751
|
Schubert D, Clarenz O, Goodrich J. Epigenetic control of plant development by Polycomb-group proteins. CURRENT OPINION IN PLANT BIOLOGY 2005; 8:553-61. [PMID: 16043386 DOI: 10.1016/j.pbi.2005.07.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 07/12/2005] [Indexed: 05/02/2023]
Abstract
Recent genetic studies indicate that the plant Polycomb-group genes play much broader roles in development than was initially apparent from their single mutant phenotypes. At the mechanistic level, evidence is accumulating that their protein products act together in complexes that direct changes in histone methylation patterns. We discuss recent studies that give clues as to how these epigenetic changes are propagated through mitosis, how they are interpreted, and how they might be reset.
Collapse
Affiliation(s)
- Daniel Schubert
- Institute of Molecular Plant Sciences, School of Biology, University of Edinburgh, Daniel Rutherford Building, Mayfield Road, Edinburgh EH9 3JH, UK.
| | | | | |
Collapse
|
752
|
Santos KF, Mazzola TN, Carvalho HF. The prima donna of epigenetics: the regulation of gene expression by DNA methylation. Braz J Med Biol Res 2005; 38:1531-41. [PMID: 16172746 DOI: 10.1590/s0100-879x2005001000010] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This review focuses on the mechanisms of DNA methylation, DNA methylation pattern formation and their involvement in gene regulation. Association of DNA methylation with imprinting, embryonic development and human diseases is discussed. Furthermore, besides considering changes in DNA methylation as mechanisms of disease, the role of epigenetics in general and DNA methylation in particular in transgenerational carcinogenesis, in memory formation and behavior establishment are brought about as mechanisms based on the cellular memory of gene expression patterns.
Collapse
Affiliation(s)
- K F Santos
- Departamento de Biologia Celular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | | |
Collapse
|
753
|
Karnik SK, Hughes CM, Gu X, Rozenblatt-Rosen O, McLean GW, Xiong Y, Meyerson M, Kim SK. Menin regulates pancreatic islet growth by promoting histone methylation and expression of genes encoding p27Kip1 and p18INK4c. Proc Natl Acad Sci U S A 2005; 102:14659-64. [PMID: 16195383 PMCID: PMC1253549 DOI: 10.1073/pnas.0503484102] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Menin, the product of the Men1 gene mutated in familial multiple endocrine neoplasia type 1 (MEN1), regulates transcription in differentiated cells. Menin associates with and modulates the histone methyltransferase activity of a nuclear protein complex to activate gene expression. However, menin-dependent histone methyltransferase activity in endocrine cells has not been demonstrated, and the mechanism of endocrine tumor suppression by menin remains unclear. Here, we show that menin-dependent histone methylation maintains the in vivo expression of cyclin-dependent kinase (CDK) inhibitors to prevent pancreatic islet tumors. In vivo expression of CDK inhibitors, including p27 and p18, and other cell cycle regulators is disrupted in mouse islet tumors lacking menin. Chromatin immunoprecipitation studies reveal that menin directly associates with regions of the p27 and p18 promoters and increases methylation of lysine 4 (Lys-4) in histone H3 associated with these promoters. Moreover, H3 Lys-4 methylation associated with p27 and p18 is reduced in islet tumors from Men1 mutant mice. Thus, H3 Lys-4 methylation is a crucial function of menin in islet tumor suppression. These studies suggest an epigenetic mechanism of tumor suppression: by promoting histone modifications, menin maintains transcription at multiple loci encoding cell cycle regulators essential for endocrine growth control.
Collapse
Affiliation(s)
- Satyajit K Karnik
- Departments of Developmental Biology and Medicine (Oncology Division), Stanford University School of Medicine, Stanford, CA 94305-5329
| | | | | | | | | | | | | | | |
Collapse
|
754
|
Sarge KD, Park-Sarge OK. Gene bookmarking: keeping the pages open. Trends Biochem Sci 2005; 30:605-10. [PMID: 16188444 DOI: 10.1016/j.tibs.2005.09.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 08/12/2005] [Accepted: 09/14/2005] [Indexed: 11/19/2022]
Abstract
'Gene bookmarking' is a mechanism of epigenetic memory that functions to transmit through mitosis the pattern of active genes and/or genes that can be activated to daughter cells. It is thought that, at a point before mitosis, genes that exist in an open, transcriptionally competent state are bound by proteins or marked by some kind of modification event. This is thought to facilitate the assembly of transcription complexes on the promoters in early G1, thereby ensuring that daughter cells have the same pattern of gene expression as the cell from which they derived. Little is known, however, about these 'bookmarking factors' and modifications or the mechanisms by which they mediate the transmission of transcriptional competence after mitosis is complete. Recent findings have provided new insights into the mechanisms, regulation and biological importance of gene bookmarking in eukaryotic cell function.
Collapse
Affiliation(s)
- Kevin D Sarge
- Department of Molecular and Cellular Biochemistry, Biomedical/Biological Sciences Research Building, 741 South Limestone Street, Lexington, KY 40536, USA.
| | | |
Collapse
|
755
|
Mito Y, Henikoff JG, Henikoff S. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 2005; 37:1090-7. [PMID: 16155569 DOI: 10.1038/ng1637] [Citation(s) in RCA: 404] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 08/01/2005] [Indexed: 11/09/2022]
Abstract
Histones of multicellular organisms are assembled into chromatin primarily during DNA replication. When chromatin assembly occurs at other times, the histone H3.3 variant replaces canonical H3. Here we introduce a new strategy for profiling epigenetic patterns on the basis of H3.3 replacement, using microarrays covering roughly one-third of the Drosophila melanogaster genome at 100-bp resolution. We identified patterns of H3.3 replacement over active genes and transposons. H3.3 replacement occurred prominently at sites of abundant RNA polymerase II and methylated H3 Lys4 throughout the genome and was enhanced on the dosage-compensated male X chromosome. Active genes were depleted of histones at promoters and were enriched in H3.3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin.
Collapse
Affiliation(s)
- Yoshiko Mito
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | | | | |
Collapse
|
756
|
Brown JL, Grau DJ, DeVido SK, Kassis JA. An Sp1/KLF binding site is important for the activity of a Polycomb group response element from the Drosophila engrailed gene. Nucleic Acids Res 2005; 33:5181-9. [PMID: 16155187 PMCID: PMC1214548 DOI: 10.1093/nar/gki827] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Polycomb-group response elements (PREs) are DNA elements through which the Polycomb-group (PcG) of transcriptional repressors act. Many of the PcG proteins are associated with two protein complexes that repress gene expression by modifying chromatin. Both of these protein complexes specifically associate with PREs in vivo, however, it is not known how they are recruited or held at the PRE. PREs are complex elements, made up of binding sites for many proteins. Our laboratory has been working to define all the sequences and DNA binding proteins required for the activity of a 181 bp PRE from the Drosophila engrailed gene. Here we show that one of the sites necessary for PRE activity, Site 2, can be bound by members of the Sp1/KLF family of zinc finger proteins. There are 10 Sp1/KLF family members in Drosophila, and nine of them bind to Site 2. We derive a consensus binding site for the Sp1/KLF Drosophila family members and show that this consensus sequence is present in most of the molecularly characterized PREs. These data suggest that one or more Sp1/KLF family members play a role in PRE function in Drosophila.
Collapse
Affiliation(s)
| | | | | | - Judith A. Kassis
- To whom correspondence should be addressed. Tel: +1 301 496 7879; Fax: +1 301 496 0243;
| |
Collapse
|
757
|
Ketel CS, Andersen EF, Vargas ML, Suh J, Strome S, Simon JA. Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes. Mol Cell Biol 2005; 25:6857-68. [PMID: 16055700 PMCID: PMC1190254 DOI: 10.1128/mcb.25.16.6857-6868.2005] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The ESC-E(Z) complex of Drosophila melanogaster Polycomb group (PcG) repressors is a histone H3 methyltransferase (HMTase). This complex silences fly Hox genes, and related HMTases control germ line development in worms, flowering in plants, and X inactivation in mammals. The fly complex contains a catalytic SET domain subunit, E(Z), plus three noncatalytic subunits, SU(Z)12, ESC, and NURF-55. The four-subunit complex is >1,000-fold more active than E(Z) alone. Here we show that ESC and SU(Z)12 play key roles in potentiating E(Z) HMTase activity. We also show that loss of ESC disrupts global methylation of histone H3-lysine 27 in fly embryos. Subunit mutations identify domains required for catalytic activity and/or binding to specific partners. We describe missense mutations in surface loops of ESC, in the CXC domain of E(Z), and in the conserved VEFS domain of SU(Z)12, which each disrupt HMTase activity but preserve complex assembly. Thus, the E(Z) SET domain requires multiple partner inputs to produce active HMTase. We also find that a recombinant worm complex containing the E(Z) homolog, MES-2, has robust HMTase activity, which depends upon both MES-6, an ESC homolog, and MES-3, a pioneer protein. Thus, although the fly and mammalian PcG complexes absolutely require SU(Z)12, the worm complex generates HMTase activity from a distinct partner set.
