801
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Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 2007; 128:735-45. [PMID: 17320510 DOI: 10.1016/j.cell.2007.02.009] [Citation(s) in RCA: 1035] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins are critical regulators of numerous developmental genes. To silence or activate gene expression, respectively, PcG and trxG proteins bind to specific regions of DNA and direct the posttranslational modification of histones. Recent work suggests that PcG proteins regulate the nuclear organization of their target genes and that PcG-mediated gene silencing involves noncoding RNAs and the RNAi machinery.
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Affiliation(s)
- Bernd Schuettengruber
- Institute of Human Genetics, CNRS, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France
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802
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Abstract
Epigenetics has recently evolved from a collection of diverse phenomena to a defined and far-reaching field of study. In this Essay, we examine the epistemology of epigenetics, provide a brief overview of underlying molecular mechanisms, and suggest future challenges for the field.
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Affiliation(s)
- Aaron D Goldberg
- Laboratory of Chromatin Biology, The Rockefeller University, New York, NY 10021, USA
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803
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Abstract
Aberrant gene function and altered patterns of gene expression are key features of cancer. Growing evidence shows that acquired epigenetic abnormalities participate with genetic alterations to cause this dysregulation. Here, we review recent advances in understanding how epigenetic alterations participate in the earliest stages of neoplasia, including stem/precursor cell contributions, and discuss the growing implications of these advances for strategies to control cancer.
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Affiliation(s)
- Peter A. Jones
- Department of Urology, Biochemistry, and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Correspondence: (P.A.J.), (S.B.B.)
| | - Stephen B. Baylin
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
- Correspondence: (P.A.J.), (S.B.B.)
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804
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Abstract
The surface of nucleosomes is studded with a multiplicity of modifications. At least eight different classes have been characterized to date and many different sites have been identified for each class. Operationally, modifications function either by disrupting chromatin contacts or by affecting the recruitment of nonhistone proteins to chromatin. Their presence on histones can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA. In this way, histone modifications have the potential to influence many fundamental biological processes, some of which may be epigenetically inherited.
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Affiliation(s)
- Tony Kouzarides
- The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB21QN, UK.
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805
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Mulder KW, Brenkman AB, Inagaki A, van den Broek NJF, Marc Timmers HT. Regulation of histone H3K4 tri-methylation and PAF complex recruitment by the Ccr4-Not complex. Nucleic Acids Res 2007; 35:2428-39. [PMID: 17392337 PMCID: PMC1874646 DOI: 10.1093/nar/gkm175] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Efficient transcription is linked to modification of chromatin. For instance, tri-methylation of lysine 4 on histone H3 (H3K4) strongly correlates with transcriptional activity and is regulated by the Bur1/2 kinase complex. We found that the evolutionarily conserved Ccr4-Not complex is involved in establishing H3K4 tri-methylation in Saccharomyces cerevisiae. We observed synthetic lethal interactions of Ccr4-Not components with BUR1 and BUR2. Further analysis indicated that the genes encoding the Not-proteins are essential for efficient regulation of H3K4me3, but not H3K4me1/2, H3K36me2 or H3K79me2/3 levels. Moreover, regulation of H3K4me3 levels by NOT4 is independent of defects in RNA polymerase II loading. We found NOT4 to be important for ubiquitylation of histone H2B via recruitment of the PAF complex, but not for recruitment or activation of the Bur1/2 complex. These results suggest a mechanism in which the Ccr4-Not complex functions parallel to or downstream of the Bur1/2 kinase to facilitate H3K4me3 via PAF complex recruitment.
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Affiliation(s)
- Klaas W. Mulder
- Department of Physiological Chemistry and Department of Physiological Chemistry Mass Spectrometry Unit, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Arjan B. Brenkman
- Department of Physiological Chemistry and Department of Physiological Chemistry Mass Spectrometry Unit, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Akiko Inagaki
- Department of Physiological Chemistry and Department of Physiological Chemistry Mass Spectrometry Unit, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Niels J. F. van den Broek
- Department of Physiological Chemistry and Department of Physiological Chemistry Mass Spectrometry Unit, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - H. Th. Marc Timmers
- Department of Physiological Chemistry and Department of Physiological Chemistry Mass Spectrometry Unit, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
- *To whom correspondence should be addressed. +31-30-2538981+31-30-2539035
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806
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Bagchi A, Papazoglu C, Wu Y, Capurso D, Brodt M, Francis D, Bredel M, Vogel H, Mills AA. CHD5 is a tumor suppressor at human 1p36. Cell 2007; 128:459-75. [PMID: 17289567 DOI: 10.1016/j.cell.2006.11.052] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 10/24/2006] [Accepted: 11/27/2006] [Indexed: 01/25/2023]
Abstract
Cancer gene discovery has relied extensively on analyzing tumors for gains and losses to reveal the location of oncogenes and tumor suppressor genes, respectively. Deletions of 1p36 are extremely common genetic lesions in human cancer, occurring in malignancies of epithelial, neural, and hematopoietic origin. Although this suggests that 1p36 harbors a gene that drives tumorigenesis when inactivated, the identity of this tumor suppressor has remained elusive. Here we use chromosome engineering to generate mouse models with gain and loss of a region corresponding to human 1p36. This approach functionally identifies chromodomain helicase DNA binding domain 5 (Chd5) as a tumor suppressor that controls proliferation, apoptosis, and senescence via the p19(Arf)/p53 pathway. We demonstrate that Chd5 functions as a tumor suppressor in vivo and implicate deletion of CHD5 in human cancer. Identification of this tumor suppressor provides new avenues for exploring innovative clinical interventions for cancer.
