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Introduction: Chromatin—a target for intracellular signalling pathways
seminars in C E L L & D E V E L OP M E N T A L B I OL OG Y , Vol 10, 1999: pp. 165]167 Article No. scdb.1999.0297, available online at http:rrwww.idealibrary.com on
Introduction: Chromatin—a target for intracellular signalling pathways Bryan M. Turner
MANY PROTEINS ASSOCIATE with DNA in the nuclei of eukaryotic cells, but few, if any, enjoy such an intimate relationship as the histones. An octamer of histones Žtwo each of H2A, H2B, H3 and H4. wraps 146bp of DNA around itself to form the nucleosome core particle, the basic unit of chromatin structure in all eukaryotic cells ŽFigure 1.. Chromatin in the nucleus can adopt a variety of higher order structures, the great majority of which consist of nucleosome arrays, and while these structures are not understood in any detail, it is clear that they can have important, and sometimes overriding effects on gene expression.1 These effects can be brought about in various ways, such as positioning a histone octamer over a crucial transcription factor binding site, changing DNA packaging to allow or inhibit access of components of the transcription apparatus or through more subtle mechanisms such as DNA looping, that can juxtapose or separate interacting DNA elements. All these possibilities, and others, have been under investigation for years, but the sheer size and complexity of the structures involved has limited progress. The problem is compounded by the fact that chromatin is a naturally dynamic structure. In most cells, DNA is going through cycles of replication, repair and condensation prior to mitosis, all of which involve major reorganisation of chromatin. To dissect out from this maelstrom, those changes relevant to the small fraction of the genome with transcriptional potential, is a formidable task. Over the last 3 years or so, chromatin research has taken a significant step forward with the identification and characterization of some of the enzymes
that mediate changes in chromatin structure. Three enzyme families have received particular attention, namely enzyme complexes that have ATP-dependent chromatin remodelling activity; histone acetyltransferases; and histone deacetylases. All these enzymes have the potential to regulate gene expression through their effects on chromatin structure and, not surprisingly, have become the focus of intensive research. However, a subject that has, as yet, received relatively little attention is that these enzymes also provide possible, mechanistic links between signal transduction pathways and their transcriptional effects. This intriguing prospect is the theme that links the articles in the present collection. Acetylation of the amino terminal domains of the core histones has been known about for over 30 years. It is a common modification, with most histone molecules going through cycles of acetylation and deacetylation with half lives varying from a few minutes to several hours. Histone acetylation clearly has the potential to alter chromatin structure and function, and a mass of evidence, albeit often circumstantial, has associated changes in histone acetylation with changes in transcription.2 More compellingly, many of the recently identified HATs and HDACs have turned out to be identical with, or homologous to, known activators or repressors of transcription. This is dealt with in the articles by Grant and Berger ŽHATs. and Johnson and Turner ŽHDACs.. Exactly how acetylation influences transcription remains something of a mystery, though much attention has recently been given to the finding, resulting from detailed crystallographic analysis of the nucleosome core particle, that the tail domain of histone H4 has the ability to link adjacent nucleosomes.3 This raises the possibility that acetylation of the H4 tail can influence such cross linking and thereby alter higher order chromatin packaging ŽFigure 1.. While HATs and HDACs change chromatin structure through
From the Department of Anatomy, Chromatin and Gene Expression Group, University of Birmingham Medical School, Birmingham B15 2TT, UK. Q1999 Academic Press 1084-9521r 99r 020165q 03 $30.00r 0
165
B. M. Turner
are subject to various levels of regulation. They are all, in vivo, multi-subunit complexes and their subunit compositions are crucial. Some complexes are now known to have both chromatin remodeling and deacetylase activity and by incorporating specific DNA binding proteins, complexes can be targeted to specific regions of the genome. Magnaghi-Jaulin et al discuss this, particularly in relation to control of cell growth and the role of Rb, the protein product of the Retinoblastoma tumour suppressor gene. Rb can associate with various complexes, including SWIrSWF homologues. Minucci and Pelicci describe the ways in which the retinoid receptors use HDACs and HATs to regulate gene activity in a ligand-dependent manner and how disruption of these interactions can lead to human disease. In this context, it is interesting to note that HDAC activity can be inhibited by an increasing variety of reagents, the therapeutic potentials of which are just beginning to be explored. The most important protein modification in intracellular signalling pathways is phosphorylation of serine, threonine or tyrosine residues, and there exists the intriguing possibility that this modification may also influence the activity of chromatin remodelling enzymes. Phosphorylation could effect these enzymes directly, by modification of the catalytic subunit, or indirectly, by influencing protein]protein interactions within the complex and thus its composition. The complex networks of protein kinases and phosphatases that regulate growth control pathways and the ways in which these might modify chromatin are considered by Thomson et al, who also describe how kinases can modify chromatin through phosphorylation of histone H3. Finally, the cell’s response to an environmental signal is often transient. Once the signal disappears, then the cell reverts to its previous state. However, in other situations, such as progression down a pathway of differentiation, the changes in gene expression specified by the signal are retained, even when the signal itself has gone. Proteins of the Polycomb ŽPc. family were first identified in the fly D. melanogaster where they have a role in stabilising the transcriptionally inactive state of certain genes during development. Jacobs and van Lohuizen describe how Polycomb group proteins can stabilise patterns of gene activity in mammals and address the crucial question of how chromatin states can operate as components of cell memory. It is clear that we are only just beginning to appreciate the many ways in which intracellular signalling pathways might impact on chromatin. It will not be
Figure 1. The lower part of the figure shows the nucleosome core particle, consisting of eight histones surrounded by DNA. The N-terminal tail domains of the histones protrude from the DNA coils Žfor clarity only four of the eight tails are shown. and are subject to various post-translational modifications, including acetylation of selected lysines. The acetylatable lysines for each of the four histones are numbered. Open and condensed chromatin conformations are shown in the middle and upper parts of the figure. The diagram illustrates the possibility that the Nterminal tail domain of H4 interacts with an acidic patch on an adjacent nucleosome, thereby encouraging chromatin condensation. Acetylated lysines Žshown as black discs. in the H4 tail inhibit such interaction, while unmodified lysines Žgrey discs. facilitate it. Histones in condensed chromatin are generally underacetylated. Chromatin condensation also involves interaction with non-histone proteins Žshown as hatched regions. that may themselves interact with the histone tails.
