401
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Abstract
Nucleosomal histones can be methylated in vivo at multiple residues and defined methylation patterns are related to distinct functional readouts of chromosomal DNA. Histone methylation has emerged as an important post-translational modification involved in transcriptional regulation and genome integrity. Recent progress in determining the cis and trans determinants of this process revealed multiple roles for histone methylation in epigenetic memory of active and silent states. The analysis of imprinted, X-linked and heterochromatic sequences disclosed mechanistic similarities for heritable transcriptional repression, pointing to a common mode of action. Moreover, the view of histone methylation as a stable modification has recently been challenged by studies revealing a number of pathways that are capable of removing histone methylation. Thus, in addition to having great in vivo complexity, this modification appears more dynamic then was previously thought.
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Affiliation(s)
- Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland.
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402
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Ringrose L, Paro R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 2005; 38:413-43. [PMID: 15568982 DOI: 10.1146/annurev.genet.38.072902.091907] [Citation(s) in RCA: 775] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the development of multicellular organisms, cells become different from one another by changing their genetic program in response to transient stimuli. Long after the stimulus is gone, "cellular memory" mechanisms enable cells to remember their chosen fate over many cell divisions. The Polycomb and Trithorax groups of proteins, respectively, work to maintain repressed or active transcription states of developmentally important genes through many rounds of cell division. Here we review current ideas on the protein and DNA components of this transcriptional memory system and how they interact dynamically with each other to orchestrate cellular memory for several hundred genes.
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403
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Srinivasan S, Armstrong JA, Deuring R, Dahlsveen IK, McNeill H, Tamkun JW. The Drosophila trithorax group protein Kismet facilitates an early step in transcriptional elongation by RNA Polymerase II. Development 2005; 132:1623-35. [PMID: 15728673 DOI: 10.1242/dev.01713] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Drosophila trithorax group gene kismet (kis) was identified in a screen for extragenic suppressors of Polycomb (Pc) and subsequently shown to play important roles in both segmentation and the determination of body segment identities. One of the two major proteins encoded by kis (KIS-L) is related to members of the SWI2/SNF2 and CHD families of ATP-dependent chromatin-remodeling factors. To clarify the role of KIS-L in gene expression, we examined its distribution on larval salivary gland polytene chromosomes. KIS-L is associated with virtually all sites of transcriptionally active chromatin in a pattern that largely overlaps that of RNA Polymerase II (Pol II). The levels of elongating Pol II and the elongation factors SPT6 and CHD1 are dramatically reduced on polytene chromosomes from kis mutant larvae. By contrast, the loss of KIS-L function does not affect the binding of PC to chromatin or the recruitment of Pol II to promoters. These data suggest that KIS-L facilitates an early step in transcriptional elongation by Pol II.
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Affiliation(s)
- Shrividhya Srinivasan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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404
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Ringrose L, Ehret H, Paro R. Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. Mol Cell 2005; 16:641-53. [PMID: 15546623 DOI: 10.1016/j.molcel.2004.10.015] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 08/30/2004] [Accepted: 09/08/2004] [Indexed: 11/21/2022]
Abstract
The Polycomb group of proteins (PcG) maintains stable epigenetic silencing of over 100 genes via PcG response elements (PREs). Here we investigate the relationship between Polycomb binding, transcriptional status, and histone H3 methylation at lysine 9 (H3K9Me) and 27 (H3K27Me) for over 30 PcG targets in Drosophila. We show that H3K9Me and H3K27Me have distinct distributions at different loci. Our data show that Polycomb binding and histone methylation at the promoter do not prevent strong transcriptional activity, and indicate instead that silencing requires methylation of both PRE and promoter. In addition, we show that trimethylated H3K9 and H3K27 peptides can compete Polycomb from polytene chromosomes, with different effects at different loci, which correlate with differences in methylation status and transcriptional activity. We use mathematical modeling to examine these data, and propose that weak Polycomb-histone tail interactions enable PcG complexes to bind dynamically to chromatin, offering opportunities for regulation.
