201
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Gorfinkiel N, Fanti L, Melgar T, García E, Pimpinelli S, Guerrero I, Vidal M. The Drosophila Polycomb group gene Sex combs extra encodes the ortholog of mammalian Ring1 proteins. Mech Dev 2004; 121:449-62. [PMID: 15147763 DOI: 10.1016/j.mod.2004.03.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Revised: 03/26/2004] [Accepted: 03/26/2004] [Indexed: 11/28/2022]
Abstract
In Drosophila, the Polycomb group (PcG) of genes is required for the maintenance of homeotic gene repression during development. Here, we have characterized the Drosophila ortholog of the products of the mammalian Ring1/Ring1A and Rnf2/Ring1B genes. We show that Drosophila Ring corresponds to the Sex combs extra (Sce), a previously described PcG gene. We find that Ring/Sce is expressed and required throughout development and that the extreme Pc embryonic phenotype due to the lack of maternal and zygotic Sce can be rescued by ectopic expression of Ring/Sce. This phenotypic rescue is also obtained by ectopic expression of the murine Ring1/Ring1A, suggesting a functional conservation of the proteins during evolution. In addition, we find that Ring/Sce binds to about 100 sites on polytene chromosomes, 70% of which overlap those of other PcG products such as Polycomb, Posterior sex combs and Polyhomeotic, and 30% of which are unique. We also show that Ring/Sce interacts directly with PcG proteins, as it occurs in mammals.
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Affiliation(s)
- Nicole Gorfinkiel
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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202
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Affiliation(s)
- James A Kennison
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Marlyland 20892-2785, USA
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203
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Huang DH, Chang YL. Isolation and characterization of CHRASCH, a polycomb-containing silencing complex. Methods Enzymol 2004; 377:267-82. [PMID: 14979031 DOI: 10.1016/s0076-6879(03)77016-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Affiliation(s)
- Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Taiwan 115, Republic of China
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204
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Bejarano F, Busturia A. Function of the Trithorax-like gene during Drosophila development. Dev Biol 2004; 268:327-41. [PMID: 15063171 DOI: 10.1016/j.ydbio.2004.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Revised: 01/05/2004] [Accepted: 01/09/2004] [Indexed: 11/20/2022]
Abstract
Maintenance of homeotic gene expression during Drosophila development relies on the Polycomb and the trithorax groups of genes. Classically, the Polycomb proteins act as repressors of homeotic gene function, whereas trithorax proteins function as activators. However, recent investigation has indicated that some of these maintenance genes may act both as repressors and activators. One of those is the Drosophila Trithorax-like gene that codes for the GAGA factor. To investigate its dual activator/repressor role, we have studied the function of the Trithorax-like throughout Drosophila development. Embryos lacking both the maternal and the zygotic Trithorax-like function do not develop suggesting that Trithorax-like might be required in oogenesis. Homozygous Trithorax-like null mutant embryos show reduced expression levels of some of the homeotic proteins. Trithorax-like mutant larval clones, however, do not show phenotypes indicative of either activation or repression of homeotic gene function. These results suggest that Trithorax-like is required during embryogenesis but not throughout larval development for the regulation of homeotic gene expression. Moreover, this temporal requirement seems also to regulate MCP-mediated silencing. Finally, lack of Trithorax-like function modulates the gain of function phenotypes caused by over-expression of homeotic genes. To explain Trithorax-like gene function, we propose a model where very early in development, GAGA factor probably establishes a chromatin ground state for transcription. The differential "on/off" transcriptional state of the homeotic genes is then established and propagated by the action of the specific regulatory proteins independently of the GAGA factor. We also suggest that GAGA factor may not have a dual activator/repressor function. Rather, Trithorax-like mutations may produce dual loss of activation and loss of repression effects.
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Affiliation(s)
- Fernando Bejarano
- Centro de Biología Molecular, CSIC-UAM, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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205
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Dukers DF, van Galen JC, Giroth C, Jansen P, Sewalt RGAB, Otte AP, Kluin-Nelemans HC, Meijer CJLM, Raaphorst FM. Unique polycomb gene expression pattern in Hodgkin's lymphoma and Hodgkin's lymphoma-derived cell lines. THE AMERICAN JOURNAL OF PATHOLOGY 2004; 164:873-81. [PMID: 14982841 PMCID: PMC1613333 DOI: 10.1016/s0002-9440(10)63175-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Human Polycomb-group (PcG) genes play a crucial role in the regulation of embryonic development and regulation of the cell cycle and hematopoiesis. PcG genes encode proteins that form two distinct PcG complexes, involved in maintenance of cell identity and gene silencing patterns. We recently showed that expression of the BMI-1 and EZH2 PcG genes is separated during normal B-cell development in germinal centers, whereas Hodgkin/Reed-Sternberg (H/RS) cells co-express BMI-1 and EZH2. In the current study, we used immunohistochemistry and immunofluorescence to determine whether the binding partners of these PcG proteins are also present in H/RS cells and H/RS-derived cell lines. PcG expression profiles were analyzed in combination with expression of the cell cycle inhibitor p16INK4a, because experimental model systems indicate that p16 is a downstream target of Bmi-1. We found that H/RS cells and HL-derived cell lines co-express all core proteins of the two known PcG complexes, including BMI-1, MEL-18, RING1, HPH1, HPC1, and -2, EED, EZH2, YY1, and the HPC2 binding partner, CtBP. Expression of HPC1 has not been found in normal mature B cells and other malignant lymphomas of B-cell origin, suggesting that the PcG expression profile of H/RS is unique. In contrast to Bmi-1 transgenic mice where p16INK4a is down-regulated, 27 of 52 BMI-1POS cases of HL revealed strong nuclear expression of p16INK4a. We propose that abnormal expression of BMI-1 and its binding partners in H/RS cells contributes to development of HL. However, abnormal expression of BMI-1 in HL is not necessarily associated with down-regulation of p16INK4a.
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Affiliation(s)
- Danny F Dukers
- Department of Pathology, Vrije Universiteit University Medical Center (VUMC), Amsterdam, The Netherlands
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206
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Sengupta AK, Kuhrs A, Müller J. General transcriptional silencing by a Polycomb response element in Drosophila. Development 2004; 131:1959-65. [PMID: 15056613 DOI: 10.1242/dev.01084] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polycomb response elements (PREs) are cis-regulatory sequences required for Polycomb repression of Hox genes in Drosophila. PREs function as potent silencers in the context of Hox reporter genes and they have been shown to partially repress a linked miniwhite reporter gene. The silencing capacity of PREs has not been systematically tested and, therefore, it has remained unclear whether only specific enhancers and promoters can respond to Polycomb silencing. Here, using a reporter gene assay in imaginal discs, we show that a PRE from the Drosophila Hox gene Ultrabithorax potently silences different heterologous enhancers and promoters that are normally not subject to Polycomb repression. Silencing of these reporter genes is abolished in PcG mutants and excision of the PRE from the reporter gene during development results in loss of silencing within one cell generation. Together, these results suggest that PREs function as general silencer elements through which PcG proteins mediate transcriptional repression.
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Affiliation(s)
- Aditya K Sengupta
- EMBL, Gene Expression Programme, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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207
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Dateki M, Mochizuki R, Yanai K, Fukamizu A. Identification of the mouse neurochondrin promoter region and the responsible region for cell type specific gene regulation. Neurosci Lett 2004; 356:107-10. [PMID: 14746875 DOI: 10.1016/j.neulet.2003.11.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neurochondrin is a cytoplasmic protein possibly involved in neurite outgrowth and chondrocyte differentiation. In the present study, we have identified 202 bp of the mouse neurochondrin minimal promoter sequences encompassing the transcriptional initiation site, and both of the activating and repressing regions in the first exon. These two regulatory regions in the first exon had a cell type dependent effect on the identified minimal promoter. In the regulatory region, the duplication of potential binding sites for GATA family transcriptional factors was observed. Prospective binding sites for sex determining region Y and c-Ets1 were also found in the minimal promoter region. These factors could be potential regulators for the mouse neurochondrin gene.
