, enhancer of Zeste, Trithorax

SFL1p:

Suppressor gene for flocculation 1

SID:

Sin3 interacting domain

Sif2p:

SIR4 interacting factor 2

Sin3:

Switch-independent three

Sir2p:

Silent information regulator 2

siRNA:

Small interfering RNA

SirT1:

Sir2-like (Sirtuin)1

SMC:

Structural maintenance of chromosomes factors

SMRT:

Silencing mediator for retionoid and thyroid hormone receptors

SNF2h:

Sucrose nonfermenting 2 homolog

Sntp:

Two SANT domains

Sp1:

Specificity protein-1

Srg3:

SWI3-related gene product 3

Sum1p:

Suppressor of uncontrolled mitosis

Suv39H1:

Suppressior of position-effect variegation 3-9 homolog 1

Swi/Snf:

Switch/sucrose nonfermenting

SWI3:

Matting-type switching defective mutant 3

TAFI68:

TBP-associated factors Pol I 68

Tax:

HTLV-1 trans-acting transcriptional activator

TBL1:

Transducin β -like protein 1

TBLR1:

Transducin β -like related protein 1

TEL complex:

Telomere complex

TFIIIB:

RNA polymerase III transcription factor B

TGF-β:

Transforming growth factor β

TSA:

Trichostatin A

Tup1:

Deoxythymidine monophosphate uptake factor 1

UbcH5:

E2 ubiquitin conjugating enzyme H5

Ume6p:

UASPHR1 multi copy enhancer six

WCRF180 (same as ACF1):

Williams syndrome transcription factor-related chromatin remodeling factor 180

XFIM:

X-linked mental retardation, zinc finger protein 261

YIL112w:

Ankyrin repeats-containing protein

YY1:

Yin-yang 1

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  1. Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ

    Alejandro Vaquero PhD, Michael Scher PhD & Danny Reinberg PhD

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  1. Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA

    Eric Verdin MD

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Vaquero, A., Scher, M., Reinberg, D. (2006). Biochemistry of Multiprotein HDAC Complexes. In: Verdin, E. (eds) Histone Deacetylases. Cancer Drug Discovery and Development. Humana Press. https://doi.org/10.1385/1-59745-024-3:23

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