their histone modifying activities, the chromatin remodelling enzymes take a more direct route by repositioning or disrupting nucleosomes in an ATP-dependent manner. Their archetype is the yeast enzyme complex designated SWIrSNF. The mammalian homologues of SWIrSNF play important roles in, among other things, growth control and tumorigenesis and are the subject of the article by Muchardt and Yaniv. Like other enzymes, SWIrSNF, HATs and HDACs 166
Introduction
References
easy to disentangle the interactions between these two complex systems, or even to unravel the terminology. Each has more than its fair share of acronyms. But the identification of chromatin modifying enzymes has provided us with potential targets that may provide the link between the kinase cascades that define cytoplasmic signalling pathways and the changes in gene expression that they induce.
1. Otte A, van Driel R, eds Ž1998. Nuclear Organization, Chromatin Structure and Gene Expression. Oxford University Press 2. Turner BM, O’Neill LP Ž1995. Histone acetylation in chromatin and chromosomes. Semin Cell Biol 6:229]236 3. Luger K, Richmond T Ž1998. The histone tails of the nucleosome. Curr Opin Genet Dev 8:140]146
167
Introduction: Chromatin—a target for intracellular signalling pathways Bryan M. Turner
MANY PROTEINS ASSOCIATE with DNA in the nuclei of eukaryotic cells, but few, if any, enjoy such an intimate relationship as the histones. An octamer of histones Žtwo each of H2A, H2B, H3 and H4. wraps 146bp of DNA around itself to form the nucleosome core particle, the basic unit of chromatin structure in all eukaryotic cells ŽFigure 1.. Chromatin in the nucleus can adopt a variety of higher order structures, the great majority of which consist of nucleosome arrays, and while these structures are not understood in any detail, it is clear that they can have important, and sometimes overriding effects on gene expression.1 These effects can be brought about in various ways, such as positioning a histone octamer over a crucial transcription factor binding site, changing DNA packaging to allow or inhibit access of components of the transcription apparatus or through more subtle mechanisms such as DNA looping, that can juxtapose or separate interacting DNA elements. All these possibilities, and others, have been under investigation for years, but the sheer size and complexity of the structures involved has limited progress. The problem is compounded by the fact that chromatin is a naturally dynamic structure. In most cells, DNA is going through cycles of replication, repair and condensation prior to mitosis, all of which involve major reorganisation of chromatin. To dissect out from this maelstrom, those changes relevant to the small fraction of the genome with transcriptional potential, is a formidable task. Over the last 3 years or so, chromatin research has taken a significant step forward with the identification and characterization of some of the enzymes
that mediate changes in chromatin structure. Three enzyme families have received particular attention, namely enzyme complexes that have ATP-dependent chromatin remodelling activity; histone acetyltransferases; and histone deacetylases. All these enzymes have the potential to regulate gene expression through their effects on chromatin structure and, not surprisingly, have become the focus of intensive research. However, a subject that has, as yet, received relatively little attention is that these enzymes also provide possible, mechanistic links between signal transduction pathways and their transcriptional effects. This intriguing prospect is the theme that links the articles in the present collection. Acetylation of the amino terminal domains of the core histones has been known about for over 30 years. It is a common modification, with most histone molecules going through cycles of acetylation and deacetylation with half lives varying from a few minutes to several hours. Histone acetylation clearly has the potential to alter chromatin structure and function, and a mass of evidence, albeit often circumstantial, has associated changes in histone acetylation with changes in transcription.2 More compellingly, many of the recently identified HATs and HDACs have turned out to be identical with, or homologous to, known activators or repressors of transcription. This is dealt with in the articles by Grant and Berger ŽHATs. and Johnson and Turner ŽHDACs.. Exactly how acetylation influences transcription remains something of a mystery, though much attention has recently been given to the finding, resulting from detailed crystallographic analysis of the nucleosome core particle, that the tail domain of histone H4 has the ability to link adjacent nucleosomes.3 This raises the possibility that acetylation of the H4 tail can influence such cross linking and thereby alter higher order chromatin packaging ŽFigure 1.. While HATs and HDACs change chromatin structure through