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Affiliation(s)
- Anindya Bagchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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807
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Dirk LMA, Flynn EM, Dietzel K, Couture JF, Trievel RC, Houtz RL. Kinetic manifestation of processivity during multiple methylations catalyzed by SET domain protein methyltransferases. Biochemistry 2007; 46:3905-15. [PMID: 17338551 DOI: 10.1021/bi6023644] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Processive versus distributive methyl group transfer was assessed for pea Rubisco large subunit methyltransferase, a SET domain protein lysine methyltransferase catalyzing the formation of trimethyllysine-14 in the large subunit of Rubisco. Catalytically competent complexes between an immobilized form of des(methyl) Rubisco and Rubisco large subunit methyltransferase were used to demonstrate enzyme release that was co-incident with and dependent on formation of trimethyllysine. Catalytic rate constants determined for formation of trimethyllysine were considerably lower ( approximately 10-fold) than rate constants determined for total radiolabel incorporation from [3H-methyl]-S-adenosylmethionine. Double-reciprocal velocity plots under catalytic conditions favoring monomethyllysine indicated a random or ordered reaction mechanism, while conditions favoring trimethyllysine suggested a hybrid ping-pong mechanism. These results were compared with double-reciprocal velocity plots and product analyses obtained for HsSET7/9 (a monomethyltransferase) and SpCLR4 (a dimethyltransferase) and suggest a predictive ability of double-reciprocal velocity plots for single versus multiple methyl group transfers by SET domain protein lysine methyltransferases. A model is proposed for SET domain protein lysine methyltransferases in which initial binding of polypeptide substrate and S-adenosylmethionine is random, with polypeptide binding followed by deprotonation of the epsilon-amine of the target lysyl residue and subsequent methylation. Following methyl group transfer, S-adenosylhomocysteine and monomethylated polypeptide dissociate from monomethyltransferases, but di- and trimethyltransferases begin a successive and catalytically obligatory deprotonation of enzyme-bound methylated lysyl intermediates, which along with binding and release of S-adenosylmethionine and S-adenosylhomocysteine is manifested as a hybrid ping-pong-like reaction mechanism.
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Affiliation(s)
- Lynnette M A Dirk
- Department of Horticulture, Plant Physiology/Biochemistry/Molecular Biology Program, 401D Plant Science Building, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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808
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Klose RJ, Zhang Y. Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol 2007; 8:307-18. [PMID: 17342184 DOI: 10.1038/nrm2143] [Citation(s) in RCA: 623] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histone methylation has important roles in regulating transcription, genome integrity and epigenetic inheritance. Historically, methylated histone arginine and lysine residues have been considered static modifications because of the low levels of methyl-group turnover in chromatin. The recent identification of enzymes that antagonize or remove histone methylation has changed this view and now the dynamic nature of these modifications is being appreciated. Here, we examine the enzymatic and structural basis for the mechanisms that these enzymes use to counteract histone methylation and provide insights into their substrate specificity and biological function.
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Affiliation(s)
- Robert J Klose
- Howard Hughes Medical Institute, 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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809
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Lee MG, Norman J, Shilatifard A, Shiekhattar R. Physical and Functional Association of a Trimethyl H3K4 Demethylase and Ring6a/MBLR, a Polycomb-like Protein. Cell 2007; 128:877-87. [PMID: 17320162 DOI: 10.1016/j.cell.2007.02.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 11/29/2006] [Accepted: 02/02/2007] [Indexed: 01/12/2023]
Abstract
Histone methylation is a posttranslational modification regulating chromatin structure and gene regulation. BHC110/LSD1 was the first histone demethylase described to reverse dimethyl histone H3 lysine 4 (H3K4). Here we show that JARID1d, a JmjC-domain-containing protein, specifically demethylates trimethyl H3K4. Detailed mapping analysis revealed that besides the JmjC domain, the BRIGHT and zinc-finger-like C(5)HC(2) domains are required for maximum catalytic activity. Importantly, isolation of native JARID1d complexes from human cells revealed the association of the demethylase with a polycomb-like protein Ring6a/MBLR. Ring6a/MBLR not only directly interacts with JARID1d but also regulates its enzymatic activity. We show that JARID1d and Ring6a occupy human Engrailed 2 gene and regulate its expression and H3K4 methylation levels. Depletion of JARID1d enhanced recruitment of the chromatin remodeling complex, NURF, and the basal transcription machinery near the transcriptional start site, revealing a role for JARID1d in regulation of transcriptional initiation through H3K4 demethylation.
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Affiliation(s)
- Min Gyu Lee
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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810
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Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The Retinoblastoma Binding Protein RBP2 Is an H3K4 Demethylase. Cell 2007; 128:889-900. [PMID: 17320163 DOI: 10.1016/j.cell.2007.02.013] [Citation(s) in RCA: 331] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 12/22/2006] [Accepted: 02/08/2007] [Indexed: 12/13/2022]
Abstract
Changes in histone methylation status regulate chromatin structure and DNA-dependent processes such as transcription. Recent studies indicate that, analogous to other histone modifications, histone methylation is reversible. Retinoblastoma binding protein 2 (RBP2), a nuclear protein implicated in the regulation of transcription and differentiation by the retinoblastoma tumor suppressor protein, contains a JmjC domain recently defined as a histone demethylase signature motif. Here we report that RBP2 is a demethylase that specifically catalyzes demethylation on H3K4, whose methylation is normally associated with transcriptionally active genes. RBP2-/- mouse cells displayed enhanced transcription of certain cytokine genes, which, in the case of SDF1, was associated with increased H3K4 trimethylation. Furthermore, RBP2 specifically demethylated H3K4 in biochemical and cell-based assays. These studies provide mechanistic insights into transcriptional regulation by RBP2 and provide the first example of a mammalian enzyme capable of erasing trimethylated H3K4.
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Affiliation(s)
- Robert J Klose
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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811
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Porras-Yakushi TR, Whitelegge JP, Clarke S. Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily: identification of Rpl23ab methylation sites and recognition motifs. J Biol Chem 2007; 282:12368-76. [PMID: 17327221 DOI: 10.1074/jbc.m611896200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal protein L23ab is specifically dimethylated at two distinct sites by the SET domain-containing enzyme Rkm1 in the yeast Saccharomyces cerevisiae. Using liquid column chromatography with electrospray-ionization mass spectrometry, we determined that Rpl23ab purified from the Deltarkm1 deletion strain demonstrated a loss in mass of approximately 56 Da when compared with Rpl23ab purified from the wild type strain. When Rpl23ab was proteolyzed, using proteinase ArgC or CNBr, and the peptides derived were analyzed by tandem mass spectrometry, no sites of methylation were found in Rpl23ab purified from the Deltarkm1 deletion strain, whereas two sites of dimethylation were observed in the wild type strain at lysine residues 105 and 109. We show that both Rpl23a and Rpl23b are expressed and methylated in vivo in yeast. Using polysomal fractionation, we demonstrate that the deletion of RKM1 has no effect on ribosomal complex formation. Comparison of SET domain methyltransferase substrates in yeast reveal sequence similarities around the lysine methylation sites and suggest that an (Asn/Pro)-Pro-Lys consensus sequence may be a target for methylation by subfamily 2 SET domain methyltransferases. Finally, we show the presence of Rkm1 homologs in fungi, plants, and mammals including humans.
