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Histone acetylation and deacetylation in yeast

Nature Reviews Molecular Cell Biology volume 4, pages 276–284 (2003)Cite this article

Key Points

  • In the yeast Saccharomyces cerevisiae, histone acetylation and deacetylation occur through both targeted and global mechanisms. In the targeted mechanism, histone acetyltransferase (HAT) and deacetylase (HDAC) enzymes are recruited to promoters by specific transcriptional activators and repressors, respectively. In the global mechanism, HATs and HDACs enzymatically modify histones throughout large chromatin domains, including coding sequences, without any apparent DNA-sequence specificity.

  • Each of five related HDACs in yeast (Hda1, Rpd3, Hos1, Hos2 and Hos3) deacetylates specific sets of genes and regions of the genome. Such 'division of labour' might organize the affected genes in functional and/or physical domains, such as the HAST (for Hda1-affected subtelomeric) domains that are deacetylated by Hda1 and contain genes that are required for growth in adverse conditions.

  • In addition to their effects on chromatin structure, specific acetylated and deacetylated lysine residues in histones function as binding sites for factors that interact with chromatin. A bromodomain is a protein motif that binds to singly or doubly acetylated histone amino termini. It is found in several eukaryotic transcription factors, as well as HATs and members of chromatin-remodelling complexes.

  • Other than transcription, histone acetylation and deacetylation function in the regulation of other DNA-based processes. In DNA replication, increased histone acetylation directly causes the earlier firing of replication origins in yeast. In DNA repair, a single acetylated lysine in histone H4 is required for the proper repair of double-strand breaks. In heterochromatin, unacetylated lysine 16 of histone H4 is required for the formation of telomeric heterochromatin, whereas acetylation of this lysine functions as a barrier to the spread of heterochromatin.

  • Contrary to the repressive role of other known deacetylases, the Hos2 HDAC binds to and deacetylates histones in the coding region of genes only during gene activity and is required for efficient transcriptional activation.

Abstract

Histone acetylation and deacetylation in the yeast Saccharomyces cerevisiae occur by targeting acetyltransferase and deacetylase enzymes to gene promoters and, in an untargeted and global manner, by affecting most nucleosomes. Recently, new roles for histone acetylation have been uncovered, not only in transcription but also in DNA replication, repair and heterochromatin formation. Interestingly, specific acetylatable lysines can function as binding sites for regulatory factors. Moreover, histone deacetylation is not only repressive but can be required for gene activity.

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Figure 1: Histone acetylation and deacetylation regulate gene transcription.
Figure 2: A cascading model for the successive recruitment of protein complexes for transcription of the human interferon-β gene.
Figure 3: Histone acetylation and deacetylation regulate the formation of heterochromatin and the distance along which it spreads.
Figure 4: A model for the role of Hos2 histone deacetylase in gene activity.

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Acknowledgements

S.K.K. is a Howard Hughes Medical Institute Physician Postdoctoral Fellow. This work was supported by Public Health Service grants from the National Institutes of Health to M.G.

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  1. Department of Biological Chemistry, University of California School of Medicine, Los Angeles, 90095, California, USA

    Siavash K. Kurdistani & Michael Grunstein

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DATABASES

InterPro

bromodomain

Swiss-Prot

Elp3

Esa1

Gcn5

Hda1

Hos1

Hos2

Hos3

Rap1

Rpd3

Sas2

Sin3

Sir2

Sir3

Sir4

Ume6

FURTHER INFORMATION

Michael Grunstein's laboratory

Glossary

ACETYLATION

The covalent addition of the acetyl chemical group to lysine residues in histones and other proteins that neutralizes the positive charge of the ε-amino group of the lysine side chain. Deacetylation removes the acetyl group, thereby restoring the positive charge.

NUCLEOSOME

The fundamental unit of chromatin, which is composed of 147 bp of DNA wrapped around an octameric core of histone proteins (two molecules each of H2A, H2B, H3 and H4).

HISTONE ACETYLTRANSFERASE

(HAT). An enzyme that catalyses the addition of acetyl groups to the lysine residues of histones.

HISTONE DEACETYLASE

(HDAC). An enzyme that catalyses the removal of acetyl groups from the lysine residues of histones.

HETEROCHROMATIN

A region of chromosome that is structurally condensed or inaccessible to molecular probes in interphase, and is generally transcriptionally silent and late replicating in S phase.

CHROMATIN IMMUNOPRECIPITATION

(ChIP). A technique that combines immunoprecipitation of chromatin fragments and polymerase chain reaction (PCR) to semi-quantifiably map sites of protein–DNA interaction in vivo.

CHROMATIN REMODELLING

An alteration in chromatin structure that is often achieved by the covalent modifications of histones and/or the action of ATP-dependent remodelling complexes. Remodelling can allow the increased access of transcription factors to chromatin.

BASAL TRANSCRIPTION

Transcription that occurs in the absence of any activating signal.

DNA MICROARRAY

A high-throughput screening method developed initially for genome-wide differential expression analysis. It involves probing known DNA sequences that are printed at high density on a glass slide.

EUCHROMATIN

Regions of the genome that are less condensed in interphase and contain most active genes.

ENHANCER

A regulatory DNA sequence that can influence the rate of transcription of a promoter at a distance.

SILENT MATING-TYPE LOCI

Two regions on yeast chromosome III that determine the mating type of a yeast cell as a or α. They are assembled into heterochromatin by proteins (for example, Rap1, Sir2–4) that also participate in the formation of telomeric heterochromatin.

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Kurdistani, S., Grunstein, M. Histone acetylation and deacetylation in yeast. Nat Rev Mol Cell Biol 4, 276–284 (2003). https://doi.org/10.1038/nrm1075

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