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Affiliation(s)
- Leonie Ringrose
- ZMBH, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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405
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Abstract
In development, cells pass on established gene expression patterns to daughter cells over multiple rounds of cell division. The cellular memory of the gene expression state is termed maintenance, and the proteins required for this process are termed maintenance proteins. The best characterized are proteins of the Polycomb and trithorax Groups that are required for silencing and maintenance of activation of target loci, respectively. These proteins act through DNA elements termed maintenance elements. Here, we re-examine the genetics and molecular biology of maintenance proteins. We discuss molecular models for the maintenance of activation and silencing, and the establishment of epigenetic marks, and suggest that maintenance proteins may play a role in propagating the mark through DNA synthesis.
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Affiliation(s)
- Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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406
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Sung S, Amasino RM. Remembering winter: toward a molecular understanding of vernalization. ANNUAL REVIEW OF PLANT BIOLOGY 2005; 56:491-508. [PMID: 15862105 DOI: 10.1146/annurev.arplant.56.032604.144307] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Exposure to the prolonged cold of winter is an important environmental cue that favors flowering in the spring in many types of plants. The process by which exposure to cold promotes flowering is known as vernalization. In Arabidopsis and certain cereals, the block to flowering in plants that have not been vernalized is due to the expression of flowering repressors. The promotion of flowering is due to the cold-mediated suppression of these repressors. Recent work has demonstrated that covalent modifications of histones in the chromatin of target loci are part of the molecular mechanism by which certain repressors are silenced during vernalization.
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Affiliation(s)
- Sibum Sung
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
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407
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Affiliation(s)
- Adone Mohd-Sarip
- Department of Biochemistry, Erasmus Medical Center, Rotterdam, Netherlands
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408
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Abstract
Proteins from the Polycomb group (PcG) are epigenetic chromatin modifiers involved in cancer development and also in the maintenance of embryonic and adult stem cells. The therapeutic potential of stem cells and the growing conviction that tumors contain stem cells highlights the importance of understanding the extrinsic and intrinsic circuitry controlling stem cell fate and their connections to cancer.
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Affiliation(s)
- Merel E Valk-Lingbeek
- The Netherlands Cancer Institute, Department of Molecular Genetics, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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409
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Chanvivattana Y, Bishopp A, Schubert D, Stock C, Moon YH, Sung ZR, Goodrich J. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 2004; 131:5263-76. [PMID: 15456723 DOI: 10.1242/dev.01400] [Citation(s) in RCA: 351] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Arabidopsis, the EMBYRONIC FLOWER2 (EMF2), VERNALISATION2 (VRN2) and FERTILISATION INDEPENDENT ENDOSPERM2 (FIS2) genes encode related Polycomb-group (Pc-G) proteins. Their homologues in animals act together with other Pc-G proteins as part of a multimeric complex, Polycomb Repressive Complex 2 (PRC2), which functions as a histone methyltransferase. Despite similarities between the fis2 mutant phenotype and those of some other plant Pc-G members, it has remained unclear how the FIS2/EMF2/VRN2 class Pc-G genes interact with the others. We have identified a weak emf2 allele that reveals a novel phenotype with striking similarity to that of severe mutations in another Pc-G gene, CURLY LEAF (CLF), suggesting that the two genes may act in a common pathway. Consistent with this, we demonstrate that EMF2 and CLF interact genetically and that this reflects interaction of their protein products through two conserved motifs, the VEFS domain and the C5 domain. We show that the full function of CLF is masked by partial redundancy with a closely related gene, SWINGER (SWN), so that null clf mutants have a much less severe phenotype than emf2 mutants. Analysis in yeast further indicates a potential for the CLF and SWN proteins to interact with the other VEFS domain proteins VRN2 and FIS2. The functions of individual Pc-G members may therefore be broader than single mutant phenotypes reveal. We suggest that plants have Pc-G protein complexes similar to the Polycomb Repressive Complex2 (PRC2) of animals, but the duplication and subsequent diversification of components has given rise to different complexes with partially discrete functions.
