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Wild Chromatin: Regulation of Eukaryotic Genes in Their Natural Chromatin Context

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Wild Chromatin: Regulation of Eukaryotic Genes in Their Natural Chromatin Context Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press MEETING REVIEW Wild chromatin: regulation of eukaryotic genes in their natural chromatin context Valerio Orlando1 and Katherine A. Jones2,3 1Dulbecco Telethon Institute, Institute of Genetics and Biophysics National Research Council, 80131 Naples, Italy; 2Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA Nearly 40 years ago, François Jacob and Jacques Monod ings highlight a key role for modification of individual provided the first genetic evidence that genes are con- nucleosomes in gene regulation. Ultimately, the stabil- trolled through the opposing actions of activators and ity of open or closed chromatin is dictated by reversible repressors on specific DNA targets. Although minimal- histone tail modifications, which occur in patterns that istic, the classic paradigm provided by the regulation of correlate with gene activation or repression. A major the Lac operon in Escherichia coli quite accurately re- task is to unravel how gene- and locus-specific patterns flects the rationale of eukaryotic gene regulation, even in of modifications are initiated and maintained. the context of highly organized chromosome structure. At the meeting, Dave Allis (University of Virginia, Transcriptional activation of most eukaryotic genes is Charlottesville, VA, USA) showed that the Saccharomy- now known to require several 10s of factors, many of ces cerevisiae Rad6 gene product regulates methylation which are responsive to developmental or environmen- at Lys 4 (K4) on histone H3, often considered a hallmark tal signaling pathways. Some regulators are enzymes of gene activation. Remarkably, RAD6 is not a histone that modify or reconfigure chromatin, whereas others methyltransferase but, rather, functions as a ubiquitin- influence the subnuclear organization of transcription conjugating enzyme specific for histone H2B-K120 (K123 factors or, in some cases, change the relative chromo- in yeast). Thus, ubiquitination of histone H2B is epi- somal environments of specific gene targets. Posttrans- static to the histone H3-K4 methylation. The converse is lational modifications of histones or enhancer factors de- not true, namely, methylation at histone H3-K4 is not fine localized chromatin domains as well as the activity required for ubiquitination of histone H2B. This example and turnover of enhancer complexes. A crucial problem illustrates the importance of nucleosomal modification in the field now is to decipher how proper regulation cross-talk, in which a modification at one site can pro- springs from combinations of positive and negative fac- foundly influence modification at nearby sites or, re- tors, generally organized in multiprotein complexes or markably, even on distant histone tails. Recent studies coupled to molecular engines, which recognize and have suggested sequence similarities between histone modify regulatory loci embedded in chromatin. deacetylase and deubiquitinating enzymes, which raises Remarkably, after an early period in which nucleo- the intriguing possibility that histone deacetylase inhibi- somal DNA was seen as a negative and somehow passive tors such as trichostain A (TSA) might impact ubiquitin- template for transcription, chromatin and chromosome dependent histone methylation pathways, which, in organization in the nucleus have now emerged as central turn, affect histone acetylation. The Allis group have parameters with direct and essential effects on the con- also found that phosphorylation at Ser 14 on histone H2B trol of gene expression. The workshop “Regulation of occurs selectively on apoptotic chromatin in vertebrates Eukaryotic Genes in Their Natural Chromatin Con- and may be mediated by Mst1 (mammalian sterile-like text,” hosted by Fundaciòn Juan March in Madrid, Spain kinase), an apoptotic-inducing kinase that acts immedi- (April 22–24, 2002), was organized by Miguel Beato and ately downstream of caspase-3s. Ken Zaret to address some of the most pressing issues Louis Mahadevan (University of Oxford, UK) ad- concerning how complex regulatory networks work in dressed whether phosphorylation of histone H3 at S10 their natural molecular environment: the chromosome. and acetylation at residues K4 and K9, which are both early events in the induction of the c-fos and c-jun genes, Histone modifications in the control of gene occur as concerted or independent events. Disruption of expression and genome plasticity the MSK1 and MSK2kinases resulted in the loss of S10 phosphorylation without affecting the overall levels of Contrary to the view that chromatin functions as a natu- histone H3 acetylation, indicating that histone phos- ral barrier to most DNA-dependent processes, new find- phorylation and acetylation may be regulated indepen- 3Corresponding author. dently. These findings contrast with previous reports E-MAIL [email protected]; FAX (858) 552-8285. Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ that phosphorylation at S10 precedes acetylation and gad.1017402. gene activation. This group also reported that whereas GENES & DEVELOPMENT 16:2039–2044 © 2002 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/02 $5.00; www.genesdev.org 2039 Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Orlando and Jones H3 phosphorylation is an inducible event, acetylation is some maintained H3-K9 methylation. This implies the continuous and dynamic, even in quiescent cells and in existence in heterochromatin of more than one type of the absence of transcription. The latter finding may be histone H3 methylation, and also indicates that more particularly relevant for maintenance programs, in than one HMT controls the methylation state of hetero- which a locus specifies an appropriate level of acetyla- chromatin. Whether histone lysine methyl groups are tion through the regulated actions of opposing enzymat- removed enzymatically is an open question at the pres- ic activities. To define the function of different chroma- ent. tin modifications in the various stages of mammalian Much discussion focused on the fact that not all his- X-chromosome inactivation, Bryan Turner (University tone modifications are created equal. In particular, K4 of Birmingham, UK) presented immunohistochemical and K9 of histone H3 can be mono-, di-, or trimethylated, evidence that global changes in the acetylation of all four and existing antisera do not appropriately distinguish core histones occur in parallel and follow down-regula- these modifications. Should these distinct methylation tion (silencing) of X-linked genes in female ES cells. Re- states differentially impact gene regulation or chromatin markably, analyses using novel antisera capable of dis- compaction, the combinatorial power of signaling tinguishing di- and trimethylated lysine residues (H3-K4, through histone modification would be enhanced signifi- H3-K9) revealed that X inactivation is accompanied by cantly. Moreover, because most in vivo studies of his- changes in the relative abundance of specific methyl- tone modification rely on chromatin immunoprecipita- ation modifications. Thus, although the inactive X-chro- tion or immunolocalization, the quality and specificity mosome (Xi) lacks H3 dimethyl K4, H3 trimethyl K4, of existing antibodies restricts our understanding of the and H3 trimethyl K9, it retains H3 dimethyl K9 in state of native chromatin. Further, Louis Mahadevan amounts equivalent to those on the active X-chromo- (University of Oxford, UK) reported that second-site some (Xa). Evidence was presented that the relatively modifications in histone tails can strongly interfere with enhanced immunostaining of Xi with certain antisera to epitope recognition. In particular, he reported the case of H3 methyl K9 is fixation-dependent, and likely reflects a commercial K9/K18 acetyl H3 antiserum that could differences in chromatin conformation rather than in- not detect the epitope if Ser10 is phosphorylated. In this creased levels of H3 methylation. case, therefore, phosphorylation at S10 would mask de- The mammalian genome undergoes extensive repro- tection of histone H3 acetylation. Bryan Turner (Univer- gramming after fertilization. The paternal genome is sity of Birmingham Medical School, Birmingham, UK) widely demethylated in the zygote, whereas the mater- has shown that antibodies raised against dimethylated nal genome is demethylated during cleavage division in H3 tail peptides share little or no cross-reactivity with the preimplantation embryo. After these epigenetic antibodies raised against the equivalent trimethylated marks are removed, a wave of de novo methylation oc- peptides, and vice versa. This issue will deserve particu- curs postimplantation. Wolf Reik (Babraham Institute, lar attention in the future, and as knowledge about com- Cambridge, UK) examined the possible relationship be- plex histone modification profiles emerges, it will be- tween DNA and histone methylation in preimplantation come crucial to develop reagents that more precisely de- embryos. K9-histone H3 methylation is asymmetric at fine the state of regulated chromatin in vivo. fertilization, and is immediately followed by DNA de- methylation of the paternal genome. Later, de novo Chromatin remodeling at activated genes in vivo DNA methylation occurs, accompanied by global his- tone H3-K9 remethylation, specifically in inner-cell- An early step in gene
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