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Affiliation(s)
- Tanya R Porras-Yakushi
- Department of Chemistry and Biochemistry, the Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1569, USA
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812
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Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 2007; 128:1077-88. [PMID: 17320160 DOI: 10.1016/j.cell.2007.02.017] [Citation(s) in RCA: 517] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 01/16/2007] [Accepted: 02/09/2007] [Indexed: 12/13/2022]
Abstract
Histone methylation regulates chromatin structure and transcription. The recently identified histone demethylase lysine-specific demethylase 1 (LSD1) is chemically restricted to demethylation of only mono- and di- but not trimethylated histone H3 lysine 4 (H3K4me3). We show that the X-linked mental retardation (XLMR) gene SMCX (JARID1C), which encodes a JmjC-domain protein, reversed H3K4me3 to di- and mono- but not unmethylated products. Other SMCX family members, including SMCY, RBP2, and PLU-1, also demethylated H3K4me3. SMCX bound H3K9me3 via its N-terminal PHD (plant homeodomain) finger, which may help coordinate H3K4 demethylation and H3K9 methylation in transcriptional repression. Significantly, several XLMR-patient point mutations reduced SMCX demethylase activity and binding to H3K9me3 peptides, respectively. Importantly, studies in zebrafish and primary mammalian neurons demonstrated a role for SMCX in neuronal survival and dendritic development and a link to the demethylase activity. Our findings thus identify a family of H3K4me3 demethylases and uncover a critical link between histone modifications and XLMR.
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Affiliation(s)
- Shigeki Iwase
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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813
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Christensen J, Agger K, Cloos PAC, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 2007; 128:1063-76. [PMID: 17320161 DOI: 10.1016/j.cell.2007.02.003] [Citation(s) in RCA: 414] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/14/2006] [Accepted: 02/02/2007] [Indexed: 12/12/2022]
Abstract
Methylation of histones has been regarded as a stable modification defining the epigenetic program of the cell, which regulates chromatin structure and transcription. However, the recent discovery of histone demethylases has challenged the stable nature of histone methylation. Here we demonstrate that the JARID1 proteins RBP2, PLU1, and SMCX are histone demethylases specific for di- and trimethylated histone 3 lysine 4 (H3K4). Consistent with a role for the JARID1 Drosophila homolog Lid in regulating expression of homeotic genes during development, we show that RBP2 is displaced from Hox genes during embryonic stem (ES) cell differentiation correlating with an increase of their H3K4me3 levels and expression. Furthermore, we show that mutation or RNAi depletion of the C. elegans JARID1 homolog rbr-2 leads to increased levels of H3K4me3 during larval development and defects in vulva formation. Taken together, these results suggest that H3K4me3/me2 demethylation regulated by the JARID1 family plays an important role during development.
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814
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Abstract
The nucleosome surface is decorated with an array of enzyme-catalysed modifications on histone tails. These modifications have well-defined roles in a variety of ongoing chromatin functions, often by acting as receptors for non-histone proteins, but their longer-term effects are less clear. Here, an attempt is made to define how histone modifications operate as part of a predictive and heritable epigenetic code that specifies patterns of gene expression through differentiation and development.
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Affiliation(s)
- Bryan M Turner
- Institute of Biomedical Research, University of Birmingham Medical School, Birmingham B15 2TT, UK.
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815
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Secombe J, Li L, Carlos L, Eisenman RN. The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev 2007; 21:537-51. [PMID: 17311883 PMCID: PMC1820896 DOI: 10.1101/gad.1523007] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Myc oncoprotein is a potent inducer of cell growth, cell cycle progression, and apoptosis. While many direct Myc target genes have been identified, the molecular determinants of Myc's transcriptional specificity remain elusive. We have carried out a genetic screen in Drosophila and identified the Trithorax group protein Little imaginal discs (Lid) as a regulator of dMyc-induced cell growth. Lid binds to dMyc and is required for dMyc-induced expression of the growth regulatory gene Nop60B. The mammalian Lid orthologs, Rbp-2 (JARID1A) and Plu-1 (JARID1B), also bind to c-Myc, indicating that Lid-Myc function is conserved. We demonstrate that Lid is a JmjC-dependent trimethyl H3K4 demethylase in vivo and that this enzymatic activity is negatively regulated by dMyc, which binds to Lid's JmjC domain. Because Myc binding is associated with high levels of trimethylated H3K4, we propose that the Lid-dMyc complex facilitates Myc binding to, or maintenance of, this chromatin context.
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Affiliation(s)
- Julie Secombe
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ling Li
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Leni Carlos
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Robert N. Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Corresponding author.E-MAIL ; FAX (206) 667-6522
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816
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Liang G, Klose RJ, Gardner KE, Zhang Y. Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nat Struct Mol Biol 2007; 14:243-5. [PMID: 17310254 DOI: 10.1038/nsmb1204] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 01/22/2007] [Indexed: 11/08/2022]
Abstract
Histone methylation is important in regulating chromatin structure and function. In budding yeast, methylation of histone H3 at Lys4 (H3-K4) is associated with active transcription and is enriched at the 5' regions of transcribed genes. Here we identify a novel budding yeast JmjC domain-containing H3-K4 demethylase, Jhd2p, that antagonizes the trimethyl modification state and contributes to regulation of telomeric silencing.
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Affiliation(s)
- Gaoyang Liang
- Howard Hughes Medical Institute, 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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817
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Schwartz YB, Pirrotta V. Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 2007; 8:9-22. [PMID: 17173055 DOI: 10.1038/nrg1981] [Citation(s) in RCA: 653] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polycomb group complexes, which are known to regulate homeotic genes, have now been found to control hundreds of other genes in mammals and insects. First believed to progressively assemble and package chromatin, they are now thought to be localized, but induce a methylation mark on histone H3 over a broad chromatin domain. Recent progress has changed our view of how these complexes are recruited, and how they affect chromatin and repress gene activity. Polycomb complexes function as global enforcers of epigenetically repressed states, balanced by an antagonistic state that is mediated by Trithorax. These epigenetic states must be reprogrammed when cells become committed to differentiation.
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Affiliation(s)
- Yuri B Schwartz
- Department of Molecular Biology and Biochemistry, Rutgers University, Nelson Laboratories, 604 Allison Road, Piscataway, New Jersey 08854, USA
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818
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Abstract
The formation of heterochromatin, which requires methylation of histone H3 at lysine 9 and the subsequent recruitment of chromodomain proteins such as heterochromatin protein HP1, serves as a model for the role of histone modifications and chromatin assembly in epigenetic control of the genome. Recent studies in Schizosaccharomyces pombe indicate that heterochromatin serves as a dynamic platform to recruit and spread a myriad of regulatory proteins across extended domains to control various chromosomal processes, including transcription, chromosome segregation and long-range chromatin interactions.
