Histone acetylation and
an epigenetic code
Bryan M. Turner
Summary
The enzyme-catalyzed acetylation of the N-terminal tail
domains of core histones provides a rich potential
source of epigenetic information. This may be used both
to mediate transient changes in transcription, through
modification of promoter-proximal nucleosomes, and
for the longer-term maintenance and modulation of
patterns of gene expression. The latter may be achieved
by setting specific patterns of histone acetylation,
perhaps involving acetylation of particular lysine resi-
dues, across relatively large chromatin domains. The
histone acetylating and deacetylating enzymes (HATs
and HDACs, respectively) can be targeted to specific
regions of the genome and show varying degrees of
substrate specificity, properties that are consistent with
a role in maintaining a dynamic, acetylation-based
epigenetic code. The code may be read (ie. exert a
functional effect) either through non-histone proteins
that bind in an acetylation-dependent manner, or through
direct effects on chromatin structure. Recent evidence
raises the interesting possibility that an acetylation-
based code may operate through both mitosis and
meiosis, providing a possible mechanism for germ-line
transmission of epigenetic changes. BioEssays
22:836±845, 2000. ß 2000 John Wiley & Sons, Inc.
Introduction
A quarter of a century has passed since the nucleosome was
first recognised as the fundamental unit of chromatin
structure in eukaryotic cells. In this time, its perceived role
has expanded from a DNA-packaging element to a crucial
determinant of virtually all aspects of genomic function.
(1)
The isolated nucleosome core particle comprises a histone
octamer, two copies each of H2A, H2B, H3 and H4, around
which is wrapped 146 base pairs of DNA. This structure is
the same in virtually all eukaryotes. However, in vivo this
extremely conserved structure is subject to numerous
enzyme-catalyzed manipulations and modifications that give
it an almost infinite capacity for variability. A major contributor
to this heterogeneity is the enzyme-catalyzed, post-transla-
tional modification of the N-terminal tails of the eight core
histones. The tails are exposed on the nucleosome surface
and can be modified by acetylation, phosphorylation,
methylation, ubiquitination and ADP-ribosylation of specific
amino acids.
(2)
Of these modifications, acetylation of the e-
amino group of defined lysine residues is the most frequently
occurring and extensively studied.
Any discussion of the possible functions of histone
modification must take account of the fact that the nucleo-
some is involved, one way or another, in virtually every
activity of nuclear DNA, including transcription, replication
and repair. It is difficult, possibly unwise, to consider these
activities in isolation. With this in mind, this review will focus
on an aspect of the subject that has received, till recently,
relatively little attention. It will explore the possibility that
histone modifications provide a mechanism for encoding and
transmitting information about genomic function from one cell
generation to the next; in other words, an epigenetic code. In
what follows, histone acetylation will provide most of the
experimental examples, but the possibilities discussed may
equally well be applied to other modifications whose analysis
is still at a relatively early stage. In fact, it is becoming
increasingly clear that important functional effects can
depend on precise combinations of modifications.
Finding coded messages
The idea that chromatin in general and patterns of histone
acetylation in particular may constitute a code that transmits
epigenetic information has been suggested before
(3±8)
, but
recent experiments have provided valuable insights into the
nature of the putative code and how it might operate. There
are several examples, some long standing, of specific
modifications that are associated with defined functional
effects. These are listed in Table 1. The potential importance
of combinations of modified residues has been emphasized
more recently by studies of phosphorylation of H3 serine10.
This residue is phosphorylated at high frequency as cells
836 BioEssays 22.9 BioEssays 22:836±845, ß 2000 John Wiley & Sons, Inc.
Chromatin and Gene Expression Group, Anatomy Department
University of Birmingham Medical School, Birmingham B15 2TT, UK.
E-mail: b.m.turner@bham.ac.uk
Abbreviations: ChIP, Chromatin ImmunPrecipitation; Fab-7, Droso-
phila DNA sequence that can activate and suppress transcription in
cis; H4Ac5 (8,12,16), Histone H4 acetylated at lysine residue 5
(8,12,16); HAT, Histone AcetylTransferase; HDAC, Histone Deacety-
lase; MBD2, Methyl Binding Domain protein 2; MeCP2, Methyl CpG-
binding Protein 2; MOF, Drosophila histone acetyltransferase named
after its mutant phenotype and chromosome location (Males-absent
On the First); Rpd3p, An important yeast transcriptional regulator and
histone deacetylase; SAGA, Yeast acetyltransferase complex named
after some of its constituent proteins; white, Drosophila gene whose
activity is necessary for the red eye colour of wild-type flies; its
mutation gives a white-eyed phenotype.
Problems and paradigms