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Affiliation(s)
- Minori Dateki
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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208
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Déjardin J, Cavalli G. Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. EMBO J 2004; 23:857-68. [PMID: 14963490 PMCID: PMC381013 DOI: 10.1038/sj.emboj.7600108] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 01/09/2004] [Indexed: 02/05/2023] Open
Abstract
Polycomb group and trithorax group proteins maintain the memory of repressed and active chromatin states by regulating chromatin of their target genes via DNA sequences termed Polycomb- and trithorax response elements. Since these elements often overlap and are able to convey the memory of both silent and active chromatin through cell division, they were also defined as cellular memory modules (CMMs). We identify here a minimal CMM of 219 bp from the Drosophila Fab-7 region that regulates the homeotic gene Abdominal-B. This CMM conveys the inheritance of active chromatin states induced by an embryonic pulse of transcriptional activation via recruitment of the trithorax group proteins Trithorax (TRX) and Brahma (BRM), the Drosophila homologue of the SWI2/SNF2 ATPase involved in chromatin remodelling. Within this CMM, DNA-binding sites for the Zeste protein are necessary for the inheritance of active chromatin through Zeste-dependent recruitment of BRM, while TRX can bind the CMM even in their absence. Thus, epigenetic inheritance of active chromatin states involves the recruitment of multiple cooperative chromatin-modifying complexes at closely spaced but distinct sites within a CMM.
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Affiliation(s)
- Jérôme Déjardin
- Institute of Human Genetics, CNRS, Montpellier Cedex 5, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, Montpellier Cedex 5, France
- Institute of Human Genetics, CNRS 141, rue de la Cardonille, F-34396 Montpellier Cedex 5, France. Tel.: +33 4 9961 9970; Fax: +33 4 9961 9901; E-mail:
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209
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Palko L, Bass HW, Beyrouthy MJ, Hurt MM. The Yin Yang-1 (YY1) protein undergoes a DNA-replication-associated switch in localization from the cytoplasm to the nucleus at the onset of S phase. J Cell Sci 2004; 117:465-76. [PMID: 14702388 DOI: 10.1242/jcs.00870] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The essential Yin Yang-1 gene (YY1) encodes a ubiquitous, conserved, multifunctional zinc-finger transcription factor in animals. The YY1 protein regulates initiation, activation, or repression of transcription from a variety of genes required for cell growth, development, differentiation, or tumor suppression, as well as from genes in some retroviruses and DNA viruses. Among the specific functions attributed to YY1 is a role in cell-cycle-specific upregulation of the replication-dependent histone genes. The YY1 protein binds to the histone alpha element, a regulatory sequence found in all replication-dependent histone genes. We therefore examined the abundance, DNA-binding activity and localization of the YY1 protein throughout the cell cycle in unperturbed, shake-off-synchronized Chinese hamster ovary and HeLa cells. We found that, whereas the DNA-binding activity of YY1 increased dramatically early in S phase, the YY1 mRNA and protein levels did not. YY1 changed subcellular distribution patterns during the cell cycle, from mainly cytoplasmic at G1 to mainly nuclear at early and middle S phase, then back to primarily cytoplasmic later in S phase. Nuclear accumulation of YY1 near the G1/S boundary coincided with both an increase in YY1 DNA-binding activity and the coordinate up-regulation of the replication-dependent histone genes. The DNA synthesis inhibitor aphidicolin caused a nearly complete loss of nuclear YY1, whereas addition of caffeine or 2-aminopurine to aphidicolin-treated cells restored both DNA synthesis and YY1 localization in the nucleus. These findings reveal a mechanism by which YY1 localization is coupled to DNA synthesis and responsive to cell-cycle signaling pathways. Taken together, our results provide insight into how YY1 might participate in the cell-cycle control over a variety of nuclear events required for cell division and proliferation.
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Affiliation(s)
- Linda Palko
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4370, USA
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210
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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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211
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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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212
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Schwartz YB, Kahn TG, Dellino GI, Pirrotta V. Polycomb silencing mechanisms in Drosophila. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:301-8. [PMID: 16117662 DOI: 10.1101/sqb.2004.69.301] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Y B Schwartz
- Department of Zoology, University of Geneva, CH-1211 Geneva, Switzerland
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213
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Pal-Bhadra M, Bhadra U, Birchler JA. Interrelationship of RNA interference and transcriptional gene silencing in Drosophila. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:433-8. [PMID: 16117678 DOI: 10.1101/sqb.2004.69.433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- M Pal-Bhadra
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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214
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Tchurikov NA, Kretova OV, Chernov BK, Golova YB, Zhimulev IF, Zykov IA. SuUR protein binds to the boundary regions separating forum domains in Drosophila melanogaster. J Biol Chem 2003; 279:11705-10. [PMID: 14702350 DOI: 10.1074/jbc.m306191200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Forum domains are 50-150 kb DNA fragments that are released during spontaneous fragmentation of chromosomes. They are separated by islands of putative heterochromatin boundary regions. The SuUR protein, which is involved in the control of chromosome organization, is localized exclusively in heterochromatin and often colocalizes on chromosomes with Polycomb group proteins. To test whether the SuUR protein is associated with boundary regions, we used gel retardation assays and found that the SuUR protein binds specifically to boundary regions and that boundary regions are under-replicated. These results suggest that the regular distribution of boundary regions in chromosomes may represent the dispersion of sites designed for chromosomal silencing.
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Affiliation(s)
- Nickolai A Tchurikov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Department of Genome Organization, Vavilov Street 32, Moscow 119991, Russia.
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215
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Ringrose L, Rehmsmeier M, Dura JM, Paro R. Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell 2003; 5:759-71. [PMID: 14602076 DOI: 10.1016/s1534-5807(03)00337-x] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Polycomb/Trithorax response elements (PRE/TREs) maintain transcriptional decisions to ensure correct cell identity during development and differentiation. There are thought to be over 100 PRE/TREs in the Drosophila genome, but only very few have been identified due to the lack of a defining consensus sequence. Here we report the definition of sequence criteria that distinguish PRE/TREs from non-PRE/TREs. Using this approach for genome-wide PRE/TRE prediction, we identify 167 candidate PRE/TREs, which map to genes involved in development and cell proliferation. We show that candidate PRE/TREs are bound and regulated by Polycomb proteins in vivo, thus demonstrating the validity of PRE/TRE prediction. Using the larger data set thus generated, we identify three sequence motifs that are conserved in PRE/TRE sequences.
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Affiliation(s)
- Leonie Ringrose
- ZMBH, Universität Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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216
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Mulholland NM, King IFG, Kingston RE. Regulation of Polycomb group complexes by the sequence-specific DNA binding proteins Zeste and GAGA. Genes Dev 2003; 17:2741-6. [PMID: 14630938 PMCID: PMC280622 DOI: 10.1101/gad.1143303] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Repression and activation of the expression of homeotic genes are maintained by proteins encoded by the Polycomb group (PcG) and trithorax group (trxG) genes. Complexes formed by these proteins are targeted by PcG or trxG response elements (PREs/TREs), which share binding sites for several of the same factors. GAGA factor and Zeste bind specifically to PREs/TREs and have been shown to act as both activators and repressors. We have used purified proteins and complexes reconstituted from recombinant subunits to characterize the effects of GAGA and Zeste proteins on PcG function using a defined in vitro system. Zeste directly associates with the PRC1 core complex (PCC) and enhances the inhibitory activity of this complex on all templates, with a preference for templates with Zeste binding sites. GAGA does not stably associate with PCC, but nucleosomal templates bound by GAGA are more efficiently bound and more efficiently inhibited by PCC. Thus Zeste and GAGA factor use distinct means to increase repression mediated by PRC1.