From the Department of Anatomy, Chromatin and Gene Expression Group, University of Birmingham Medical School, Birmingham B15 2TT, UK. Q1999 Academic Press 1084-9521r 99r 020165q 03 $30.00r 0
165
B. M. Turner
are subject to various levels of regulation. They are all, in vivo, multi-subunit complexes and their subunit compositions are crucial. Some complexes are now known to have both chromatin remodeling and deacetylase activity and by incorporating specific DNA binding proteins, complexes can be targeted to specific regions of the genome. Magnaghi-Jaulin et al discuss this, particularly in relation to control of cell growth and the role of Rb, the protein product of the Retinoblastoma tumour suppressor gene. Rb can associate with various complexes, including SWIrSWF homologues. Minucci and Pelicci describe the ways in which the retinoid receptors use HDACs and HATs to regulate gene activity in a ligand-dependent manner and how disruption of these interactions can lead to human disease. In this context, it is interesting to note that HDAC activity can be inhibited by an increasing variety of reagents, the therapeutic potentials of which are just beginning to be explored. The most important protein modification in intracellular signalling pathways is phosphorylation of serine, threonine or tyrosine residues, and there exists the intriguing possibility that this modification may also influence the activity of chromatin remodelling enzymes. Phosphorylation could effect these enzymes directly, by modification of the catalytic subunit, or indirectly, by influencing protein]protein interactions within the complex and thus its composition. The complex networks of protein kinases and phosphatases that regulate growth control pathways and the ways in which these might modify chromatin are considered by Thomson et al, who also describe how kinases can modify chromatin through phosphorylation of histone H3. Finally, the cell’s response to an environmental signal is often transient. Once the signal disappears, then the cell reverts to its previous state. However, in other situations, such as progression down a pathway of differentiation, the changes in gene expression specified by the signal are retained, even when the signal itself has gone. Proteins of the Polycomb ŽPc. family were first identified in the fly D. melanogaster where they have a role in stabilising the transcriptionally inactive state of certain genes during development. Jacobs and van Lohuizen describe how Polycomb group proteins can stabilise patterns of gene activity in mammals and address the crucial question of how chromatin states can operate as components of cell memory. It is clear that we are only just beginning to appreciate the many ways in which intracellular signalling pathways might impact on chromatin. It will not be
Figure 1. The lower part of the figure shows the nucleosome core particle, consisting of eight histones surrounded by DNA. The N-terminal tail domains of the histones protrude from the DNA coils Žfor clarity only four of the eight tails are shown. and are subject to various post-translational modifications, including acetylation of selected lysines. The acetylatable lysines for each of the four histones are numbered. Open and condensed chromatin conformations are shown in the middle and upper parts of the figure. The diagram illustrates the possibility that the Nterminal tail domain of H4 interacts with an acidic patch on an adjacent nucleosome, thereby encouraging chromatin condensation. Acetylated lysines Žshown as black discs. in the H4 tail inhibit such interaction, while unmodified lysines Žgrey discs. facilitate it. Histones in condensed chromatin are generally underacetylated. Chromatin condensation also involves interaction with non-histone proteins Žshown as hatched regions. that may themselves interact with the histone tails.
their histone modifying activities, the chromatin remodelling enzymes take a more direct route by repositioning or disrupting nucleosomes in an ATP-dependent manner. Their archetype is the yeast enzyme complex designated SWIrSNF. The mammalian homologues of SWIrSNF play important roles in, among other things, growth control and tumorigenesis and are the subject of the article by Muchardt and Yaniv. Like other enzymes, SWIrSNF, HATs and HDACs 166
Introduction
References
easy to disentangle the interactions between these two complex systems, or even to unravel the terminology. Each has more than its fair share of acronyms. But the identification of chromatin modifying enzymes has provided us with potential targets that may provide the link between the kinase cascades that define cytoplasmic signalling pathways and the changes in gene expression that they induce.
1. Otte A, van Driel R, eds Ž1998. Nuclear Organization, Chromatin Structure and Gene Expression. Oxford University Press 2. Turner BM, O’Neill LP Ž1995. Histone acetylation in chromatin and chromosomes. Semin Cell Biol 6:229]236 3. Luger K, Richmond T Ž1998. The histone tails of the nucleosome. Curr Opin Genet Dev 8:140]146
167