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Affiliation(s)
- Yindee Chanvivattana
- Institute of Molecular Plant Science, School of Biology, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JH, UK
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410
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Breiling A, O'Neill LP, D'Eliseo D, Turner BM, Orlando V. Epigenome changes in active and inactive polycomb-group-controlled regions. EMBO Rep 2004; 5:976-82. [PMID: 15448640 PMCID: PMC1299157 DOI: 10.1038/sj.embor.7400260] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 08/10/2004] [Accepted: 08/25/2004] [Indexed: 01/28/2023] Open
Abstract
The Polycomb group (PcG) of proteins conveys epigenetic inheritance of repressed transcriptional states. In Drosophila, the Polycomb repressive complex 1 (PRC1) maintains the silent state by inhibiting the transcription machinery and chromatin remodelling at core promoters. Using immunoprecipitation of in vivo formaldehyde-fixed chromatin in phenotypically diverse cultured cell lines, we have mapped PRC1 components, the histone methyl transferase (HMT) Enhancer of zeste (E(z)) and histone H3 modifications in active and inactive PcG-controlled regions. We show that PRC1 components are present in both cases, but at different levels. In particular, active target promoters are nearly devoid of E(z) and Polycomb. Moreover, repressed regions are trimethylated at lysines 9 and 27, suggesting that these histone modifications represent a mark for inactive PcG-controlled regions. These PcG-specific repressive marks are maintained by the action of the E(z) HMT, an enzyme that has an important role not only in establishing but also in maintaining PcG repression.
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Affiliation(s)
- Achim Breiling
- Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Laura P O'Neill
- Chromatin and Gene Expression Group, Institute of Biomedical Research, University of Birmingham Medical School, Birmingham B15 2TT, UK
| | - Donatella D'Eliseo
- Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Bryan M Turner
- Chromatin and Gene Expression Group, Institute of Biomedical Research, University of Birmingham Medical School, Birmingham B15 2TT, UK
| | - Valerio Orlando
- Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Via Pietro Castellino 111, 80131 Naples, Italy
- Tel: +39 081 6132361; Fax: +39 081 6132702; E-mail:
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411
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Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y. Role of histone H2A ubiquitination in Polycomb silencing. Nature 2004; 431:873-8. [PMID: 15386022 DOI: 10.1038/nature02985] [Citation(s) in RCA: 1272] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Accepted: 09/02/2004] [Indexed: 11/09/2022]
Abstract
Covalent modification of histones is important in regulating chromatin dynamics and transcription. One example of such modification is ubiquitination, which mainly occurs on histones H2A and H2B. Although recent studies have uncovered the enzymes involved in histone H2B ubiquitination and a 'cross-talk' between H2B ubiquitination and histone methylation, the responsible enzymes and the functions of H2A ubiquitination are unknown. Here we report the purification and functional characterization of an E3 ubiquitin ligase complex that is specific for histone H2A. The complex, termed hPRC1L (human Polycomb repressive complex 1-like), is composed of several Polycomb-group proteins including Ring1, Ring2, Bmi1 and HPH2. hPRC1L monoubiquitinates nucleosomal histone H2A at lysine 119. Reducing the expression of Ring2 results in a dramatic decrease in the level of ubiquitinated H2A in HeLa cells. Chromatin immunoprecipitation analysis demonstrated colocalization of dRing with ubiquitinated H2A at the PRE and promoter regions of the Drosophila Ubx gene in wing imaginal discs. Removal of dRing in SL2 tissue culture cells by RNA interference resulted in loss of H2A ubiquitination concomitant with derepression of Ubx. Thus, our studies identify the H2A ubiquitin ligase, and link H2A ubiquitination to Polycomb silencing.
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Affiliation(s)
- Hengbin Wang
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA
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412
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Zhang Y, Cao R, Wang L, Jones RS. Mechanism of Polycomb group gene silencing. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:309-17. [PMID: 16117663 DOI: 10.1101/sqb.2004.69.309] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Y Zhang
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA
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413
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Muyrers-Chen I, Hernández-Muñoz I, Lund AH, Valk-Lingbeek ME, van der Stoop P, Boutsma E, Tolhuis B, Bruggeman SWM, Taghavi P, Verhoeven E, Hulsman D, Noback S, Tanger E, Theunissen H, van Lohuizen M. Emerging roles of Polycomb silencing in X-inactivation and stem cell maintenance. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:319-26. [PMID: 16117664 DOI: 10.1101/sqb.2004.69.319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- I Muyrers-Chen
- The Netherlands Cancer Institute, Division of Molecular Genetics, 1066 CX Amsterdam, The Netherlands
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