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  • 1
    Publication Date: 2010-05-04
    Description: Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1-4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182123/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182123/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheuermann, Johanna C -- de Ayala Alonso, Andres Gaytan -- Oktaba, Katarzyna -- Ly-Hartig, Nga -- McGinty, Robert K -- Fraterman, Sven -- Wilm, Matthias -- Muir, Tom W -- Muller, Jurg -- R01 GM086868/GM/NIGMS NIH HHS/ -- R01 GM086868-13/GM/NIGMS NIH HHS/ -- RC2 CA148354/CA/NCI NIH HHS/ -- RC2 CA148354-02/CA/NCI NIH HHS/ -- RC2CA148354/CA/NCI NIH HHS/ -- England -- Nature. 2010 May 13;465(7295):243-7. doi: 10.1038/nature08966. Epub 2010 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20436459" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Biocatalysis ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/embryology/*enzymology/genetics/metabolism ; Gene Silencing ; Genes, Homeobox/genetics ; Genes, Insect/genetics ; Genetic Complementation Test ; Histones/*metabolism ; Humans ; Multiprotein Complexes/chemistry/isolation & purification/*metabolism ; Nucleosomes/chemistry/metabolism ; Polycomb Repressive Complex 1 ; Repressor Proteins/genetics/isolation & purification/*metabolism ; Ubiquitin/metabolism ; Ubiquitin Thiolesterase/chemistry/genetics/*metabolism ; Ubiquitination/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2008-05-02
    Description: Numerous post-translational modifications of histones have been described in organisms ranging from yeast to humans. Growing evidence for dynamic regulation of these modifications, position- and modification-specific protein interactions, and biochemical crosstalk between modifications has strengthened the 'histone code' hypothesis, in which histone modifications are integral to choreographing the expression of the genome. One such modification, ubiquitylation of histone H2B (uH2B) on lysine 120 (K120) in humans, and lysine 123 in yeast, has been correlated with enhanced methylation of lysine 79 (K79) of histone H3 (refs 5-8), by K79-specific methyltransferase Dot1 (KMT4). However, the specific function of uH2B in this crosstalk pathway is not understood. Here we demonstrate, using chemically ubiquitylated H2B, a direct stimulation of hDot1L-mediated intranucleosomal methylation of H3 K79. Two traceless orthogonal expressed protein ligation (EPL) reactions were used to ubiquitylate H2B site-specifically. This strategy, using a photolytic ligation auxiliary and a desulphurization reaction, should be generally applicable to the chemical ubiquitylation of other proteins. Reconstitution of our uH2B into chemically defined nucleosomes, followed by biochemical analysis, revealed that uH2B directly activates methylation of H3 K79 by hDot1L. This effect is mediated through the catalytic domain of hDot1L, most likely through allosteric mechanisms. Furthermore, asymmetric incorporation of uH2B into dinucleosomes showed that the enhancement of methylation was limited to nucleosomes bearing uH2B. This work demonstrates a direct biochemical crosstalk between two modifications on separate histone proteins within a nucleosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774535/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774535/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McGinty, Robert K -- Kim, Jaehoon -- Chatterjee, Champak -- Roeder, Robert G -- Muir, Tom W -- GM07739/GM/NIGMS NIH HHS/ -- R01 GM086868/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 5;453(7196):812-6. doi: 10.1038/nature06906. Epub 2008 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18449190" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Catalytic Domain ; Histones/chemical synthesis/*metabolism ; Humans ; Lysine/metabolism ; Methylation ; Methyltransferases/genetics/*metabolism ; Nucleosomes/chemistry/*metabolism ; Ubiquitin/*metabolism ; Xenopus
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1994-11-04
    Description: A simple technique has been devised that allows the direct synthesis of native backbone proteins of moderate size. Chemoselective reaction of two unprotected peptide segments gives an initial thioester-linked species. Spontaneous rearrangement of this transient intermediate yields a full-length product with a native peptide bond at the ligation site. The utility of native chemical ligation was demonstrated by the one-step preparation of a cytokine containing multiple disulfides. The polypeptide ligation product was folded and oxidized to form the native disulfide-containing protein molecule. Native chemical ligation is an important step toward the general application of chemistry to proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dawson, P E -- Muir, T W -- Clark-Lewis, I -- Kent, S B -- GM 50969-01/GM/NIGMS NIH HHS/ -- GM48870-03/GM/NIGMS NIH HHS/ -- GM48897-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 4;266(5186):776-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Humans ; Interleukin-8/*chemical synthesis/chemistry ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Conformation ; *Protein Folding ; Proteins/*chemical synthesis/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2006-11-11
    Description: Potassium channels are K+-selective protein pores in cell membrane. The selectivity filter is the functional unit that allows K+ channels to distinguish potassium (K+) and sodium (Na+) ions. The filter's structure depends on whether K+ or Na+ ions are bound inside it. We synthesized a K+ channel containing the d-enantiomer of alanine in place of a conserved glycine and found by x-ray crystallography that its filter maintains the K+ (conductive) structure in the presence of Na+ and very low concentrations of K+. This channel conducts Na+ in the absence of K+ but not in the presence of K+. These findings demonstrate that the ability of the channel to adapt its structure differently to K+ and Na+ is a fundamental aspect of ion selectivity, as is the ability of multiple K+ ions to compete effectively with Na+ for the conductive filter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valiyaveetil, Francis I -- Leonetti, Manuel -- Muir, Tom W -- Mackinnon, Roderick -- EB001991/EB/NIBIB NIH HHS/ -- GM43949/GM/NIGMS NIH HHS/ -- GM55843/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):1004-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Neurobiology and Biophysics and Synthetic Protein Chemistry, Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095703" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Electrophysiology ; Lipid Bilayers ; Liposomes ; Models, Molecular ; Potassium/*metabolism ; Potassium Channels/*chemistry/*metabolism ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2013-03-30