Collapse
Affiliation(s)
- Carrie S Ketel
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, 55455, USA
| | | | | | | | | | | |
Collapse
|
758
|
Abstract
In the universe of science, two worlds have recently collided-those of RNA and chromatin. The intersection of these two fields has been impending, but evidence for such a meaningful collision has only recently become apparent. In this review, we discuss the implications for noncoding RNAs and the formation of specialized chromatin domains in various epigenetic processes as diverse as dosage compensation, RNA interference-mediated heterochromatin assembly and gene silencing, and programmed DNA elimination. While mechanistic details as to how the RNA and chromatin worlds connect remain unclear, intriguing parallels exist in the overall design and machinery used in model organisms from all eukaryotic kingdoms. The role of potential RNA-binding chromatin-associated proteins will be discussed as one possible link between RNA and chromatin.
Collapse
Affiliation(s)
- Emily Bernstein
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | | |
Collapse
|
759
|
Nolz JC, Gomez TS, Billadeau DD. The Ezh2 methyltransferase complex: actin up in the cytosol. Trends Cell Biol 2005; 15:514-7. [PMID: 16126384 DOI: 10.1016/j.tcb.2005.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 07/18/2005] [Accepted: 08/15/2005] [Indexed: 11/26/2022]
Abstract
Ezh2, a polycomb group protein, is known to function in histone methylation, thereby regulating gene expression. However, in a recent study by Su et al., the Ezh2-containing complex has been given an additional role in cellular regulation. Cytosolic Ezh2 methyltransferase complexes were shown to associate with Vav1 and control receptor-induced actin polymerization and proliferation in a methylation-dependent manner. Overall, these findings implicate lysine methylation as a posttranslational modification crucial for receptor-mediated signal transduction events.
Collapse
Affiliation(s)
- Jeffrey C Nolz
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | | |
Collapse
|
760
|
Nekrasov M, Wild B, Müller J. Nucleosome binding and histone methyltransferase activity of Drosophila PRC2. EMBO Rep 2005; 6:348-53. [PMID: 15776017 PMCID: PMC1299286 DOI: 10.1038/sj.embor.7400376] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 02/10/2005] [Accepted: 02/15/2005] [Indexed: 11/08/2022] Open
Abstract
The Drosophila Polycomb group protein E(z) is a histone methyltransferase (HMTase) that is essential for maintaining HOX gene silencing during development. E(z) exists in a multiprotein complex called Polycomb repressive complex 2 (PRC2) that also contains Su(z)12, Esc and Nurf55. Reconstituted recombinant PRC2 methylates nucleosomes in vitro, but recombinant E(z) on its own shows only poor HMTase activity on nucleosomes. Here, we investigate the function of the PRC2 subunits. We show that PRC2 binds to nucleosomes in vitro but that individual PRC2 subunits alone do not bind to nucleosomes. By analysing PRC2 subcomplexes, we show that Su(z)12-Nurf55 is the minimal nucleosome-binding module of PRC2 and that Esc contributes to high-affinity binding of PRC2 nucleosomes. We find that nucleosome binding of PRC2 is not sufficient for histone methylation and that only complexes that contain Esc protein show robust HMTase activity. These observations suggest that different subunits provide mechanistically distinct functions within the PRC2 HMTase: the nucleosome-binding subunits Su(z)12 and Nurf55 anchor the E(z) enzyme on chromatin substrates, whereas Esc is needed to boost enzymatic activity.
