Histone deacetylases (HDACs): characterization of the classical HDAC family

RUIJTER, Annemieke J.M. de; GENNIP, Albert H. van; CARON, Huib N.; KEMP, Stephan; KUILENBURG, André B.P. van

doi:10.1042/bj20021321

Cited by 3,114Histone Deacetylase Inhibitors ResearchGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

Histone deacetylases (HDACs): characterization of the classical HDAC family

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RUIJTER, Annemieke J.M. de, GENNIP, Albert H. van, CARON, Huib N., KEMP, Stephan, KUILENBURG, André B.P. van·2003·Biochemical Journal

DOI 10.1042/bj20021321PMC PMC1223209

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Abstract

Transcriptional regulation in eukaryotes occurs within a chromatin setting, and is strongly influenced by the post-translational modification of histones, the building blocks of chromatin, such as methylation, phosphorylation and acetylation. Acetylation is probably the best understood of these modifications: hyperacetylation leads to an increase in the expression of particular genes, and hypoacetylation has the opposite effect. Many studies have identified several large, multisubunit enzyme complexes that are responsible for the targeted deacetylation of histones. The aim of this review is to give a comprehensive overview of the structure, function and tissue distribution of members of the classical histone deacetylase (HDAC) family, in order to gain insight into the regulation of gene expression through HDAC activity. SAGE (serial analysis of gene expression) data show that HDACs are generally expressed in almost all tissues investigated. Surprisingly, no major differences were observed between the expression pattern in normal and malignant tissues. However, significant variation in HDAC expression was observed within tissue types. HDAC inhibitors have been shown to induce specific changes in gene expression and to influence a variety of other processes, including growth arrest, differentiation, cytotoxicity and induction of apoptosis. This challenging field has generated many fascinating results which will ultimately lead to a better understanding of the mechanism of gene transcription as a whole.

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HDACs are usually associated with transcriptionally silent chromatin.
“HDACs, the enzymes responsible for histone deacetylation, are usually associated with transcriptionally silent chromatin and are often the easiest to study as numerous HDAC inhibitors are available for use in anxiety animal models (de Ruijter et al., 2003).”
From The Epigenetics of Anxiety Pathophysiology: A DNA Methylation and Histone Modification Focused Review (2023) · cites this paper as de Ruijter et al., 2003
The Introduction and Mechanism of action sections link HDAC-mediated deacetylation to tighter chromatin and transcriptional repression, supporting the quoted claim. The Introduction also describes numerous HDAC inhibitors, but the cited sentence additionally says HDACs are easy to study using inhibitors in anxiety animal models; our copy does not establish that use or comparison. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Class I and IV enzymes are primarily located in the nucleus, class IIa enzymes shuttle between nucleus and cytosol, and class IIb enzymes are mainly localized to the cytosol.
“Among the eleven zinc-dependent enzymes, class I and IV enzymes are primarily located in the nucleus, class IIa enzymes are shuttling between nucleus and cytosol, and class IIb enzymes are mainly localized to the cytosol (de Ruijter et al., 2003).”
From Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase (2018) · cites this paper as de Ruijter et al., 2003
Most often, acetylated histones are associated with transcriptionally active chromatin, while deacetylated histones are associated with inactive transcription, though there are repressive acetyl marks.
“Most often, acetylated histones are associated with transcriptionally active chromatin, as it allows increased access of transcription factors to exposed gene promoters and transcription start sites (TSSs), while deacetylated histones are associated with inactive transcription, though there are repressive acetyl marks (de Ruijter et al., 2003).”
From The Epigenetics of Anxiety Pathophysiology: A DNA Methylation and Histone Modification Focused Review (2023) · cites this paper as de Ruijter et al., 2003

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Richon, V. M., Sandhoff, T. W., Rifkind, R. A. and Marks, P. A. (2000) Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation. Proc. Natl. Acad. Sci. U.S.A. 97, 10014-10019 124

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“116 The former includes three phylogenetic classes: I (HDAC1, 2, 3, and 8), II (HDAC4, 5, 6, 7, 9, and 10), and IV (HDAC11).”
Background
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Authors: RUIJTER, A. J. M. D., GENNIP, A. H. V., CARON, H. N., KEMP, S., & KUILENBURG, A. B. P. V.
Affiliations: Amsterdam UMC Location University of Amsterdam (NL)
ORCID: CARON, Huib N.
KEMP, Stephan
KUILENBURG, André B.P. van
Venue: Biochemical Journal
Publisher: Portland Press Ltd.
Published: 2003-03-15
Volume: 370
Issue: 3
Pages: 737-749
ISSN: 0264-6021 (ISSN-L)
1470-8728
DOI: 10.1042/bj20021321
PMC: PMC1223209
OpenAlex: W2107733280
Cited by: 3,114
References: 130
Citations by year: 2026: 70 · 2025: 115 · 2024: 128 · 2023: 122 · 2022: 124 · 2021: 142 · 2020: 168 · 2019: 152 · 2018: 157 · 2017: 154 · 2016: 153 · 2015: 171 · 2014: 141 · 2013: 171 · 2012: 165
FWCI: 8.66
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Biochemical Journal (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Pure Amsterdam UMC (publishedVersion)
Data Archiving and Networked Services (DANS) (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: histone deacetylase, histone acetylation, chromatin, transcriptional regulation, gene expression regulation, histone deacetylase inhibitors, tissue distribution, histone modifications, apoptosis, growth arrest, differentiation
MeSH terms: Acetylation, Gene Expression Regulation, Histone Deacetylases, Histones, Humans, Isoenzymes, Models, Genetic, Neoplasms, Repressor Proteins, Tissue Distribution, Transcription, Genetic, Molecular Structure, Signal Transduction, Evolution, Molecular

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Histone deacetylases (HDACs): characterization of the classical HDAC family

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