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Affiliation(s)
- Niveen M Mulholland
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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217
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Violot S, Hong SS, Rakotobe D, Petit C, Gay B, Moreau K, Billaud G, Priet S, Sire J, Schwartz O, Mouscadet JF, Boulanger P. The human polycomb group EED protein interacts with the integrase of human immunodeficiency virus type 1. J Virol 2003; 77:12507-22. [PMID: 14610174 PMCID: PMC262565 DOI: 10.1128/jvi.77.23.12507-12522.2003] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2003] [Accepted: 08/23/2003] [Indexed: 11/20/2022] Open
Abstract
Human EED, a member of the superfamily of WD-40 repeat proteins and of the Polycomb group proteins, has been identified as a cellular partner of the human immunodeficiency virus type 1 (HIV-1) matrix (MA) protein (R. Peytavi et al., J. Biol. Chem. 274:1635-1645, 1999). In the present study, EED was found to interact with HIV-1 integrase (IN) both in vitro and in vivo in yeast. In vitro, data from mutagenesis studies, pull-down assays, and phage biopanning suggested that EED-binding site(s) are located in the C-terminal domain of IN, between residues 212 and 264. In EED, two putative discrete IN-binding sites were mapped to its N-terminal moiety, at a distance from the MA-binding site, but EED-IN interaction also required the integrity of the EED last two WD repeats. EED showed an apparent positive effect on IN-mediated DNA integration reaction in vitro, in a dose-dependent manner. In situ analysis by immunoelectron microscopy (IEM) of cellular distribution of IN and EED in HIV-1-infected cells (HeLa CD4(+) cells or MT4 lymphoid cells) showed that IN and EED colocalized in the nucleus and near nuclear pores, with maximum colocalization events occurring at 6 h postinfection (p.i.). Triple colocalizations of IN, EED, and MA were also observed in the nucleoplasm of infected cells at 6 h p.i., suggesting the ocurrence of multiprotein complexes involving these three proteins at early steps of the HIV-1 virus life cycle. Such IEM patterns were not observed with a noninfectious, envelope deletion mutant of HIV-1.
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Affiliation(s)
- Sébastien Violot
- Laboratoire de Virologie and Pathogénèse Virale, Faculté de Médecine RTH Laennec, CNRS UMR-5537, France
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218
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Bloyer S, Cavalli G, Brock HW, Dura JM. Identification and characterization of polyhomeotic PREs and TREs. Dev Biol 2003; 261:426-42. [PMID: 14499651 DOI: 10.1016/s0012-1606(03)00314-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyhomeotic (ph) gene is a member of the Polycomb group of genes (Pc-G), which are required for the maintenance of the spatial expression pattern of homeotic genes. In contrast to homeotic genes, ph is ubiquitously expressed and it is quantitatively regulated. ph is negatively regulated by the Pc-G genes, except Psc, and positively regulated by the antagonist trithorax group of genes (trx-G), suggesting that Pc-G and trx-G response elements (PREs and TREs) exist at the ph locus. In this study, we have functionally characterized PREs and TREs at the ph locus that function in transgenic constructs. We have identified a strong PRE and TRE in the ph proximal unit as well as a weak one in the ph distal unit. The PRE/TRE of both ph units appear atypical compared with the well-defined homeotic maintenance elements because the minimal ph proximal response element activity requires at least 2 kb of sequence and does not work at long range. We have used chromatin immunoprecipitation experiments on cultured cells and embryos to show that Pc-G proteins are located in restricted regions, close to the ph promoters that overlap functionally defined PRE/TREs. Our data suggest that ph PRE/TREs are cis-acting DNA elements that modulate rather than silence Pc-G- and trx-G-mediated regulation, enlarging the role of these two groups of genes in transcriptional regulation.
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Affiliation(s)
- Sébastien Bloyer
- Institut de Génétique Humaine, C.N.R.S.-U.P.R. 1142, 141 rue de la Cardonille, 34396 5, Montpellier Cedex, France
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219
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Mahmoudi T, Zuijderduijn LMP, Mohd-Sarip A, Verrijzer CP. GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response element. Nucleic Acids Res 2003; 31:4147-56. [PMID: 12853632 PMCID: PMC167640 DOI: 10.1093/nar/gkg479] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polycomb response elements (PREs) are chromosomal elements, typically comprising thousands of base pairs of poorly defined sequences that confer the maintenance of gene expression patterns by Polycomb group (PcG) repressors and trithorax group (trxG) activators. Genetic studies have indicated a synergistic requirement for the trxG protein GAGA and the PcG protein Pleiohomeotic (PHO) in silencing at several PREs. However, the molecular basis of this cooperation remains unknown. Here, using DNaseI footprinting analysis, we provide a high-resolution map of sites for the sequence- specific DNA-binding PcG protein PHO, trxG proteins GAGA and Zeste and the gap protein Hunchback (HB) on the 1.6 kb Ultrabithorax (Ubx) PRE. Although these binding elements are present throughout the PRE, they display clear patterns of clustering, suggestive of functional collaboration at the level of PRE binding. We found that while GAGA could efficiently bind to a chromatinized PRE, PHO alone was incapable of binding to chromatin. However, PHO binding to chromatin, but not naked DNA, was strongly facilitated by GAGA, indicating interdependence between GAGA and PHO already at the level of PRE binding. These results provide a biochemical explanation for the in vivo cooperation between GAGA and PHO and suggest that PRE function involves the integrated activities of genetically antagonistic trxG and PcG proteins.
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Affiliation(s)
- Tokameh Mahmoudi
- Department of Molecular and Cell Biology, Center for Biomedical Genetics, Leiden University Medical Center, PO Box 9503, 2300 RA, Leiden, The Netherlands
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220
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Kwon HJ, Chung HM. Yin Yang 1, a vertebrate polycomb group gene, regulates antero-posterior neural patterning. Biochem Biophys Res Commun 2003; 306:1008-13. [PMID: 12821143 DOI: 10.1016/s0006-291x(03)01071-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polycomb group (PcG) genes are required for the stable repression of the homeotic genes and other developmentally regulated genes. Yin Yang 1 (YY1), a vertebrate homolog of the Drosophila PcG pleiohomeotic (Pho), is a multifunctional protein that can act as a repressor or activator of transcription. Xenopus YY1 (XYY1) protein was localized in the central nervous system (CNS), particularly anterior neural tube of tailbud stage embryos. To elucidate the role of endogenous XYY1, loss-of-function studies were performed using XYY1 antisense morpholino oligonucleotide (XYY1 MO). Inhibition of XYY1 function resulted in embryos with antero-posterior axial patterning defects and reduction of head structures. XYY1 MO also reduced the expression of En2, a midbrain/hindbrain junction marker, which was rescued by co-injection of XYY1 mRNA. However, XYY1 MO-injection did not affect the expression of HoxB9, a spinal cord marker. These results suggest that YY1 controls antero-posterior patterning of the CNS during Xenopus embryonic development.
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Affiliation(s)
- Hye-Joo Kwon
- School of Biological Sciences, Seoul National University, San 56-1, Shillim-dong, Kwanak-gu, Seoul 151-747, Republic of Korea
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221
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Abstract
Cell identity is determined by selective gene activation and by the maintenance of other regulated genes in a silent state. Although activation mechanisms have been dissected in considerable depth, great strides towards an understanding of the molecular control of gene silencing have been made only recently. Molecular hallmarks of silent chromatin and proteins involved in its assembly and maintenance have been identified through genetic, cytological and biochemical studies in a variety of organisms. Immunologists are now beginning to use this knowledge to elucidate mechanisms underlying cell fate decisions and key developmental steps. This review surveys the current knowledge of gene silencing, with an emphasis on studies in lymphocytes that are advancing our general understanding of silencing mechanisms during development.
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Affiliation(s)
- Stephen T Smale
- Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095-1662, USA.
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222
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Lessard J, Sauvageau G. Polycomb group genes as epigenetic regulators of normal and leukemic hemopoiesis. Exp Hematol 2003; 31:567-85. [PMID: 12842702 DOI: 10.1016/s0301-472x(03)00081-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Epigenetic modification of chromatin structure underlies the differentiation of pluripotent hemopoietic stem cells (HSCs) into their committed/differentiated progeny. Compelling evidence indicates that Polycomb group (PcG) genes play a key role in normal and leukemic hemopoiesis through epigenetic regulation of HSC self-renewal/proliferation and commitment. The PcG proteins are constituents of evolutionary highly conserved molecular pathways regulating cell fate in several other tissues through diverse mechanisms, including 1) regulation of self-renewal/proliferation, 2) regulation of senescence/immortalization, 3) interaction with the initiation transcription machinery, 4) interaction with chromatin-condensation proteins, 5) modification of histones, 6) inactivation of paternal X chromosome, and 7) regulation of cell death. It is therefore not surprising that PcG genes lead to pleiotropic phenotypes when mutated and have been associated with malignancies in several systems in both mice and humans. Although much remains to be learned regarding the PcG mechanism(s) of action, advances in identifying the functional domains and enzymatic activities of these multimeric protein complexes have provided insights into how PcG proteins accomplish such processes. Some of the new insights into a role for the PcG cellular memory system in regulating normal and leukemic hemopoiesis are reviewed here, with special emphasis on their potential involvement in epigenetic regulation of gene expression through modification of chromatin structure.
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Affiliation(s)
- Julie Lessard
- Laboratory of Molecular Genetics of Hemopoietic Stem Cells, Clinical Research Institute of Montreal, Montreal, Quebec, Canada
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223
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Abstract
Yin Yang 1 (YY1) is a highly conserved and multifunctional transcription factor. The diverse activities of YY1 are regulated and sometimes modified by interaction with various other proteins. By using a yeast two-hybrid screening system, SAP30 was identified as a protein that associates with YY1 and it is able to enhance YY1-mediated repression in a dose-dependent manner. SAP30 is a 30kDa nuclear protein and is a component of the human histone deacetylase complex. In this study, the interaction of SAP30 and YY1 was confirmed both by in vitro and in vivo assays. The interaction domains between YY1 and SAP30 were mapped to the C-terminal segment of YY1 (295-414) and the C-terminal 91 amino acid region of SAP30. The observation that YY1, SAP30, and HDAC1 form a complex in vivo provides evidence that YY1 also recruits HDAC1 indirectly via its binding to SAP30. These results describe a novel mechanism for YY1-mediated repression.
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Affiliation(s)
- Nu En Huang
- Graduate Institute of Life Sciences, National Defense Medical Center, ROC, Taipei, Taiwan
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224
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Gordon SJ, Saleque S, Birshtein BK. Yin Yang 1 is a lipopolysaccharide-inducible activator of the murine 3' Igh enhancer, hs3. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:5549-57. [PMID: 12759432 DOI: 10.4049/jimmunol.170.11.5549] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 3' Igh enhancers, DNase I hypersensitive site (hs) 3B and/or hs4, are required for germline transcription, and hence, class switch recombination for multiple isotypes. A number of hs3-binding transcription factors have been identified by EMSA, including octamer and NF-kappa B family members, and Pax5. We have found that the binding of the transcription factor, Yin Yang 1 (YY1), to hs3 and to the mu E1 site of the intronic enhancer, E mu, is induced in primary splenic B cells after approximately 48 h in response to LPS and other activators of class switch recombination. Transient transfection experiments in B cell lines indicate that YY1 is an activator of hs3. Interestingly, levels of YY1 expression are unchanged in resting and LPS-stimulated B cells. Mixing experiments followed by EMSA showed that a protein present in resting B cells prevented binding of YY1 to DNA. We found that recombinant retinoblastoma protein (Rb) inhibited binding of YY1 to hs3 in a dose-dependent manner, and we have identified complexes of endogenous YY1 with the Rb in resting B cells, but not in LPS-stimulated B cells. A difference in Rb phosphorylation state was also confirmed between resting (G(0)) B cells and LPS-stimulated B cells. These observations suggest that the interaction of YY1 with hypophosphorylated Rb in resting B cells prevents interaction of YY1 with DNA. After stimulation with class-switching activators, such as LPS, Rb becomes hyperphosphorylated and YY1 is released and can then bind to the hs3 enhancer and E mu.
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Affiliation(s)
- Steven J Gordon
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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225
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Mishra K, Chopra VS, Srinivasan A, Mishra RK. Trl-GAGA directly interacts with lola like and both are part of the repressive complex of Polycomb group of genes. Mech Dev 2003; 120:681-9. [PMID: 12834867 DOI: 10.1016/s0925-4773(03)00046-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Epigenetic inheritance to maintain the expression state of the genome is essential during development. In Drosophila, the cis regulatory elements, called the Polycomb Response Elements (PREs) function to mark the epigenetic cellular memory of the corresponding genomic region with the help of PcG and trxG proteins. While the PcG genes code for the repressor proteins, the trxG genes encode activator proteins. The observations that some proteins may function both as PcG and trxG member and that both these group of proteins act upon common cis elements indicate at least a partial functional overlap among these proteins. Trl-GAGA was initially identified as a trxG member but later was shown to be essential for PcG function on several PREs. In order to understand how Trl-GAGA functions in PcG context, we have looked for the interactors of this protein. We identified lola like, aka batman, as a strong interactor of GAGA factor in a yeast two-hybrid screen. lolal also interacts with polyhomeotic and, like Trl, both lolal and ph are needed for iab-7PRE mediated pairing dependent silencing of mini-white transgene. These observations suggest a possible mechanism of how Trl-GAGA plays a role in maintaining the repressed state of target genes involving lolal, which may function as a mediator to recruit PcG complexes.
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Affiliation(s)
- Krishnaveni Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, 500007 Hyderabad, India
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226
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Boccuni P, MacGrogan D, Scandura JM, Nimer SD. The human L(3)MBT polycomb group protein is a transcriptional repressor and interacts physically and functionally with TEL (ETV6). J Biol Chem 2003; 278:15412-20. [PMID: 12588862 DOI: 10.1074/jbc.m300592200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
H-L(3)MBT, the human homolog of the Drosophila lethal(3)malignant brain tumor protein, is a member of the polycomb group (PcG) of proteins, which function as transcriptional regulators in large protein complexes. Homozygous mutations in the l(3)mbt gene cause brain tumors in Drosophila, identifying l(3)mbt as a tumor suppressor gene. The h-l(3)mbt gene maps to chromosome 20q12, within a common deleted region associated with myeloid hematopoietic malignancies. H-L(3)MBT contains three repeats of 100 residues called MBT repeats, whose function is unknown, and a C-terminal alpha-helical structure, the SPM (SCM, PH, MBT domain, which is structurally similar to the SAM (sterile alpha motif) protein-protein interaction domain, found in several ETS transcription factors, including TEL (translocation Ets leukemia). We report that H-L(3)MBT is a transcriptional repressor and that its activity is largely dependent on the presence of a region containing the three MBT repeats. H-L(3)MBT acts as a histone deacetylase-independent transcriptional repressor, based on its lack of sensitivity to trichostatin A. We found that H-L(3)MBT binds in vivo to TEL, and we have mapped the region of interaction to their respective SPM/SAM domains. We show that the ability of TEL to repress TEL-responsive promoters is enhanced by the presence of H-L(3)MBT, an effect dependent on the H-L(3)MBT and the TEL interacting domains. These experiments suggest that histone deacetylase-independent transcriptional repression by TEL depends on the recruitment of PcG proteins. We speculate that the interaction of TEL with H-L(3)MBT can direct a PcG complex to genes repressed by TEL, stabilizing their repressed state.
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Affiliation(s)
- Piernicola Boccuni
- Laboratory of Molecular Aspects of Hematopoiesis, Sloan Kettering Institute for Cancer Research, New York, New York 10021, USA
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227
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Hiromura M, Choi CH, Sabourin NA, Jones H, Bachvarov D, Usheva A. YY1 is regulated by O-linked N-acetylglucosaminylation (O-glcNAcylation). J Biol Chem 2003; 278:14046-52. [PMID: 12588874 DOI: 10.1074/jbc.m300789200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
YY1 is a zinc finger DNA-binding transcription factor that influences expression of a wide variety of cellular and viral genes. YY1 is essential for the development of mammalian embryos. It regulates the expression of genes with important functions in DNA replication, protein synthesis, and cellular response to external stimuli during cell growth and differentiation. How YY1 accomplishes such a variety of functions is unknown. Here, we show that a subset of the nuclear YY1 appears to be O-GlcNAcylated regardless of the differentiation status of the cells. We found that glucose strongly stimulates O-linked N-acetylglucosaminylation (O-GlcNAcylation) on YY1. Glycosylated YY1 no longer binds the retinoblastoma protein (Rb). Upon dissociation from Rb, the glycosylated YY1 is free to bind DNA. The ability of the O-glycosylation on YY1 to disrupt the complex with Rb leads us to propose that O-glycosylation might have a profound effect on cell cycle transitions that regulate the YY1-Rb heterodimerization and promote the activity of YY1. Our observations provide strong evidence that YY1-regulated transcription is very likely connected to the pathway of glucose metabolism that culminates in the O-GlcNAcylation on YY1, changing its function in transcription.
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Affiliation(s)
- Makoto Hiromura
- Beth Israel Deaconess Medical Center, Department of Medicine, Endocrinology, Harvard Medical School, Boston, Massachussetts 02215, USA
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228
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Atchison L, Ghias A, Wilkinson F, Bonini N, Atchison ML. Transcription factor YY1 functions as a PcG protein in vivo. EMBO J 2003; 22:1347-58. [PMID: 12628927 PMCID: PMC151054 DOI: 10.1093/emboj/cdg124] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Polycomb group (PcG) proteins function as high molecular weight complexes that maintain transcriptional repression patterns during embryogenesis. The vertebrate DNA binding protein and transcriptional repressor, YY1, shows sequence homology with the Drosophila PcG protein, pleiohomeotic (PHO). YY1 might therefore be a vertebrate PcG protein. We used Drosophila embryo and larval/imaginal disc transcriptional repression systems to determine whether YY1 repressed transcription in a manner consistent with PcG function in vivo. YY1 repressed transcription in Drosophila, and this repression was stable on a PcG-responsive promoter, but not on a PcG-non-responsive promoter. PcG mutants ablated YY1 repression, and YY1 could substitute for PHO in repressing transcription in wing imaginal discs. YY1 functionally compensated for loss of PHO in pho mutant flies and partially corrected mutant phenotypes. Taken together, these results indicate that YY1 functions as a PcG protein. Finally, we found that YY1, as well as Polycomb, required the co-repressor protein CtBP for repression in vivo. These results provide a mechanism for recruitment of vertebrate PcG complexes to DNA and demonstrate new functions for YY1.
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Affiliation(s)
| | - Ayesha Ghias
- Department of Biology, Chestnut Hill College, 9601 Germantown Avenue, Philadelphia, PA 19118,
Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104 and Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA Corresponding author e-mail:
| | - Frank Wilkinson
- Department of Biology, Chestnut Hill College, 9601 Germantown Avenue, Philadelphia, PA 19118,
Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104 and Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA Corresponding author e-mail:
| | - Nancy Bonini
- Department of Biology, Chestnut Hill College, 9601 Germantown Avenue, Philadelphia, PA 19118,
Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104 and Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA Corresponding author e-mail:
| | - Michael L. Atchison
- Department of Biology, Chestnut Hill College, 9601 Germantown Avenue, Philadelphia, PA 19118,
Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104 and Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA Corresponding author e-mail:
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229
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Cunliffe VT. Memory by modification: the influence of chromatin structure on gene expression during vertebrate development. Gene 2003; 305:141-50. [PMID: 12609734 DOI: 10.1016/s0378-1119(03)00386-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multicellular development is programmed by regulated interactions between transcription factors and target genes. Target genes function as nucleosomal arrays whose higher order structure, composition and accessibility to transcription machinery are strictly and dynamically controlled. Several classes of chromatin-associated proteins generate or remove localized, covalent chromatin modifications that signify gene expression status, whereas others modulate nucleosome organization and so regulate template availability for transcription. In vertebrates, covalent modification of the DNA template itself also has dramatic impacts on gene expression and development. Here I review recent discoveries that improve our understanding of the influence of chromatin structure on gene expression and I discuss their relevance to mechanisms of vertebrate development.
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Affiliation(s)
- Vincent T Cunliffe
- Centre for Developmental Genetics, School of Medicine and Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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230
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Brown JL, Fritsch C, Mueller J, Kassis JA. The Drosophila pho-like gene encodes a YY1-related DNA binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 2003; 130:285-94. [PMID: 12466196 DOI: 10.1242/dev.00204] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polycomb group proteins (PcG) repress homeotic genes in cells where these genes must remain inactive during Drosophila and vertebrate development. This repression depends on cis-acting silencer sequences, called Polycomb group response elements (PREs). Pleiohomeotic (Pho), the only known sequence-specific DNA-binding PcG protein, binds to PREs but pho mutants show only mild phenotypes compared with other PcG mutants. We characterize pho-like, a gene encoding a protein with high similarity to Pho. Pho-like binds to Pho-binding sites in vitro and pho-like, pho double mutants show more severe misexpression of homeotic genes than do the single mutants. These results suggest that Pho and Pho-like act redundantly to repress homeotic genes. We examined the distribution of five PcG proteins on polytene chromosomes from pho-like, pho double mutants. Pc, Psc, Scm, E(z) and Ph remain bound to polytene chromosomes at most sites in the absence of Pho and Pho-like. At a few chromosomal locations, however, some of the PcG proteins are no longer present in the absence of Pho and Pho-like, suggesting that Pho-like and Pho may anchor PcG protein complexes to only a subset of PREs. Alternatively, Pho-like and Pho may not participate in the anchoring of PcG complexes, but may be necessary for transcriptional repression mediated through PREs. In contrast to Pho and Pho-like, removal of Trithorax-like/GAGA factor or Zeste, two other DNA-binding proteins implicated in PRE function, does not cause misexpression of homeotic genes or reporter genes in imaginal disks.
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Affiliation(s)
- J Lesley Brown
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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231
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Mohrmann L, Kal AJ, Verrijzer CP. Characterization of the extended Myb-like DNA-binding domain of trithorax group protein Zeste. J Biol Chem 2002; 277:47385-92. [PMID: 12354778 DOI: 10.1074/jbc.m202341200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Zeste is a Drosophila sequence-specific DNA-binding protein that performs a variety of functions during chromatin-directed gene regulation. Its DNA-binding domain (DBD) was previously identified, but no similarities to established DNA-binding structures are known. Here we present sequence comparisons suggesting that the Zeste-DBD is a novel variant of the tri-helical Myb-DBD. Using band shift assays, we mapped the Zeste-DBD to 76 residues, corresponding to a single Myb repeat of only 50 residues. All residues involved in formation of the hydrophobic core of the Myb domain are conserved in Zeste, suggesting it forms an extended Myb domain. Mutagenesis studies determined (T/C/g)GAGTG(A/G/c) as the consensus Zeste recognition sequence. Reconstituted transcription experiments established that deviations from this optimal consensus compromise transcriptional activation by Zeste. In addition, flanking DNA is critical because Zeste-DBD binding requires a DNA sequence of minimally 16 base pairs, which is much longer than the consensus site. The DNA flanking the consensus is contacted by Zeste through sequence-independent backbone contacts. Interestingly, hydroxyl radical footprinting revealed that the Zeste-DNA backbone contacts all map to one face of the DNA. We compare the DNA-binding properties of Zeste with those of classical tri-helical DBDs harboring a helix-turn-helix motif and suggest a model for Zeste-DNA recognition.