Collapse
Affiliation(s)
- Maxim Nekrasov
- Gene Expression Programme, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Brigitte Wild
- Gene Expression Programme, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jürg Müller
- Gene Expression Programme, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Tel: +49 6221 387 629; Fax: +49 6221 387 424; E-mail:
| |
Collapse
|
761
|
Tie F, Siebold AP, Harte PJ. The N-terminus of Drosophila ESC mediates its phosphorylation and dimerization. Biochem Biophys Res Commun 2005; 332:622-32. [PMID: 15896722 DOI: 10.1016/j.bbrc.2005.04.157] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 04/29/2005] [Indexed: 11/17/2022]
Abstract
The ESC protein, like other Polycomb Group proteins, is required for heritable silencing of the homeotic genes. ESC is phosphorylated in vivo, but the region of ESC that is phosphorylated and its consequences are not known. Here, we show that the amino-terminal region of ESC (residues 1-60) mediates its phosphorylation and dimerization. Phosphorylation of ESC1-60 in vitro by CK1 and CK2 strongly enhances its dimerization. Both phosphorylation and dimerization are conserved in the mammalian ESC homolog EED, suggesting that they play important roles in vivo. One role is suggested by the effect of phosphatase treatment on native ESC complexes, which does not affect the integrity of the 600 kDa ESC/E(Z) complex, but eliminates the 1 MDa ESC/E(Z) complex, which is distinguished from the former by the presence of the additional subunits PCL and RPD3. Thus, stability and perhaps assembly of larger ESC complexes may depend on ESC phosphorylation.
Collapse
Affiliation(s)
- Feng Tie
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | |
Collapse
|
762
|
Abstract
The mixed-lineage leukemia (MLL) gene is a trithorax group (trxG) gene that was originally identified at chromosomal translocations in patients developing acute leukemia. Although Polycomb group (PcG) genes, which counteract trxG genes, were found to play essential roles in hematopoiesis, little has been understood about the roles of trxG genes in hematopoiesis except for MLL. MLL has been found fused with 1 of more than 30 different partner genes to yield a diverse collection of MLL fusion oncoproteins that lead to the aberrant expression of HOX genes. Recent studies have revealed that MLL assembles, as do some trxG proteins, into a chromatin-modifying transcriptional regulatory supercomplex to regulate epigenetic pathways, including the methylation of histone H3 lysine 4, which is conferred by the Su (var)3-9, enhancer of zeste, and tritho-rax (SET) domain. Other studies also indicated that MLL plays a nonredundant and essential role in definitive hematopoiesis and induces the proliferation and differentiation of hematopoietic progenitors by maintaining appropriate up-regulation of HOX genes. Further progress in the field will provide novel insights into trxG- and PcG-mediated hematopoiesis and help us understand the epigenetic process by which developing stem cells coordinate proliferation and differentiation.
Collapse
Affiliation(s)
- Ryoichi Ono
- Division of Hematopoietic Factors, The Institute of Medical Science, The University of Tokyo, Japan
| | | | | |
Collapse
|
763
|
Abstract
Gene expression, differentiation and the specialized function of various cell types are controlled epigenetically by post-translational histone modifications. These modifications establish a "histone code" that is recognized by various regulatory proteins, thereby creating a stable pattern of gene expression. The focus of this review is to discuss how the chromatin modifications regulate immunoglobulin gene rearrangement and B cell differentiation.
Collapse
Affiliation(s)
- I-hsin Su
- Laboratory of Lymphocyte Signalling, The Rockefeller University, 1230 York Avenue, Box 301, New York, NY 10021, USA.
| | | |
Collapse
|
764
|
Abstract
Stem cells are unique in their capacity to self-renew and generate differentiated progeny to maintain tissues throughout life. A common molecular program for stem cells has remained elusive. We discuss what the molecular logic of stemness may be. We suggest that it may not be coupled to distinct cellular properties such as self-renewal or multipotency, but rather to the stable suspension at a specific developmental stage. In this view, the stem cell niche allows a cell to maintain a transcriptional accessibility enabling the generation of specific differentiated progeny.
Collapse
Affiliation(s)
- Harald Mikkers
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Stockholm, Sweden
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Box 285, 17177 Stockholm, Sweden. Tel.: +46 8 524 87562; Fax: +46 8 324927; E-mail:
| |
Collapse
|
765
|
Mathieu O, Probst AV, Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 2005; 24:2783-91. [PMID: 16001083 PMCID: PMC1182238 DOI: 10.1038/sj.emboj.7600743] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 06/15/2005] [Indexed: 11/09/2022] Open
Abstract
Transcriptional activity and structure of chromatin are correlated with patterns of covalent DNA and histone modification. Previous studies have revealed that high levels of histone H3 dimethylation at lysine 9 (H3K9me2), characteristic of transcriptionally silent heterochromatin in Arabidopsis, require hypermethylation of DNA at CpG sites. Here, we report that CpG hypermethylation characteristic of heterochromatin specifically prevented H3K27 trimethylation (H3K27me3). H3K27 mono- and dimethylation mark silent heterochromatin independently of DNA methylation. Upon loss of CpG methylation, there was target-specific enrichment of H3K27me3 in heterochromatin that correlated with transcriptional reactivation. Moreover, using the kyp mutant affected in H3K9me2, we showed that changes in H3K27me3 occurred independently of the levels of H3K9me2. Therefore, CpG methylation provides distinct and direct information for a specific subset of histone methylation marks. The observed independence of the regulation of H3K9 and H3K27 methylation by CpG methylation refines the recently proposed combinatorial histone code involving these two marks.
Collapse
Affiliation(s)
- Olivier Mathieu
- Laboratory of Plant Genetics, University of Geneva, Geneva, Switzerland.
| | | | | |
Collapse
|
766
|
Deschamps J, van Nes J. Developmental regulation of the Hox genes during axial morphogenesis in the mouse. Development 2005; 132:2931-42. [PMID: 15944185 DOI: 10.1242/dev.01897] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Hox genes confer positional information to the axial and paraxial tissues as they emerge gradually from the posterior aspect of the vertebrate embryo. Hox genes are sequentially activated in time and space, in a way that reflects their organisation into clusters in the genome. Although this co-linearity of expression of the Hox genes has been conserved during evolution, it is a phenomenon that is still not understood at the molecular level. This review aims to bring together recent findings that have advanced our understanding of the regulation of the Hox genes during mouse embryonic development. In particular, we highlight the integration of these transducers of anteroposterior positional information into the genetic network that drives tissue generation and patterning during axial elongation.
Collapse
Affiliation(s)
- Jacqueline Deschamps
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | | |
Collapse
|
767
|
Hennig L, Bouveret R, Gruissem W. MSI1-like proteins: an escort service for chromatin assembly and remodeling complexes. Trends Cell Biol 2005; 15:295-302. [PMID: 15953547 DOI: 10.1016/j.tcb.2005.04.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 04/04/2005] [Accepted: 04/20/2005] [Indexed: 10/25/2022]
Abstract
MSI1-like WD40 repeat proteins are subunits of many protein complexes controlling chromatin dynamics. These proteins do not have any catalytic activity, but several recent studies using loss-of-function mutants established specific functions during development. Here, we review the current knowledge of MSI1-like proteins, including their phylogenetic history, expression patterns, biochemical interactions and mutant phenotypes. MSI1-like proteins, which are often targets or partners of tumor-suppressor proteins, are required during cell proliferation and differentiation in flies, nematodes and plants. We discuss the possibility that MSI1-like proteins could function to maintain epigenetic memory during development by targeting silencing complexes to chromatin during nucleosome assembly.
Collapse
Affiliation(s)
- Lars Hennig
- Institute of Plant Sciences, Swiss Federal Institute of Technology and Zürich-Basel Plant Science Center, ETH Center, CH-8092 Zürich.
| | | | | |
Collapse
|
768
|
Abstract
Changes in protein conformation drive most biological processes, but none have seized the imagination of scientists and the public alike as have the self-replicating conformations of prions. Prions transmit lethal neurodegenerative diseases by means of the food chain. However, self-replicating protein conformations can also constitute molecular memories that transmit genetic information. Here, we showcase definitive evidence for the prion hypothesis and discuss examples in which prion-encoded heritable information has been harnessed during evolution to confer selective advantages. We then describe situations in which prion-enciphered events might have essential roles in long-term memory formation, transcriptional memory and genome-wide expression patterns.
Collapse
Affiliation(s)
- James Shorter
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
| | | |
Collapse
|
769
|
Prouteau M, Colot V. [Epigenetic control, development and natural genetic variation in plants]. Med Sci (Paris) 2005; 21:422-7. [PMID: 15811308 DOI: 10.1051/medsci/2005214422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plant life strategies differ radically from those of most animals. Plants are not motile, and can only face stress by developing appropriate physiological responses. In addition, many developmental decisions take place during post-embryonic life in plants, whereas vertebrate and invertebrate development is nearly complete by the time of birth. For instance, while the germ line is typically set aside early during embryogenesis in animals, plants produce gametes from stem cell populations that were previously used for the vegetative growth of shoots. Nevertheless, plants and animals have similar nuclear organization, chromatin constitution and gene content, which raises the question as to whether or not fundamental differences in the use of genetic information underlie their distinct life strategies. More specifically, we would like to know if chromatin and the epigenetically defined, heritable cell fates that it can confer play comparable roles in plants and animals. Here we review our current knowledge on chromatin-mediated epigenetic processes in plants. Based on available evidence, we argue that epigenetic regulation of gene expression plays a relatively minor role in plants compared to mammals. Conversely, plants appear to be more prone than other multicellular organisms to the induction of chromatin-based, epigenetically modified gene activity states that can be transmitted over many generations. These so-called "epimutations" may therefore represent a significant proportion of the natural genetic variation seen in plants. In humans, epimutations are frequently observed in cancers, and given their metastable nature, they could also play an important role in familial disorders that do not demonstrate clear Mendelian inheritance.
Collapse
Affiliation(s)
- Manoël Prouteau
- Unité de Recherche en Génomique végétale, UMR INRA 1165-CNRS 8114-UEVE, 2, rue Gaston-Crémieux, 91057 Evry Cedex, France
| | | |
Collapse
|
770
|
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.
Collapse
Affiliation(s)
- Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland.
| | | |
Collapse
|
771
|
van der Knaap JA, Kumar BRP, Moshkin YM, Langenberg K, Krijgsveld J, Heck AJR, Karch F, Verrijzer CP. GMP Synthetase Stimulates Histone H2B Deubiquitylation by the Epigenetic Silencer USP7. Mol Cell 2005; 17:695-707. [PMID: 15749019 DOI: 10.1016/j.molcel.2005.02.013] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Revised: 01/17/2005] [Accepted: 02/08/2005] [Indexed: 11/16/2022]
Abstract
The packaging of eukaryotic genomic DNA into chromatin is modulated through a range of posttranslational histone modifications. Among these, the role of histone ubiquitylation remains poorly understood. Here, we show that the essential Drosophila ubiquitin-specific protease 7 (USP7) contributes to epigenetic silencing of homeotic genes by Polycomb (Pc). We purified USP7 from embryo nuclear extracts as a stable heteromeric complex with guanosine 5'-monophosphate synthetase (GMPS). The USP7-GMPS complex catalyzed the selective deubiquitylation of histone H2B, but not H2A. Biochemical assays confirmed the tight association between USP7 and GMPS in Drosophila embryo extracts. Similar to USP7, mutations in GMPS acted as enhancers of Pc in vivo. USP7 binding to GMPS was required for histone H2B deubiquitylation and strongly augmented deubiquitylation of the human tumor suppressor p53. Thus, GMPS can regulate the activity of a ubiquitin protease. Collectively, these results implicate a biosynthetic enzyme in chromatin control via ubiquitin regulation.
Collapse
Affiliation(s)
- Jan A van der Knaap
- Department of Biochemistry, Center for Biomedical Genetics, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
772
|
Schmitt S, Prestel M, Paro R. Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 2005; 19:697-708. [PMID: 15741315 PMCID: PMC1065723 DOI: 10.1101/gad.326205] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Polycomb group response elements (PREs) mediate the mitotic inheritance of gene expression programs and thus maintain determined cell fates. By default, PREs silence associated genes via the targeting of Polycomb group (PcG) complexes. Upon an activating signal, however, PREs recruit counteracting trithorax group (trxG) proteins, which in turn maintain target genes in a transcriptionally active state. Using a transgenic reporter system, we show that the switch from the silenced to the activated state of a PRE requires noncoding transcription. Continuous transcription through the PRE induced by an actin promoter prevents the establishment of PcG-mediated silencing. The maintenance of epigenetic activation requires transcription through the PRE to proceed at least until embryogenesis is completed. At the homeotic bithorax complex of Drosophila, intergenic PRE transcripts can be detected not only during embryogenesis, but also at late larval stages, suggesting that transcription through endogenous PREs is required continuously as an anti-silencing mechanism to prevent the access of repressive PcG complexes to the chromatin. Furthermore, all other PREs outside the homeotic complex we tested were found to be transcribed in the same tissue as the mRNA of the corresponding target gene, suggesting that anti-silencing by transcription is a fundamental aspect of the cellular memory system.
Collapse
Affiliation(s)
- Sabine Schmitt
- Zentrum für Molekular Biologie Heidelberg (ZMBH), University of Heidelberg, D-69120 Heidelberg, Germany
| | | | | |
Collapse
|
773
|
Abstract
Chromosomal aberrations that affect the MLL (Mixed Lineage Leukemia) gene at the locus 11q23 are associated with an aggressive subtype of leukemia. These alterations create MLL fusion derivatives with an active transforming potential. This review summarizes recent advances in our knowledge about normal and malignant MLL proteins with special emphasis on epigenetic processes affected by these molecules.
Collapse
|
774
|
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.
Collapse
Affiliation(s)
- Shrividhya Srinivasan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | | | | | | | | |
Collapse
|
775
|
Martens JHA, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, Jenuwein T. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 2005; 24:800-12. [PMID: 15678104 PMCID: PMC549616 DOI: 10.1038/sj.emboj.7600545] [Citation(s) in RCA: 512] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Accepted: 12/13/2004] [Indexed: 12/12/2022] Open
Abstract
Histone lysine methylation has been shown to index silenced chromatin regions at, for example, pericentric heterochromatin or of the inactive X chromosome. Here, we examined the distribution of repressive histone lysine methylation states over the entire family of DNA repeats in the mouse genome. Using chromatin immunoprecipitation in a cluster analysis representing repetitive elements, our data demonstrate the selective enrichment of distinct H3-K9, H3-K27 and H4-K20 methylation marks across tandem repeats (e.g. major and minor satellites), DNA transposons, retrotransposons, long interspersed nucleotide elements and short interspersed nucleotide elements. Tandem repeats, but not the other repetitive elements, give rise to double-stranded (ds) RNAs that are further elevated in embryonic stem (ES) cells lacking the H3-K9-specific Suv39h histone methyltransferases. Importantly, although H3-K9 tri- and H4-K20 trimethylation appear stable at the satellite repeats, many of the other repeat-associated repressive marks vary in chromatin of differentiated ES cells or of embryonic trophoblasts and fibroblasts. Our data define a profile of repressive histone lysine methylation states for the repetitive complement of four distinct mouse epigenomes and suggest tandem repeats and dsRNA as primary triggers for more stable chromatin imprints.
Collapse
Affiliation(s)
- Joost H A Martens
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Roderick J O'Sullivan
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Ulrich Braunschweig
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Susanne Opravil
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Martin Radolf
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Peter Steinlein
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
| | - Thomas Jenuwein
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), The Vienna Biocenter, Dr Bohrgasse 7, 1030 Vienna, Austria. Tel.: +43 1 797 30 474; Fax: +43 1 798 7153; E-mail:
| |
Collapse
|
776
|
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.
Collapse
Affiliation(s)
- Leonie Ringrose
- ZMBH, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
777
|
Abstract
The developmental programs of eukaryotic organisms involve the programmed transcription of genes. A characteristic gene expression pattern is established and preserved in each different cell type. Therefore, gene activation at a particular time and its maintenance during cell division are significant for cellular differentiation and individual development. Although many studies have sought to explain the molecular mechanisms of gene expression regulation, the mechanism through which gene expression states are inherited during cell division has not been fully elucidated yet. This review illustrates the general principles and the complexities involved in the establishment and maintenance of active transcription through cell cycles. It focuses on the most-recent findings about the ways in which molecular memory marks for active transcription are coordinated with cell cycle events, such as replication, mitosis and nuclear organization, to mediate transcription memory across cell division events, which may establish a unifying memory process of active transcription.
Collapse
Affiliation(s)
- Guo-Ling Zhou
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R.China
| | | | | |
Collapse
|
778
|
Affiliation(s)
- Adone Mohd-Sarip
- Department of Biochemistry, Erasmus Medical Center, Rotterdam, Netherlands
| | | |
Collapse
|
779
|
Fan HY, Narlikar GJ, Kingston RE. Noncovalent modification of chromatin: different remodeled products with different ATPase domains. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:183-92. [PMID: 16117648 DOI: 10.1101/sqb.2004.69.183] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- H-Y Fan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | | | | |
Collapse
|