Dynamic nucleosomes and gene transcription

doi:10.1016/j.tig.2006.03.008

Trends in Genetics

Volume 22, Issue 6, June 2006, Pages 320-329

https://doi.org/10.1016/j.tig.2006.03.008 Get rights and content

Gene transcription occurs on a nucleosomal template known as chromatin. The recruitment of the transcriptional regulators and the transcription machinery to promoter chromatin is coordinated by a genetic code on the DNA and an epigenetic code on the histone proteins. Chromatin is not a stable environment; rather, the histones, the transcription regulatory proteins and the enzymes that modify and mobilise nucleosomes are in a dynamic state. Thus, at any one time, the factors associated with a region will cooperate or compete to change the rate of inter-conversion between permissive and non-permissive chromatin states, leading to activation or repression of transcription. Here, new concepts such as dynamic nucleosomes and a dynamic histone code in gene transcription are explored.

Introduction

In eukaryotes, the packaging of DNA into chromatin, in which the DNA is wound around a core of four basic histone proteins to form nucleosomes, has long been thought to be a major obstacle to transcription, replication, recombination and repair in the nucleus. Indeed a large and growing number of chaperones, histone modifying enzymes, nucleosomal ATPases and variant histone proteins (see Glossary) are dedicated to facilitating events on the DNA and maintaining the nucleosomal organisation. However, we now see nucleosomes as a vital component of these processes, rather than a mere passive obstacle.

In addition to the genetic information encoded within the DNA, a second epigenetic code, known as the histone code [1], exists on each nucleosome to direct and control transcription, replication, recombination and repair (Figure 1). This code comprises interdependent combinatorial post-translational covalent modifications at multiple sites on each of the four core histone proteins within a nucleosome 2, 3, 4. These marks are likely to have at least two roles: to provide heritable chromosome-specific epigenetic marks (i.e. who am I?) and to provide more localised control over events on chromatin in real time (i.e. what is happening to me now?). Some of these modifications are known to act as sites for recruitment of structural proteins and enzymes directly to the chromatin, complementing the recruitment of sequence-specific-binding proteins to sites on the DNA 5, 6.

Over the past year or so, it has become clear that the association of sequence-specific DNA- binding proteins with the chromatin template, the position of nucleosomes and their composition (in terms of covalent modifications and variant histones) are highly dynamic. We should think of a chromosome, even when condensed during mitosis, as a dynamic structure that responds to a wide range of biological signals 7, 8. Here, I will discuss the role of these dynamic changes in marking and, importantly, controlling the various stages of gene activation, expression and repression in the context of the gene.

It is clear that the dynamic events leading to gene activation are complex and that even for the initiation of transcription from one promoter in one cell type, there is redundancy in the combination of factors that are chosen and in the order in which they are recruited to regulate any one cycle of transcription. Furthermore, it is evident that there is a high degree of precision in setting up a chromatin template, and small changes to a single nucleosome can have dramatic consequences. Finally, the question of whether genes have a molecular memory of the last time they were transcribed will be discussed, that is, whether heritable epigenetic marks are present on the chromatin in newly born cells. Implicit in this is the importance of both nucleosome modifications and positioning in the repressed state in controlling subsequent rounds of gene activation.

Section snippets

The dynamic state of chromatin

On a eukaryotic chromosome there are regions of heterochromatin, associated with the epigenetic silencing of genes, and euchromatin, a more open structure in which genes are often expressed. Both forms of chromatin are generally considered to be stable, heritable states, but the idea of a stable structure has been challenged by in vivo experiments using fluorescence recovery after photobleaching (FRAP), which measures the time it takes for new fluorescently labelled molecules to return to a

The dynamics of the core histones within nucleosomes

Although most chromatin-associated proteins diffuse freely within the nucleus and show relatively transient binding to chromatin (modulated in response to changes in cell physiology and other stimuli), the core histones, H2A, H2B, H3 and H4 (the major structural components of the chromatin) exchange much more slowly in HeLa cells. For example, the residence time for H2B measured by FRAP is in the order of hours rather than seconds 7, 9. In a mammalian cell, the majority of H2B falls into two

Stable H3–H4 tetramers

Global analysis indicates that H3–H4 tetramers are ∼20 times more stable than H2A–H2B dimers [19], even within transcriptionally active genes [20]. This is despite the replication-independent replacement of H3.1 with a variant form, H3.3, at transcriptionally active loci that occurs in some organisms 21, 22, 23, 24. Because H3 is known to be subject to extensive covalent modifications, both on active genes [e.g. H3 lysine 4 trimethylation (K4^me3) and H3 K36 trimethylation (K36^me3) Box 2] and

Reversible covalent histone modifications to histones H3 and H4

Although reversible covalent modification to histones is a well established concept, until the recent discovery of histone demethylases [25], methylation was generally considered as a stable modification, well suited as an epigenetic mark to persist through cell generations [26]. Now, mechanisms to explain how methyl groups can be removed from methylated arginine (R^me1) 27, 28, H3 K4^me2 [25] and H3 K36^me2 [29], together with demonstrations of dynamic arginine 30, 31 and lysine methylation 32, 33

Linking stable methylation of histone H3 to dynamic cycles of histone H3 and H4 acetylation and deacetylation

Although the H3–H4 tetramer is a relatively stable component of the chromatin over most active genes when assessed by FRAP, it nevertheless undergoes dynamic changes from one state to another by virtue of reversible covalent modifications such as acetylation and deacetylation. Furthermore, persistent marks such as K4^me3 and K36^me3 control this dynamic by recruiting the HATs [33] and HDACs 35, 36, 37 to the chromatin. Lysine methylation at positions 4 and 36 on histone H3 are important and