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Affiliation(s)
- Lisette Mohrmann
- Department of Molecular and Cell Biology, Center for Biomedical Genetics, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden, The Netherlands
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232
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Mohd-Sarip A, Venturini F, Chalkley GE, Verrijzer CP. Pleiohomeotic can link polycomb to DNA and mediate transcriptional repression. Mol Cell Biol 2002; 22:7473-83. [PMID: 12370294 PMCID: PMC135681 DOI: 10.1128/mcb.22.21.7473-7483.2002] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polycomb group (PcG) proteins function through cis-acting DNA elements called PcG response elements (PREs) to stably silence developmental regulators, including the homeotic genes. However, the mechanism by which they are targeted to PREs remains largely unclear. Pleiohomeotic (PHO) is a sequence-specific DNA-binding PcG protein and therefore may function to tether other PcG proteins to the DNA. Here, we show that PHO can directly bind to a Polycomb (PC)-containing complex as well as the Brahma (BRM) chromatin-remodeling complex. PHO contacts the BRM complex through its zinc finger DNA-binding domain and a short N-terminal region. A distinct domain of PHO containing a conserved motif contacts the PcG proteins PC and Polyhomeotic (PH). With mobility shift assays and DNA pulldown experiments, we demonstrated that PHO is able to link PC, which lacks sequence-specific DNA-binding activity, to the DNA. Importantly, we found that the PC-binding domain of PHO can mediate transcriptional repression in transfected Drosophila Schneider cells. Concomitant overexpression of PC resulted in stronger PHO-directed repression that was dependent on its PC-binding domain. Together, these results suggest that PHO can contribute to PRE-mediated silencing by direct recruitment of a PC complex to repress transcription.
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Affiliation(s)
- Adone Mohd-Sarip
- Department of Molecular and Cell Biology, Centre for Biomedical Genetics, Leiden University Medical Center, 2300 RA Leiden, The Netherlands
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233
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Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 2002; 111:185-96. [PMID: 12408863 DOI: 10.1016/s0092-8674(02)00975-3] [Citation(s) in RCA: 1159] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enhancer of Zeste is a Polycomb Group protein essential for the establishment and maintenance of repression of homeotic and other genes. In the early embryo it is found in a complex that includes ESC and is recruited to Polycomb Response Elements. We show that this complex contains a methyltransferase activity that methylates lysine 9 and lysine 27 of histone H3, but the activity is lost when the E(Z) SET domain is mutated. The lysine 9 position is trimethylated and this mark is closely associated with Polycomb binding sites on polytene chromosomes but is also found in centric heterochromatin, chromosome 4, and telomeric sites. Histone H3 methylated in vitro by the E(Z)/ESC complex binds specifically to Polycomb protein.
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Affiliation(s)
- Birgit Czermin
- Adolf-Butenandt Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
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234
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Maurange C, Paro R. A cellular memory module conveys epigenetic inheritance of hedgehog expression during Drosophila wing imaginal disc development. Genes Dev 2002; 16:2672-83. [PMID: 12381666 PMCID: PMC187463 DOI: 10.1101/gad.242702] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In Drosophila, the Trithorax-group (trxG) and Polycomb-group (PcG) proteins interact with chromosomal elements, termed Cellular Memory Modules (CMMs). By modifying chromatin, this ensures a stable heritable maintenance of the transcriptional state of developmental regulators, like the homeotic genes, that is defined embryonically. We asked whether such CMMs could also control expression of genes involved in patterning imaginal discs during larval development. Our results demonstrate that expression of the hedgehog gene, once activated, is maintained by a CMM. In addition, our experiments indicate that the switching of such CMMs to an active state during larval stages, in contrast to embryonic stages, may require specific trans-activators. Our results suggest that the patterning of cells in particular developmental fields in the imaginal discs does not only rely on external cues from morphogens, but also depends on the previous history of the cells, as the control by CMMs ensures a preformatted gene expression pattern.
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Affiliation(s)
- Cédric Maurange
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), University of Heidelberg, D-69120 Heidelberg, Germany
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235
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Arnosti DN. Design and function of transcriptional switches in Drosophila. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2002; 32:1257-1273. [PMID: 12225917 DOI: 10.1016/s0965-1748(02)00089-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Extensive genetic and biochemical analysis of Drosophila melanogaster has made this system an important model for characterization of transcriptional regulatory elements and factors. Given the striking conservation of transcriptional controls in metazoans, general principles derived from studies of Drosophila are expected to continue to illuminate transcriptional regulation in other systems, including vertebrates. With improvement in technologies for genetic manipulation of insects, research in Drosophila will also aid the design of systems for controlled expression of genes in other hosts. This review focuses on recent advances from Drosophila in analysis of the functional components of transcriptional switches, including basal promoters, enhancers, boundary elements, and maintenance elements.
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Affiliation(s)
- D N Arnosti
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824-1319, USA.
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236
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Schwendemann A, Lehmann M. Pipsqueak and GAGA factor act in concert as partners at homeotic and many other loci. Proc Natl Acad Sci U S A 2002; 99:12883-8. [PMID: 12271134 PMCID: PMC130554 DOI: 10.1073/pnas.202341499] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Drosophila GAGA factor (GAF) controls transcription and other chromosome functions by altering chromatin structure. We found that a second GAGA-binding protein of Drosophila, Pipsqueak (Psq), can directly bind to GAF and is associated with GAF in vivo. Genetic interaction studies provide evidence that Psq and GAF act together in the transcriptional activation and silencing of homeotic genes. A complete colocalization of Psq and GAF on polytene interphase chromosomes and mitotic chromosomes suggests that the two proteins cooperate as general partners not only at homeotic loci, but also at hundreds of other chromosomal sites.
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Affiliation(s)
- Alexander Schwendemann
- Institut für Biologie, Genetik, Freie Universität Berlin, Arnimallee 7, D-14195 Berlin, Germany
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237
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Abstract
DNA repetitions may provoke heterochromatinization. We explore here a model in which multiple cis-acting sequences that display no silencing activity on their own (protosilencers) may cooperate to establish and maintain a heterochromatin domain efficiently. Protosilencers, first defined in budding yeast, have now been found in a wide range of genomes where they appear to stabilize and to extend the propagation of heterochromatin domains. Strikingly, isolated or moderately repeated protosilencers can also be found in promoters where they participate in transcriptional activation and have insulation functions. This suggests that the proper juxtaposition of a threshold number of protosilencers converts them from neutral or transactivating elements into ones that nucleate heterochromatin. Interactions might be transient or permanent, and are likely to occur over distances by looping. This model provides a conceptual framework for as varied phenomena as telomere-driven silencing in Drosophila, X inactivation in mammals, and rDNA silencing in S. cerevisiae. It may also account for the silencing that occurs when multiple copies of a transgene are inserted in tandem.
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238
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Huang DH, Chang YL, Yang CC, Pan IC, King B. pipsqueak encodes a factor essential for sequence-specific targeting of a polycomb group protein complex. Mol Cell Biol 2002; 22:6261-71. [PMID: 12167718 PMCID: PMC134006 DOI: 10.1128/mcb.22.17.6261-6271.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Polycomb (Pc) group (Pc-G) of repressors is essential for transcriptional silencing of homeotic genes that determine the axial development of metazoan animals. It is generally believed that the multimeric complexes formed by these proteins nucleate certain chromatin structures to silence promoter activity upon binding to Pc-G response elements (PRE). Little is known, however, about the molecular mechanism involved in sequence-specific binding of these complexes. Here, we show that an immunoaffinity-purified Pc protein complex contains a DNA binding activity specific to the (GA)n motif in a PRE from the bithoraxoid region. We found that this activity can be attributed primarily to the large protein isoform encoded by pipsqueak (psq) instead of to the well-characterized GAGA factor. The functional relevance of psq to the silencing mechanism is strongly supported by its synergistic interactions with a subset of Pc-G that cause misexpression of homeotic genes.
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Affiliation(s)
- Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.
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239
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Gilthorpe J, Vandromme M, Brend T, Gutman A, Summerbell D, Totty N, Rigby PWJ. Spatially specific expression of Hoxb4 is dependent on the ubiquitous transcription factor NFY. Development 2002; 129:3887-99. [PMID: 12135926 DOI: 10.1242/dev.129.16.3887] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Understanding how boundaries and domains of Hox gene expression are determined is critical to elucidating the means by which the embryo is patterned along the anteroposterior axis. We have performed a detailed analysis of the mouse Hoxb4 intron enhancer to identify upstream transcriptional regulators. In the context of an heterologous promoter, this enhancer can establish the appropriate anterior boundary of mesodermal expression but is unable to maintain it, showing that a specific interaction with its own promoter is important for maintenance. Enhancer function depends on a motif that contains overlapping binding sites for the transcription factors NFY and YY1. Specific mutations that either abolish or reduce NFY binding show that it is crucial for enhancer activity. The NFY/YY1 motif is reiterated in the Hoxb4 promoter and is known to be required for its activity. As these two factors are able to mediate opposing transcriptional effects by reorganizing the local chromatin environment, the relative levels of NFY and YY1 binding could represent a mechanism for balancing activation and repression of Hoxb4 through the same site.
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Affiliation(s)
- Jonathan Gilthorpe
- Division of Eukaryotic Molecular Genetics, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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240
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Sawa C, Yoshikawa T, Matsuda-Suzuki F, Deléhouzée S, Goto M, Watanabe H, Sawada JI, Kataoka K, Handa H. YEAF1/RYBP and YAF-2 are functionally distinct members of a cofactor family for the YY1 and E4TF1/hGABP transcription factors. J Biol Chem 2002; 277:22484-90. [PMID: 11953439 DOI: 10.1074/jbc.m203060200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor hGABP/E4TF1 is a heterotetrameric complex composed of two DNA-binding subunits (hGABP alpha/E4TF1-60) and two transactivating subunits (hGABP beta/E4TF1-53). In order to understand the molecular mechanism of transcriptional regulation by hGABP, we searched for proteins that interact with the non-DNA-binding subunit, hGABP beta, using yeast two-hybrid screening. We identified a human cDNA encoding a protein related to YAF-2 (YY1-associated factor 2), which was previously isolated as an interacting partner of the Ying-Yang-1 (YY1) transcription factor. Reflecting this similarity, both YAF-2 and this novel protein (named YEAF1 for YY1- and E4TF1/hGABP-associated factor-1) interacted with hGABP beta and YY1 in vitro and in vivo, indicating that YEAF1 and YAF-2 constitute a cofactor family for these two structurally distinct transcription factors. By using yeast three-hybrid assay, we demonstrated that hGABP beta and YY1 formed a complex only in the presence of YEAF1, indicating that YEAF1 is a bridging factor of these two transcription factors. These cofactors are functionally different in that YAF-2 positively regulates the transcriptional activity of hGABP but YEAF1 negatively regulates this activity. Also, YAF-2 mRNA is highly expressed in skeletal muscle, whereas YEAF1 mRNA is highly expressed in placenta. We speculate that the transcriptional activity of hGABP is in part regulated by the expression levels of these tissue-specific cofactors. These results provide a novel mechanism of transcriptional regulation by functionally distinct cofactor family members.
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Affiliation(s)
- Chika Sawa
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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241
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Lagger G, O'Carroll D, Rembold M, Khier H, Tischler J, Weitzer G, Schuettengruber B, Hauser C, Brunmeir R, Jenuwein T, Seiser C. Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression. EMBO J 2002; 21:2672-81. [PMID: 12032080 PMCID: PMC126040 DOI: 10.1093/emboj/21.11.2672] [Citation(s) in RCA: 597] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Histone deacetylases (HDACs) modulate chromatin structure and transcription, but little is known about their function in mammalian development. HDAC1 was implicated previously in the repression of genes required for cell proliferation and differentiation. Here we show that targeted disruption of both HDAC1 alleles results in embryonic lethality before E10.5 due to severe proliferation defects and retardation in development. HDAC1-deficient embryonic stem cells show reduced proliferation rates, which correlate with decreased cyclin-associated kinase activities and elevated levels of the cyclin-dependent kinase inhibitors p21(WAF1/CIP1) and p27(KIP1). Similarly, expression of p21 and p27 is up-regulated in HDAC1-null embryos. In addition, loss of HDAC1 leads to significantly reduced overall deacetylase activity, hyperacetylation of a subset of histones H3 and H4 and concomitant changes in other histone modifications. The expression of HDAC2 and HDAC3 is induced in HDAC1-deficient cells, but cannot compensate for loss of the enzyme, suggesting a unique function for HDAC1. Our study provides the first evidence that a histone deacetylase is essential for unrestricted cell proliferation by repressing the expression of selective cell cycle inhibitors.
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Affiliation(s)
- Gerda Lagger
- Institute of Medical Biochemistry, Division of Molecular Biology, University of Vienna, Vienna Biocenter, Dr Bohr-Gasse 9/2, A-1030 Vienna, Austria
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242
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Abstract
Diverse post-translational modifications of histone amino termini represent an important epigenetic mechanism for the organisation of chromatin structure and the regulation of gene activity. Within the past two years, great progress has been made in understanding the functional implications of histone methylation; in particular through the characterisation of histone methyltransferases that direct the site-specific methylation of, for example, lysine 9 and lysine 4 positions in the histone H3 amino terminus. All known histone methyltransferases of this type contain the evolutionarily conserved SET domain and appear to be able to stimulate either gene repression or gene activation. Methylation of H3 Lys9 and Lys4 has been visualised in native chromatin, indicating opposite roles in structuring repressive or accessible chromatin domains. For example, at the mating-type loci in Schizosaccharomyces pombe, at pericentric heterochromatin and at the inactive X chromosome in mammals, striking differences between these distinct marks have been observed. H3 Lys9 methylation is also important to direct additional epigenetic signals such as DNA methylation--for example, in Neurospora crassa and in Arabidopsis thaliana. Together, the available data strongly establish histone lysine methylation as a central modification for the epigenetic organisation of eukaryotic genomes.
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Affiliation(s)
- Monika Lachner
- Research Institute of Molecular Pathology, The Vienna Biocenter, Dr Bohrgasse 7, A-1030 Vienna, Austria
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243
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Americo J, Whiteley M, Brown JL, Fujioka M, Jaynes JB, Kassis JA. A complex array of DNA-binding proteins required for pairing-sensitive silencing by a polycomb group response element from the Drosophila engrailed gene. Genetics 2002; 160:1561-71. [PMID: 11973310 PMCID: PMC1462036 DOI: 10.1093/genetics/160.4.1561] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Regulatory DNA from the Drosophila gene engrailed causes silencing of a linked reporter gene (mini-white) in transgenic Drosophila. This silencing is strengthened in flies homozygous for the transgene and has been called "pairing-sensitive silencing." The pairing-sensitive silencing activities of a large fragment (2.6 kb) and a small subfragment (181 bp) were explored. Since pairing-sensitive silencing is often associated with Polycomb group response elements (PREs), we tested the activities of each of these engrailed fragments in a construct designed to detect PRE activity in embryos. Both fragments were found to behave as PREs in a bxd-Ubx-lacZ reporter construct, while the larger fragment showed additional silencing capabilities. Using the mini-white reporter gene, a 139-bp minimal pairing-sensitive element (PSE) was defined. DNA mobility-shift assays using Drosophila nuclear extracts suggested that there are eight protein-binding sites within this 139-bp element. Mutational analysis showed that at least five of these sites are important for pairing-sensitive silencing. One of the required sites is for the Polycomb group protein Pleiohomeotic and another is GAGAG, a sequence bound by the proteins GAGA factor and Pipsqueak. The identity of the other proteins is unknown. These data suggest a surprising degree of complexity in the DNA-binding proteins required for PSE function.