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Affiliation(s)
- Shiv I S Grewal
- Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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819
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Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 2007; 25:15-30. [PMID: 17218268 DOI: 10.1016/j.molcel.2006.12.014] [Citation(s) in RCA: 856] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Cells employ elaborate mechanisms to introduce structural and chemical variation into chromatin. Here, we focus on one such element of variation: methylation of lysine 4 in histone H3 (H3K4). We assess a growing body of literature, including treatment of how the mark is established, the patterns of methylation, and the functional consequences of this epigenetic signature. We discuss structural aspects of the H3K4 methyl recognition by the downstream effectors and propose a distinction between sequence-specific recruitment mechanisms and stabilization on chromatin through methyl-lysine recognition. Finally, we hypothesize how the unique properties of the polyvalent chromatin fiber and associated effectors may amplify small differences in methyl-lysine recognition, simultaneously allowing for a dynamic chromatin architecture.
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820
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Abstract
Recent studies demonstrated that histone methylation is not static but is dynamically regulated by histone methyltransferases and the newly discovered histone demethylases. This review discusses the chemical mechanisms for the known and potentially new classes of demethylases, the roles of these demethylases in chromatin and transcription, and their potential biological functions and connections to human diseases.
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821
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Reader JC, Meekins JS, Gojo I, Ning Y. A novel NUP98-PHF23 fusion resulting from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia. Leukemia 2007; 21:842-4. [PMID: 17287853 DOI: 10.1038/sj.leu.2404579] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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822
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Wissmann M, Yin N, Müller JM, Greschik H, Fodor BD, Jenuwein T, Vogler C, Schneider R, Günther T, Buettner R, Metzger E, Schüle R. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol 2007; 9:347-53. [PMID: 17277772 DOI: 10.1038/ncb1546] [Citation(s) in RCA: 462] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 01/02/2007] [Indexed: 01/27/2023]
Abstract
Posttranslational modifications of histones, such as methylation, regulate chromatin structure and gene expression. Recently, lysine-specific demethylase 1 (LSD1), the first histone demethylase, was identified. LSD1 interacts with the androgen receptor and promotes androgen-dependent transcription of target genes by ligand-induced demethylation of mono- and dimethylated histone H3 at Lys 9 (H3K9) only. Here, we identify the Jumonji C (JMJC) domain-containing protein JMJD2C as the first histone tridemethylase regulating androgen receptor function. JMJD2C interacts with androgen receptor in vitro and in vivo. Assembly of ligand-bound androgen receptor and JMJD2C on androgen receptor-target genes results in demethylation of trimethyl H3K9 and in stimulation of androgen receptor-dependent transcription. Conversely, knockdown of JMJD2C inhibits androgen-induced removal of trimethyl H3K9, transcriptional activation and tumour cell proliferation. Importantly, JMJD2C colocalizes with androgen receptor and LSD1 in normal prostate and in prostate carcinomas. JMJD2C and LSD1 interact and both demethylases cooperatively stimulate androgen receptor-dependent gene transcription. In addition, androgen receptor, JMJD2C and LSD1 assemble on chromatin to remove methyl groups from mono, di and trimethylated H3K9. Thus, our data suggest that specific gene regulation requires the assembly and coordinate action of demethylases with distinct substrate specificities.
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MESH Headings
- Animals
- Cell Line
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Chlorocebus aethiops
- Gene Expression Regulation/drug effects
- HeLa Cells
- Histone Demethylases
- Histones/metabolism
- Humans
- Jumonji Domain-Containing Histone Demethylases
- Male
- Metribolone/pharmacology
- MicroRNAs/genetics
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Prostate-Specific Antigen/genetics
- Prostate-Specific Antigen/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Protein Binding/drug effects
- RNA, Small Interfering/genetics
- Receptors, Androgen/analysis
- Receptors, Androgen/metabolism
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Response Elements/genetics
- Tissue Kallikreins/genetics
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transfection
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Affiliation(s)
- Melanie Wissmann
- Universitäts-Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
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823
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Abstract
The posttranslational modification of histones plays an important role in chromatin regulation. Histone methylation influences constitutive heterochromatin, genomic imprinting, X-chromosome inactivation and gene transcription. Histone demethylase catalyzes the removal of methyl groups on lysine or arginine residues of histones. Two kinds of histone lysine demethylases have been identified, including lysine specific demethylase 1 and Jumonji C (JmjC) domain family proteins. These histone demethylases are involved in the regulation of gene expression. Histone modification is a dynamic process, and the imbalance of histone methylation has been linked to cancers. Therefore, histone demethylases may represent a new target for anti-cancer therapy.
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Affiliation(s)
- Xiaoqing Tian
- Shanghai Jiaotong University School of Medicine, Renji Hospital, Shanghai Institute of Digestive Disease, Shanghai 200001, China
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824
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Kouzarides T. Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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825
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Kouzarides T. Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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826
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Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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827
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Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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828
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Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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829
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Kouzarides T. Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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830
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Kouzarides T. Chromatin Modifications and Their Function. Cell 2007. [DOI: 10.1016/j.cell.2007.02.005 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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831
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Gangaraju VK, Bartholomew B. Mechanisms of ATP dependent chromatin remodeling. Mutat Res 2007; 618:3-17. [PMID: 17306844 PMCID: PMC2584342 DOI: 10.1016/j.mrfmmm.2006.08.015] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 08/14/2006] [Indexed: 11/21/2022]
Abstract
The inter-relationship between DNA repair and ATP dependent chromatin remodeling has begun to become very apparent with recent discoveries. ATP dependent remodeling complexes mobilize nucleosomes along DNA, promote the exchange of histones, or completely displace nucleosomes from DNA. These remodeling complexes are often categorized based on the domain organization of their catalytic subunit. The biochemical properties and structural information of several of these remodeling complexes are reviewed. The different models for how these complexes are able to mobilize nucleosomes and alter nucleosome structure are presented incorporating several recent findings. Finally the role of histone tails and their respective modifications in ATP-dependent remodeling are discussed.
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Affiliation(s)
- Vamsi K Gangaraju
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL. 62901-4413, USA
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832
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Hogan C, Varga-Weisz P. The regulation of ATP-dependent nucleosome remodelling factors. Mutat Res 2007; 618:41-51. [PMID: 17306842 DOI: 10.1016/j.mrfmmm.2006.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 07/18/2006] [Indexed: 11/17/2022]
Abstract
The plasticity of chromatin is governed by multi-subunit protein complexes that enzymatically regulate chromosomal structure and activity. Such complexes include ATP-dependent chromatin remodelling factors that are involved in many fundamental processes such as transcription, DNA repair, replication and chromosome structure maintenance. Because ATP-dependent chromatin remodelling factors play important roles, it is not surprising to find that their functions are regulated in a plethora of ways, including post-translational modifications of their subunits and subunit composition changes. The activity of these enzymes is modulated by many factors, including linker histones, histone variants, histone chaperones, non-histone chromatin constituents such as HMG-proteins and secondary messengers, such as inositolpolyphosphates. Additionally, specific histone modifications and interaction with site-specific transcriptional regulators direct the targeting of these activities. Understanding the network of mechanisms that control ATP-dependent chromatin remodelling will constitute an important challenge towards our understanding of chromatin dynamics.
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833
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Abstract
DNA is under constant attack from intracellular and external mutagens. Sites of DNA damage need to be pinpointed so that the DNA repair machinery can be mobilized to the proper location. The identification of damaged sites, recruitment of repair factors, and assembly of repair "factories" is orchestrated by posttranslational modifications (PTMs). These PTMs include phosphorylation, ubiquitination, sumoylation, acetylation, and methylation. Here we discuss recent data surrounding the roles of arginine and lysine methylation in DNA repair processes.
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Affiliation(s)
- Aimee N Lake
- The University of Texas MD Anderson Cancer Center, Science Park-Research Division, Smithville, TX 78957, USA.
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834
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Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 2007; 24:785-796. [PMID: 17157260 PMCID: PMC4690528 DOI: 10.1016/j.molcel.2006.10.026] [Citation(s) in RCA: 248] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/22/2006] [Accepted: 10/19/2006] [Indexed: 12/31/2022]
Abstract
Posttranslational histone modifications participate in modulating the structure and function of chromatin. Promoters of transcribed genes are enriched with K4 trimethylation and hyperacetylation on the N-terminal tail of histone H3. Recently, PHD finger proteins, like Yng1 in the NuA3 HAT complex, were shown to interact with H3K4me3, indicating a biochemical link between K4 methylation and hyperacetylation. By using a combination of mass spectrometry, biochemistry, and NMR, we detail the Yng1 PHD-H3K4me3 interaction and the importance of NuA3-dependent acetylation at K14. Furthermore, genome-wide ChIP-Chip analysis demonstrates colocalization of Yng1 and H3K4me3 in vivo. Disrupting the K4me3 binding of Yng1 altered K14ac and transcription at certain genes, thereby demonstrating direct in vivo evidence of sequential trimethyl binding, acetyltransferase activity, and gene regulation by NuA3. Our data support a general mechanism of transcriptional control through which histone acetylation upstream of gene activation is promoted partially through availability of H3K4me3, "read" by binding modules in select subunits.
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Affiliation(s)
- Sean D Taverna
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Serge Ilin
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Jason C Tanny
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Heather Lavender
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Haitao Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Lindsey Baker
- Laboratory of Chromatin Biology, The Rockefeller University
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington 98103
| | - Lauren P Blair
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University.
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835
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Huq MDM, Tsai NP, Khan SA, Wei LN. Lysine trimethylation of retinoic acid receptor-alpha: a novel means to regulate receptor function. Mol Cell Proteomics 2007; 6:677-88. [PMID: 17205979 DOI: 10.1074/mcp.m600223-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Retinoic acid receptors (RARs) belong to the nuclear receptor superfamily. The mechanism of ligand-dependent activation of RARs is well known. The effect of protein phosphorylation on the activity of RARs has also been demonstrated. However, it is unclear whether other types of modifications exist and if so whether they can affect the activity of RARs. In a mass spectrometric analysis of mouse RARalpha expressed in insect cells, we identified a trimethylation site on Lys(347) in the ligand binding domain. The modification site was verified in mammalian cells, and site-directed mutagenesis studies revealed the functionality of Lys(347) methylation in vivo. Constitutive negative mutants, mimicking hypomethylated RARalpha, were prepared by replacing methylated Lys(347) with either alanine or glutamine. A constitutive positive mutant partially mimicking the hypermethylated RARalpha was generated by replacing the methylated lysine residue with phenylalanine, a bulky hydrophobic amino acid, to introduce a site-specific hydrophobicity similar to that contributed by lysine methylation. Studies of these mutants revealed that trimethylation of Lys(347) of RARalpha facilitated its interactions with cofactors p300/CREB-binding protein-associated factor and receptor-interacting protein 140 as well as its heterodimeric partner retinoid X receptor, suggesting that site-specific hydrophobicity at Lys(347) enhanced molecular interaction of RARalpha with its modulators. This study uncovers the first example of lysine trimethylation on a mammalian non-histone protein that has an important biological consequence. Our finding also provides the evidence for lysine methylation for the family of nuclear receptors for the first time.
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Affiliation(s)
- M D Mostaqul Huq
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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836
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Seeds AM, Frederick JP, Tsui MMK, York JD. Roles for inositol polyphosphate kinases in the regulation of nuclear processes and developmental biology. ACTA ACUST UNITED AC 2007; 47:10-25. [PMID: 17467778 PMCID: PMC3258027 DOI: 10.1016/j.advenzreg.2006.12.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | - John D. York
- To whom correspondence should be addressed: Department of Pharmacology and Cancer Biology, Howard Hughes Medical Institute, Duke University Medical Center, DUMC 3813, Durham, NC 27710, Tel: 919-681-6414, Fax: 919-668-0991, E-mail:
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837
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Wang S, He F, Xiong W, Gu S, Liu H, Zhang T, Yu X, Chen Y. Polycomblike-2-deficient mice exhibit normal left–right asymmetry. Dev Dyn 2007; 236:853-61. [PMID: 17266133 DOI: 10.1002/dvdy.21070] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Polycomb group (PcG) proteins are required for maintaining the repressed state of developmentally important genes such as homeotic genes. Polycomblike (Pcl), a member of PcG genes with two characteristic PHD finger motifs, was shown to strongly enhance the effects of PcG genes in Drosophila. Three Pcl genes exist in the mouse genome, with their function largely unknown. Our previous studies demonstrate that the chick Pcl2 is essential for the left-right asymmetry by silencing Shh expression in the right side of the node (Wang et al., [2004b] Development 131:4381-4391). To elucidate the in vivo role of mouse Pcl2, we generated Pcl2 mutant mice. Phenotypic analyses indicate the normal development of left-right asymmetry in the Pcl2 mutant mice. However, Pcl2 mutant mice exhibit posterior transformation of axial skeletons and other phenotypic defects, with a relatively low penetrance. These results demonstrate that Pcl2 is dispensable for the normal left-right axis development in mice.
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Affiliation(s)
- Shusheng Wang
- Division of Developmental Biology, Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, USA
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838
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Greb T, Mylne JS, Crevillen P, Geraldo N, An H, Gendall AR, Dean C. The PHD Finger Protein VRN5 Functions in the Epigenetic Silencing of Arabidopsis FLC. Curr Biol 2007; 17:73-8. [PMID: 17174094 DOI: 10.1016/j.cub.2006.11.052] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 11/13/2006] [Accepted: 11/14/2006] [Indexed: 11/23/2022]
Abstract
Vernalization, the acceleration of flowering by the prolonged cold of winter, ensures that plants flower in favorable spring conditions. During vernalization in Arabidopsis, cold temperatures repress FLOWERING LOCUS C (FLC) expression in a mechanism involving VERNALIZATION INSENSITIVE 3 (VIN3), and this repression is epigenetically maintained by a Polycomb-like chromatin regulation involving VERNALIZATION 2 (VRN2), a Su(z)12 homolog, VERNALIZATION 1 (VRN1), and LIKE-HETEROCHROMATIN PROTEIN 1. In order to further elaborate how cold repression triggers epigenetic silencing, we have targeted mutations that result in FLC misexpression both at the end of the prolonged cold and after subsequent development. This identified VERNALIZATION 5 (VRN5), a PHD finger protein and homolog of VIN3. Our results suggest that during the prolonged cold, VRN5 and VIN3 form a heterodimer necessary for establishing the vernalization-induced chromatin modifications, histone deacetylation, and H3 lysine 27 trimethylation required for the epigenetic silencing of FLC. Double mutant and FLC misexpression analyses reveal additional VRN5 functions, both FLC-dependent and -independent, and indicate a spatial complexity to FLC epigenetic silencing with VRN5 acting as a common component in multiple pathways.
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Affiliation(s)
- Thomas Greb
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
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839
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Kitamura E, Igarashi J, Morohashi A, Hida N, Oinuma T, Nemoto N, Song F, Ghosh S, Held WA, Yoshida-Noro C, Nagase H. Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics 2006; 89:326-37. [PMID: 17188838 PMCID: PMC1847344 DOI: 10.1016/j.ygeno.2006.11.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/26/2006] [Accepted: 11/06/2006] [Indexed: 10/23/2022]
Abstract
Alterations in DNA methylation have been implicated in mammalian development. Hence, the identification of tissue-specific differentially methylated regions (TDMs) is indispensable for understanding its role. Using restriction landmark genomic scanning of six mouse tissues, 150 putative TDMs were identified and 14 were further analyzed. The DNA sequences of the 14 mouse TDMs are analyzed in this study. Six of the human homologous regions show TDMs to both mouse and human and genes in five of these regions have conserved tissue-specific expression: preferential expression in testis. A TDM, DDX4, is further analyzed in nine testis tissues. An increase in methylation of the promoter region is significantly associated with a marked reduction of the gene expression and defects in spermatogenesis, suggesting that hypomethylation of the DDX4 promoter region regulates DDX4 gene expression in spermatogenic cells. Our results indicate that some genomic regions with tissue-specific methylation and expression are conserved between mouse and human and suggest that DNA methylation may have an important role in regulating differentiation and tissue-/cell-specific gene expression of some genes.
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Affiliation(s)
- Eiko Kitamura
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Jun Igarashi
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Aiko Morohashi
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Naoko Hida
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Toshinori Oinuma
- Department of Pathology, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Norimichi Nemoto
- Department of Pathology, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Fei Song
- Department of Molecular and Cellular Biology, Elm and Carlton Streets, Buffalo, NY 14263
| | - Srimoyee Ghosh
- Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263
| | - William A. Held
- Department of Molecular and Cellular Biology, Elm and Carlton Streets, Buffalo, NY 14263
| | - Chikako Yoshida-Noro
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Hiroki Nagase
- Life Science, Advanced Research Institute for the Sciences and Humanities, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
- Cancer Genetics, Nihon, University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
- Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263
- *Corresponding author. Life Science, Advanced Research Institute for the Sciences and Humanities, Cancer Genetics, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo, 173-8610. Tel/Fax: +81-3-3972-8337. E-mail address: (H. Nagase)
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840
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Affiliation(s)
- Robert J Sims
- Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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841
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Wysocka J. Identifying novel proteins recognizing histone modifications using peptide pull-down assay. Methods 2006; 40:339-43. [PMID: 17101446 PMCID: PMC4491501 DOI: 10.1016/j.ymeth.2006.05.028] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 05/27/2006] [Indexed: 01/31/2023] Open
Abstract
Post-translational modifications of histones have been correlated with virtually all chromatin-templated processes, including gene expression regulation, DNA replication, mitosis and meiosis, and DNA repair. In order to better understand the mechanistic basis by which histone modifications participate in the control of cellular processes, it is essential to identify and characterize downstream effector proteins, or "readers", that are responsible for recognizing different marks and translating them into specific biological outcomes. Ideally, identification of potential histone-binding effectors should occur in an unbiased fashion. Although in the recent years much progress has been made in identifying readers of histone modifications, in particular methylation, recognition of the majority of known histone marks is still poorly understood. Here I describe a simple and unbiased biochemical pull-down assay that allows for the identification of novel histone effector proteins and utilizes biotinylated histone peptides modified at various residues. I provide detailed protocols and suggestions for troubleshooting.
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Affiliation(s)
- Joanna Wysocka
- Department of Molecular Pharmacology and Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, USA.
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842
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Shi X, Kachirskaia I, Walter KL, Kuo JHA, Lake A, Davrazou F, Chan SM, Martin DGE, Fingerman IM, Briggs SD, Howe L, Utz PJ, Kutateladze TG, Lugovskoy AA, Bedford MT, Gozani O. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem 2006; 282:2450-5. [PMID: 17142463 PMCID: PMC2735445 DOI: 10.1074/jbc.c600286200] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PHD finger motif is a signature chromatin-associated motif that is found throughout eukaryotic proteomes. Here we have determined the histone methyl-lysine binding activity of the PHD fingers present within the Saccharomyces cerevisiae proteome. We provide evidence on the genomic scale that PHD fingers constitute a general class of effector modules for histone H3 trimethylated at lysine 4 (H3K4me3) and histone H3 trimethylated at lysine 36 (H3K36me3). Structural modeling of PHD fingers demonstrates a conserved mechanism for recognizing the trimethyl moiety and provides insight into the molecular basis of affinity for the different methyl-histone ligands. Together, our study suggests that a common function for PHD fingers is to transduce methyl-lysine events and sheds light on how a single histone modification can be linked to multiple biological outcomes.
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Affiliation(s)
- Xiaobing Shi
- Department of Biological Sciences, Stanford University, Stanford, California 94305
| | - Ioulia Kachirskaia
- Department of Biological Sciences, Stanford University, Stanford, California 94305
| | - Kay L. Walter
- Department of Biological Sciences, Stanford University, Stanford, California 94305
| | - Jen-Hao A. Kuo
- Department of Biological Sciences, Stanford University, Stanford, California 94305
| | - Aimee Lake
- Department of Biological Sciences, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957
| | - Foteini Davrazou
- Department of Pharmacology, University Colorado Health Sciences Center, Aurora, Colorado 80045
| | - Steve M. Chan
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305
| | - David G. E. Martin
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ian M. Fingerman
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Scott D. Briggs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - LeAnn Howe
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University Colorado Health Sciences Center, Aurora, Colorado 80045
| | - Alexey A. Lugovskoy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Mark T. Bedford
- Department of Biological Sciences, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957
| | - Or Gozani
- Department of Biological Sciences, Stanford University, Stanford, California 94305
- Recipient of a Burroughs Wellcome Career Development Award in Biomedical Sciences. To whom correspondence should be addressed. Tel.: 650-799-0306; Fax: 650-725-8309; E-mail:
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843
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Palacios A, Garcia P, Padró D, López-Hernández E, Martín I, Blanco FJ. Solution structure and NMR characterization of the binding to methylated histone tails of the plant homeodomain finger of the tumour suppressor ING4. FEBS Lett 2006; 580:6903-8. [PMID: 17157298 DOI: 10.1016/j.febslet.2006.11.055] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 11/17/2006] [Accepted: 11/19/2006] [Indexed: 12/30/2022]
Abstract
Plant homeodomain (PHD) fingers are frequently present in proteins involved in chromatin remodelling, and some of them bind to histones. The family of proteins inhibitors of growth (ING) contains a PHD finger that bind to histone-3 trimethylated at lysine 4, and those of ING1 and ING2 also act as nuclear phosphoinositide receptors. We have determined the structure of ING4 PHD, and characterised its binding to phosphoinositides and histone methylated tails. In contrast to ING2, ING4 is not a phosphoinositide receptor and binds with similar affinity to the different methylation states of histone-3 at lysine 4.
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Affiliation(s)
- Alicia Palacios
- NMR Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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844
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Addis M, Meloni C, Congiu R, Santaniello S, Emma F, Zuffardi O, Ciccone R, Cao A, Melis MA, Cau M. A novel interstitial deletion in Xq25, identified by array-CGH in a patient with Lowe syndrome. Eur J Med Genet 2006; 50:79-84. [PMID: 17142121 DOI: 10.1016/j.ejmg.2006.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 10/17/2006] [Indexed: 11/15/2022]
Abstract
The oculocerebrorenal syndrome of Lowe (OCRL) (MIM:309000) is an X-linked multisystemic disorder affecting the eyes, nervous system and kidneys due to mutations in OCRL1 gene. The gene contains 24 exons, and encodes a 105kDa phosphatydylinositol 4,5-biphosphate [PtdIns(4,5)P(2)] 5-phosphatase localized primarily in the trans-Golgi network and the lysosomes. The large majority of the OCRL1 mutations producing Lowe syndrome are either missense mutations localized mainly in the catalytic domain or non-sense/frameshift mutations resulting in truncated proteins. Rarely, in about 6% of the cases, the disease results from large gene deletions occurring in the 5' part of the gene. Here we report a new case of a patient with Lowe syndrome due to a deletion of about 4Mb, encompassing the OCRL1 gene, detected by PCR and CGH array. The mother was carrier of the same deletion.
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Affiliation(s)
- Maria Addis
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, Via Jenner s/n, 09134 Cagliari, Italy
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845
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Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD. The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Mol Cell Biol 2006; 27:721-31. [PMID: 17088384 PMCID: PMC1800795 DOI: 10.1128/mcb.01628-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me). This modification marks the 5' end of transcribed genes in a 5'-to-3' tri- to di- to monomethyl gradient and promotes association of chromatin-remodeling and histone-modifying enzymes. Here we show that Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II), regulates H3K4 methylation. We found that CTK1 deletion nearly abolished H3K4 monomethylation yet caused a significant increase in H3K4 di- and trimethylation. Both in individual genes and genome-wide, loss of CTK1 disrupted the H3K4 methylation patterns normally observed. H3K4me2 and H3K4me3 spread 3' into the bodies of genes, while H3K4 monomethylation was diminished. These effects were dependent on the catalytic activity of Ctk1 but are independent of Set2-mediated H3K36 methylation. Furthermore, these effects are not due to spurious transcription initiation in the bodies of genes, to changes in RNAP II occupancy, to changes in serine 5 CTD phosphorylation patterns, or to "transcriptional stress." These data show that Ctk1 acts to restrict the spread of H3K4 methylation through a mechanism that is independent of a general transcription defect. The evidence presented suggests that Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone deacetylation, and preventing the 3' spread of H3K4 trimethylation, a mark associated with transcriptional initiation.
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Affiliation(s)
- Tiaojiang Xiao
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, 405 Mary Ellen Jones, Chapel Hill, NC 27599-7260, USA
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846
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Couture JF, Trievel RC. Histone-modifying enzymes: encrypting an enigmatic epigenetic code. Curr Opin Struct Biol 2006; 16:753-60. [PMID: 17070031 DOI: 10.1016/j.sbi.2006.10.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 09/14/2006] [Accepted: 10/13/2006] [Indexed: 10/24/2022]
Abstract
Histone-modifying enzymes catalyze a diverse array of post-translational modifications of core and linker histones within chromatin. These modifications govern a multitude of genomic functions, particularly gene expression, and are believed to constitute an epigenetic code. Histone-modifying enzymes inscribe this code by catalyzing site-selective modifications, which are subsequently interpreted by effector proteins that recognize specific covalent marks. The substrate specificity of these enzymes is of fundamental biological importance because it underpins this epigenetic code. Recently, the structural basis of this specificity has been examined with regards to recently determined structures of GCN5 acetyltransferases and SET domain methyltransferases in complex with their cognate histone substrates.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0606, USA
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847
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Dacwag CS, Ohkawa Y, Pal S, Sif S, Imbalzano AN. The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling. Mol Cell Biol 2006; 27:384-94. [PMID: 17043109 PMCID: PMC1800640 DOI: 10.1128/mcb.01528-06] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Skeletal muscle differentiation requires the coordinated activity of transcription factors, histone modifying enzymes, and ATP-dependent chromatin remodeling enzymes. The type II protein arginine methyltransferase Prmt5 symmetrically dimethylates histones H3 and H4 and numerous nonchromatin proteins, and prior work has implicated Prmt5 in transcriptional repression. Here we demonstrate that MyoD-induced muscle differentiation requires Prmt5. One of the first genes activated during differentiation encodes the myogenic regulator myogenin. Prmt5 and dimethylated H3R8 (histone 3 arginine 8) are localized at the myogenin promoter in differentiating cells. Modification of H3R8 required Prmt5, and reduction of Prmt5 resulted in the abrogation of promoter binding by the Brg1 ATPase-associated with the SWI/SNF chromatin remodeling enzymes and all subsequent events associated with gene activation, including increases in chromatin accessibility and stable binding by MyoD. Prmt5 and dimethylated H3R8 were also associated with the myogenin promoter in activated satellite cells isolated from muscle tissue, further demonstrating the physiological relevance of these observations. The data indicate that Prmt5 facilitates myogenesis because it is required for Brg1-dependent chromatin remodeling and gene activation at a locus essential for differentiation. We therefore conclude that a histone modifying enzyme is necessary to permit an ATP-dependent chromatin remodeling enzyme to function.
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Affiliation(s)
- Caroline S Dacwag
- Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
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848
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Lee S, Lee DK, Dou Y, Lee J, Lee B, Kwak E, Kong YY, Lee SK, Roeder RG, Lee JW. Coactivator as a target gene specificity determinant for histone H3 lysine 4 methyltransferases. Proc Natl Acad Sci U S A 2006; 103:15392-7. [PMID: 17021013 PMCID: PMC1622834 DOI: 10.1073/pnas.0607313103] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Activating signal cointegrator-2 (ASC-2), a coactivator of multiple transcription factors that include retinoic acid receptor (RAR), associates with histone H3-K4 methyltranferases (H3K4MTs) MLL3 and MLL4 in mixed-lineage leukemia. Here, we show that mice expressing a SET domain mutant of MLL3 share phenotypes with isogenic ASC2+/- mice and that expression and H3-K4 trimethylation of RAR target gene RAR-beta2 are impaired in ASC-2-null mouse embryo fibroblasts (MEFs) or in MEFs expressing siRNAs against both MLL3 and MLL4. We also show that MLL3 and MLL4 are found in distinct ASC-2-containing complexes rather than in a common ASC-2 complex, and they are recruited to RAR-beta2 by ASC-2. In contrast, RAR-beta2 expression is intact in MEFs devoid of menin, a component of MLL1 and MLL2 H3K4MT complexes. These results suggest that ASC-2 confers target gene specificity to MLL3 and MLL4 H3K4MT complexes and that recruitment of H3K4MTs to their target genes generally involves interactions between integral components of H3K4MT complexes and transcription factors.
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Affiliation(s)
| | - Dong-Kee Lee
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, and
| | - Yali Dou
- Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, NY 10021; and
| | - Jeongkyung Lee
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, and
| | - Bora Lee
- *Deparment of Molecular and Cellular Biology
| | - Eunyee Kwak
- Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Young-Yun Kong
- Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Soo-Kyung Lee
- *Deparment of Molecular and Cellular Biology
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Robert G. Roeder
- Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, NY 10021; and
- To whom correspondence may be addressed. E-mail:
| | - Jae W. Lee
- *Deparment of Molecular and Cellular Biology
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, and
- **To whom correspondence may be addressed at: Department of Medicine, Baylor College of Medicine, Houston, TX 77030. E-mail:
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849
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Gearhart MD, Corcoran CM, Wamstad JA, Bardwell VJ. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol Cell Biol 2006; 26:6880-9. [PMID: 16943429 PMCID: PMC1592854 DOI: 10.1128/mcb.00630-06] [Citation(s) in RCA: 265] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The corepressor BCOR potentiates transcriptional repression by the proto-oncoprotein BCL6 and suppresses the transcriptional activity of a common mixed-lineage leukemia fusion partner, AF9. Mutations in human BCOR cause male lethal, X-linked oculofaciocardiodental syndrome. We identified a BCOR complex containing Polycomb group (PcG) and Skp-Cullin-F-box subcomplexes. The PcG proteins include RING1, RYBP, NSPC1, a Posterior Sex Combs homolog, and RNF2, an E3 ligase for the mono-ubiquitylation of H2A. BCOR complex components and mono-ubiquitylated H2A localize to BCL6 targets, indicating that the BCOR complex employs PcG proteins to expand the repertoire of enzymatic activities that can be recruited by BCL6. This also suggests that BCL6 can target PcG proteins to DNA. In addition, the BCOR complex contains components of a second ubiquitin E3 ligase, namely, SKP1 and FBXL10 (JHDM1B). We show that BCOR coimmunoprecipitates isoforms of FBXL10 which contain a JmjC domain that recently has been determined to have histone H3K36 demethylase activity. The recruitment of two distinct classes of E3 ubiquitin ligases and a histone demethylase by BCOR suggests that BCOR uses a unique combination of epigenetic modifications to direct gene silencing.
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Affiliation(s)
- Micah D Gearhart
- Department of Genetics, Cell Biology and Development, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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850
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Porras-Yakushi TR, Whitelegge JP, Clarke S. A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10. J Biol Chem 2006; 281:35835-45. [PMID: 17005568 DOI: 10.1074/jbc.m606578200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal protein L12ab (Rpl12ab) in Saccharomyces cerevisiae is modified by methylation at both arginine and lysine residues. Although the enzyme responsible for the modification reaction at arginine 66 has been identified (Rmt2), the enzyme(s) responsible for the lysine modification(s) has not been found, and the site(s) of methylation has not been determined. Here we demonstrate, using a combination of mass spectrometry and labeling assays, that the yeast gene YDR198c encodes the enzyme responsible for the predominant epsilon-trimethylation at lysine 10 in Rpl12ab. An additional site of predominant epsilon-dimethylation is observed at lysine 3; the enzyme catalyzing this modification is not known. The YDR198c gene encodes a SET domain similar to that of the Rkm1 enzyme responsible for modifying Rpl23ab, and we have now designated the YDR198c gene product as Rkm2 (ribosomal lysine methyltransferase 2). The effect of the loss of the enzyme on ribosomal complex stability was studied by polysomal fractionation. However, no difference was observed between the Deltarkm2 deletion strain and its parent wild type strain. With the identification of this enzyme, it appears that the 12 SET domain family members in yeast can now be divided into two subfamilies based on function and amino acid sequence identity. One branch includes enzymes that modify histones, including Set1 and Set2; the other branch includes Rkm1, Rkm2, and Ctm1, the cytochrome c methyltransferase. These studies suggest that the remaining seven SET domain proteins may also be lysine methyltransferases.
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Affiliation(s)
- Tanya R Porras-Yakushi
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569, USA
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