    Description: Sequencing of pediatric gliomas has identified missense mutations Lys27Met (K27M) and Gly34Arg/Val (G34R/V) in genes encoding histone H3.3 (H3F3A) and H3.1 (HIST3H1B). We report that human diffuse intrinsic pontine gliomas (DIPGs) containing the K27M mutation display significantly lower overall amounts of H3 with trimethylated lysine 27 (H3K27me3) and that histone H3K27M transgenes are sufficient to reduce the amounts of H3K27me3 in vitro and in vivo. We find that H3K27M inhibits the enzymatic activity of the Polycomb repressive complex 2 through interaction with the EZH2 subunit. In addition, transgenes containing lysine-to-methionine substitutions at other known methylated lysines (H3K9 and H3K36) are sufficient to cause specific reduction in methylation through inhibition of SET-domain enzymes. We propose that K-to-M substitutions may represent a mechanism to alter epigenetic states in a variety of pathologies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951439/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951439/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, Peter W -- Muller, Manuel M -- Koletsky, Matthew S -- Cordero, Francisco -- Lin, Shu -- Banaszynski, Laura A -- Garcia, Benjamin A -- Muir, Tom W -- Becher, Oren J -- Allis, C David -- DP2OD007447/OD/NIH HHS/ -- GM040922/GM/NIGMS NIH HHS/ -- R01 GM040922/GM/NIGMS NIH HHS/ -- R01 GM107047/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 17;340(6134):857-61. doi: 10.1126/science.1232245. Epub 2013 Mar 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539183" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Brain Neoplasms/*enzymology/*genetics ; Child ; *Epigenesis, Genetic ; Glioblastoma/*enzymology/*genetics ; HEK293 Cells ; Histones/*genetics/metabolism ; Humans ; Lysine/genetics ; Methionine/genetics ; Methylation ; Mice ; Mutation, Missense ; Polycomb Repressive Complex 2/*antagonists & inhibitors/metabolism ; Transgenes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2016-05-14
    Description: Several types of pediatric cancers reportedly contain high-frequency missense mutations in histone H3, yet the underlying oncogenic mechanism remains poorly characterized. Here we report that the H3 lysine 36-to-methionine (H3K36M) mutation impairs the differentiation of mesenchymal progenitor cells and generates undifferentiated sarcoma in vivo. H3K36M mutant nucleosomes inhibit the enzymatic activities of several H3K36 methyltransferases. Depleting H3K36 methyltransferases, or expressing an H3K36I mutant that similarly inhibits H3K36 methylation, is sufficient to phenocopy the H3K36M mutation. After the loss of H3K36 methylation, a genome-wide gain in H3K27 methylation leads to a redistribution of polycomb repressive complex 1 and de-repression of its target genes known to block mesenchymal differentiation. Our findings are mirrored in human undifferentiated sarcomas in which novel K36M/I mutations in H3.1 are identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Chao -- Jain, Siddhant U -- Hoelper, Dominik -- Bechet, Denise -- Molden, Rosalynn C -- Ran, Leili -- Murphy, Devan -- Venneti, Sriram -- Hameed, Meera -- Pawel, Bruce R -- Wunder, Jay S -- Dickson, Brendan C -- Lundgren, Stefan M -- Jani, Krupa S -- De Jay, Nicolas -- Papillon-Cavanagh, Simon -- Andrulis, Irene L -- Sawyer, Sarah L -- Grynspan, David -- Turcotte, Robert E -- Nadaf, Javad -- Fahiminiyah, Somayyeh -- Muir, Tom W -- Majewski, Jacek -- Thompson, Craig B -- Chi, Ping -- Garcia, Benjamin A -- Allis, C David -- Jabado, Nada -- Lewis, Peter W -- DP2CA174499/CA/NCI NIH HHS/ -- DP2OD007447/OD/NIH HHS/ -- K08CA151660/CA/NCI NIH HHS/ -- K08CA181475/CA/NCI NIH HHS/ -- P01CA196539/CA/NCI NIH HHS/ -- P30CA008748/CA/NCI NIH HHS/ -- R01GM110174/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2016 May 13;352(6287):844-9. doi: 10.1126/science.aac7272.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. ; Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA. ; Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. ; Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. ; Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. ; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. ; University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Surgical Oncology and Division of Orthopedic Surgery, Princess Margaret Hospital, University of Toronto, Toronto, Ontario M5T 2M9, Canada. ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. ; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada. ; Department of Medical Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada. ; Division of Orthopaedic Surgery, Montreal General Hospital, McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada. ; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA. ; Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. ; Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu. ; Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. Department of Pediatrics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu. ; Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27174990" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2013-08-26
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2009-06-18
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2012-04-23
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2004-11-24
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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