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Affiliation(s)
- Jeffrey Americo
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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244
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Tuckfield A, Clouston DR, Wilanowski TM, Zhao LL, Cunningham JM, Jane SM. Binding of the RING polycomb proteins to specific target genes in complex with the grainyhead-like family of developmental transcription factors. Mol Cell Biol 2002; 22:1936-46. [PMID: 11865070 PMCID: PMC135618 DOI: 10.1128/mcb.22.6.1936-1946.2002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2001] [Accepted: 12/14/2001] [Indexed: 01/01/2023] Open
Abstract
The Polycomb group (PcG) of proteins represses homeotic gene expression through the assembly of multiprotein complexes on key regulatory elements. The mechanisms mediating complex assembly have remained enigmatic since most PcG proteins fail to bind DNA. We now demonstrate that the human PcG protein dinG interacts with CP2, a mammalian member of the grainyhead-like family of transcription factors, in vitro and in vivo. The functional consequence of this interaction is repression of CP2-dependent transcription. The CP2-dinG interaction is conserved in evolution with the Drosophila factor grainyhead binding to dring, the fly homologue of dinG. Electrophoretic mobility shift assays demonstrate that the grh-dring complex forms on regulatory elements of genes whose expression is repressed by grh but not on elements where grh plays an activator role. These observations reveal a novel mechanism by which PcG proteins may be anchored to specific regulatory elements in developmental genes.
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Affiliation(s)
- Annabel Tuckfield
- Rotary Bone Marrow Research Laboratory, Royal Melbourne Hospital Research Foundation, c/o RMH Post Office, Grattan Street, Parkville, Victoria 3050, Australia
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245
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Abstract
Polycomb proteins form DNA-binding protein complexes with gene-suppressing activity. They maintain cell identity but, also, contribute to the regulation of cell proliferation. Mice with mutated Polycomb-group genes exhibit various hematological disorders, ranging from the loss of mature B and T cells to development of lymphomas. Lymphopoiesis in humans is associated with characteristic expression patterns of Polycomb-group genes in defined lymphocyte populations. Collectively, these results indicate that Polycomb-group genes encode novel gene regulators involved in the differentiation of lymphocytes. The underlying mechanism is related, most probably, to gene silencing by chromatin modification, and might affect proliferative behavior and account for the irreversibility of lineage choice.
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Affiliation(s)
- F M Raaphorst
- VU Medical Center, Department of Pathology, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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246
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O'Connell S, Wang L, Robert S, Jones CA, Saint R, Jones RS. Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein. J Biol Chem 2001; 276:43065-73. [PMID: 11571280 DOI: 10.1074/jbc.m104294200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The products of Polycomb group (PcG) genes are required for the epigenetic repression of a number of important developmental regulatory genes, including homeotic genes. Enhancer of zeste (E(Z)) is a Drosophila PcG protein that previously has been shown to bind directly to another PcG protein, Extra Sex Combs (ESC), and is present along with ESC in a 600-kDa complex in Drosophila embryos. Using yeast two-hybrid and in vitro binding assays, we show that E(Z) binds directly to another PcG protein, Polycomblike (PCL). PCL.E(Z) interaction is shown to be mediated by the plant homeodomain (PHD) fingers domain of PCL, providing evidence that this motif can act as an independent protein interaction domain. An association was also observed between PHF1 and EZH2, human homologs of PCL and E(Z), respectively, demonstrating the evolutionary conservation of this interaction. E(Z) was found to not interact with the PHD domains of three Drosophila trithorax group (trxG) proteins, which function to maintain the transcriptional activity of homeotic genes, providing evidence for the specificity of the interaction of E(Z) with the PCL PHD domain. Coimmunoprecipitation and gel filtration experiments demonstrate in vivo association of PCL with E(Z) and ESC in Drosophila embryos. We discuss the implications of PCL association with ESC.E(Z) complexes and the possibility that PCL may either be a subunit of a subset of ESC.E(Z) complexes or a subunit of a separate complex that interacts with ESC.E(Z) complexes.
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Affiliation(s)
- S O'Connell
- Centre for the Molecular Genetics of Development and Department of Genetics, University of Adelaide, Adelaide, South Australia 5005, Australia
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247
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Abstract
YY1 is a sequence-specific DNA-binding transcription factor that has many important biological roles. It activates or represses many genes during cell growth and differentiation and is also required for the normal development of mammalian embryos. Previous studies have established that YY1 interacts with histone acetyltransferases p300 and CREB-binding protein (CBP) and histone deacetylase 1 (HDAC1), HDAC2, and HDAC3. Here, we present evidence that the activity of YY1 is regulated through acetylation by p300 and PCAF and through deacetylation by HDACs. YY1 was acetylated in two regions: both p300 and PCAF acetylated the central glycine-lysine-rich domain of residues 170 to 200, and PCAF also acetylated YY1 at the C-terminal DNA-binding zinc finger domain. Acetylation of the central region was required for the full transcriptional repressor activity of YY1 and targeted YY1 for active deacetylation by HDACs. However, the C-terminal region of YY1 could not be deacetylated. Rather, the acetylated C-terminal region interacted with HDACs, which resulted in stable HDAC activity associated with the YY1 protein. Finally, acetylation of the C-terminal zinc finger domain decreased the DNA-binding activity of YY1. Our findings suggest that in the natural context, YY1 activity is regulated through intricate mechanisms involving negative feedback loops, histone deacetylation, and recognition of the cognate DNA sequence affected by acetylation and deacetylation of the YY1 protein.
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248
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Bannasch D, Mädge B, Schwab M. Functional interaction of Yaf2 with the central region of MycN. Oncogene 2001; 20:5913-9. [PMID: 11593398 DOI: 10.1038/sj.onc.1204747] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2001] [Revised: 06/13/2001] [Accepted: 06/18/2001] [Indexed: 11/09/2022]
Abstract
MYCN is often amplified in advanced-stage neuroblastomas with the consequence of enhanced MycN protein expression. By employing the yeast two-hybrid system we found that Yaf2 binds to the central region of MycN. Binding was also seen in vitro and in vivo. Ectopically expressed Yaf2, like MycN, is localized in the nuclei of neuroblastoma cells. Endogenous Yaf2 is expressed in all three tested neuroblastoma cell lines, all of which also express MycN. Yaf2 was able to enhance MycN-mediated transactivation from an E-box promoter, deletion of the Yaf2 binding region in MycN abrogates this effect. Thus, the binding of Yaf2 to the central region of MycN is functional in mammalian cells.
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Affiliation(s)
- D Bannasch
- Division of Cytogenetics-H0400, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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249
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Abstract
YY1 is a sequence-specific DNA-binding transcription factor that has many important biological roles. It activates or represses many genes during cell growth and differentiation and is also required for the normal development of mammalian embryos. Previous studies have established that YY1 interacts with histone acetyltransferases p300 and CREB-binding protein (CBP) and histone deacetylase 1 (HDAC1), HDAC2, and HDAC3. Here, we present evidence that the activity of YY1 is regulated through acetylation by p300 and PCAF and through deacetylation by HDACs. YY1 was acetylated in two regions: both p300 and PCAF acetylated the central glycine-lysine-rich domain of residues 170 to 200, and PCAF also acetylated YY1 at the C-terminal DNA-binding zinc finger domain. Acetylation of the central region was required for the full transcriptional repressor activity of YY1 and targeted YY1 for active deacetylation by HDACs. However, the C-terminal region of YY1 could not be deacetylated. Rather, the acetylated C-terminal region interacted with HDACs, which resulted in stable HDAC activity associated with the YY1 protein. Finally, acetylation of the C-terminal zinc finger domain decreased the DNA-binding activity of YY1. Our findings suggest that in the natural context, YY1 activity is regulated through intricate mechanisms involving negative feedback loops, histone deacetylation, and recognition of the cognate DNA sequence affected by acetylation and deacetylation of the YY1 protein.
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Affiliation(s)
- Y L Yao
- Department of Medical Microbiology and Immunology, Interdisciplinary Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, College of Medicine, University of South Florida, Tampa, FL 33612, USA
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250
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Mattick JS, Gagen MJ. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 2001; 18:1611-30. [PMID: 11504843 DOI: 10.1093/oxfordjournals.molbev.a003951] [Citation(s) in RCA: 295] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.
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Affiliation(s)
- J S Mattick
- Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
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