Dynamic H2A–H2B dimers

A small fraction (3%) of the H2A–H2B in cells has been observed using FRAP to exchange rapidly (residence time ∼6 minutes), which probably reflects DNA replication-independent exchange of the H2A–H2B dimers, primarily at transcriptionally active loci 18, 20. Thus, the nucleosome over transcriptionally active genes can be visualised as having two distinct components, a fluid H2A–H2B dimer and a stable H3–H4 tetramer. Support for the fluidity of the H2A–H2B dimers during transcription comes from

Chromatin remodelling ATPases drive nucleosome dynamics directed by transcription factors

A very nice example of how a fluid H2A–H2B dimer influences nucleosome dynamics, and therefore gene expression, is provided by the mouse mammary tumour virus (MMTV) promoter, one of the best studied promoters in mammals. UV laser cross-linking was used to probe in vitro the interactions between the glucocorticoid receptor (GR), a transcription factor that binds specifically to the MMTV promoter, and a nucleosome array assembled on the MMTV promoter [52]. These experiments revealed that the

Dynamic and redundant events control cycles of transcription in the cell

Events at the promoter of the mammalian oestrogen-regulated pS2 gene, which encodes the trefoil factor (TFF1) involved in mucosal restitution, illustrate very clearly both the idea of dynamic cycles of transcription and the degree of redundancy that manages these cycles in the cell 30, 53. In this study 30, 53, chromatin was prepared from cells treated with the RNA synthesis inhibitor α amanitin, which was removed as the hormonal inducer was added to give synchronous induction. Chromatin was

There are no rules for the sequence of events necessary for gene activation

The next question is whether events at the pS2 promoter are atypical of promoters in other systems. This question is hard to address, because no other system is as completely described as the pS2 promoter, but dynamic patterns of histone modification in mammals at the promoters of the liver-regulated HNF-4α gene [62], a collagenase gene [63], an IFN-β gene [64], a chicken lysozyme gene [41] or the yeast SUC2 and MET16 genes 33, 65 suggest that the order in which histone modifications and

Concluding remarks

Here, I have used a limited number of examples to illustrate some of the recent work that challenges our thinking about chromatin, and introduced the concept of the dynamic nucleosome. The armoury of tools available to the cell for controlling nucleosome dynamics include ATP-dependent chromatin remodelling enzymes, histone modifying enzymes, linker histones, variant histones, transcription factors and histone chaperones. Many of these factors act transiently and redundantly making analysis of

Glossary

Chromatin remodelling:: several energy-dependent alterations to the structure of a nucleosome, catalysed in an ATP-dependent reaction by one of many ATPases often found in large protein complexes [71]. Although the outcome of any one remodelling reaction can appear very different from another, these probably represent variations on one basic mechanism.
Epigenetics:: changes in patterns of gene expression that are heritable but that do not result from mutation or changes to the DNA sequence.

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Trends in Genetics

Dynamic nucleosomes and gene transcription

Introduction

Section snippets

The dynamic state of chromatin

The dynamics of the core histones within nucleosomes

Stable H3–H4 tetramers

Reversible covalent histone modifications to histones H3 and H4

Linking stable methylation of histone H3 to dynamic cycles of histone H3 and H4 acetylation and deacetylation

Dynamic H2A–H2B dimers

Chromatin remodelling ATPases drive nucleosome dynamics directed by transcription factors

Dynamic and redundant events control cycles of transcription in the cell

There are no rules for the sequence of events necessary for gene activation

Concluding remarks

Glossary

Selective use of H4 acetylation sites in the yeast Saccharomyces cerevisiae

Biochem. J.

Histones and histone modifications

Curr. Biol.

Regulated nucleosome mobility and the histone code

Nat. Struct. Mol. Biol.

The language of covalent histone modifications

Nature

Trypanosoma cruzi histone H1 is phosphorylated in a typical cyclin dependent kinase site accordingly to the cell cycle

Mol. Biochem. Parasitol.

Translating the histone code

Science

Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins

J. Cell Biol.

The Dynamics of Histone H1 Function in Chromatin

Mol. Cell

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins

Mol. Cell. Biol.

H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain

J. Biol. Chem.

Rapid exchange of histone H1.1 on chromatin in living human cells

Nature

Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin

Mol. Cell. Biol.

Linker histone binding and displacement: versatile mechanism for transcriptional regulation

FASEB J.

Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller

EMBO Rep.

The F Box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing

Cell

Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy

Methods Enzymol.

Complex role of histone H1 in transactivation of MMTV promoter chromatin by progesterone receptor

J Steroid Biochem Mol Biol.

Histone dynamics in living cells revealed by photobleaching

DNA Repair (Amst.)

Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B

J. Cell Biol.

Replication-independent core histone dynamics at transcriptionally active loci in vivo

Genes Dev.

Histone variants, nucleosome assembly and epigenetic inheritance

Trends Genet.

Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis

Cell

Histone H3.3 deposition at E2F-regulated genes is linked to transcription

EMBO Rep.

Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division

EMBO Rep.

Histone demethylation mediated by the nuclear amine oxidase homolog LSD1

Cell

Histone lysine methylation: a signature for chromatin function

Trends Genet.

Histone deimination antagonizes arginine methylation

Cell

Human PAD4 regulates histone arginine methylation levels via demethylimination

Science

Histone demethylation by a family of JmjC domain-containing proteins

Nature

Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter

Cell

Transcriptional complexes engaged by apo-estrogen receptor-αisoforms have divergent outcomes

EMBO J.

Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A

Oncogene

Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription