How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers

[1]  Wolfgang Fischle,et al.  Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. , 2007, Molecular cell.

[2]  John A Latham,et al.  Cross-regulation of histone modifications , 2007, Nature Structural &Molecular Biology.

[3]  Yingming Zhao,et al.  JMJD6 Is a Histone Arginine Demethylase , 2007, Science.

[4]  Jürg Bähler,et al.  Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation , 2007, Nature.

[5]  E. Guccione,et al.  Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive , 2007, Nature.

[6]  Matthias Mann,et al.  Selective Anchoring of TFIID to Nucleosomes by Trimethylation of Histone H3 Lysine 4 , 2007, Cell.

[7]  T. Swigut,et al.  H3K27 Demethylases, at Long Last , 2007, Cell.

[8]  B. Cairns,et al.  Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. , 2007, Molecular cell.

[9]  Min Gyu Lee,et al.  p53 is regulated by the lysine demethylase LSD1 , 2007, Nature.

[10]  C. Allis,et al.  Chromatin remodeling and cancer, Part I: Covalent histone modifications. , 2007, Trends in molecular medicine.

[11]  V. Pirrotta,et al.  CHD1 Motor Protein Is Required for Deposition of Histone Variant H3.3 into Chromatin in Vivo , 2007, Science.

[12]  B. Chait,et al.  Methylation of a histone mimic within the histone methyltransferase G9a regulates protein complex assembly. , 2007, Molecular cell.

[13]  Yang Shi,et al.  Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression , 2007, Nature.

[14]  C. Allis,et al.  DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA , 2007, Nature.

[15]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[16]  Monika S. Kowalczyk,et al.  Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX , 2007, Proceedings of the National Academy of Sciences.

[17]  R. Young,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[18]  S. Khorasanizadeh,et al.  Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect , 2007, Proceedings of the National Academy of Sciences.

[19]  M. Nussenzweig,et al.  Chromatin dynamics and the preservation of genetic information , 2007, Nature.

[20]  J. Gaudet,et al.  Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity. , 2007, Cancer cell.

[21]  Neil L Kelleher,et al.  Pervasive combinatorial modification of histone H3 in human cells , 2007, Nature Methods.

[22]  D. Reinberg,et al.  L3MBTL1, a Histone-Methylation-Dependent Chromatin Lock , 2007, Cell.

[23]  S. Berger.  The complex language of chromatin regulation during transcription , 2007, Nature.

[24]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

[25]  Bing Li,et al.  Combined Action of PHD and Chromo Domains Directs the Rpd3S HDAC to Transcribed Chromatin , 2007, Science.

[26]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[27]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[28]  Alan J Tackett,et al.  Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini , 2007, Proceedings of the National Academy of Sciences.

[29]  M. Horikoshi,et al.  Structural polymorphism of chromodomains in Chd1. , 2007, Journal of molecular biology.

[30]  Yang Shi,et al.  Dynamic regulation of histone lysine methylation by demethylases. , 2007, Molecular cell.

[31]  C. Allis,et al.  Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. , 2007, Molecular cell.

[32]  Georges Mer,et al.  Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair , 2006, Cell.

[33]  John D Aitchison,et al.  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. , 2006, Molecular cell.

[34]  Michael Grunstein,et al.  Histone H2B deacetylation at lysine 11 is required for yeast apoptosis induced by phosphorylation of H2B at serine 10. , 2006, Molecular cell.

[35]  Alexey Bochkarev,et al.  Structural basis for molecular recognition and presentation of histone H3 By WDR5 , 2006, The EMBO journal.

[36]  Yi Zhang,et al.  JmjC-domain-containing proteins and histone demethylation , 2006, Nature Reviews Genetics.

[37]  Michael Grunstein,et al.  Genome-wide patterns of histone modifications in yeast , 2006, Nature Reviews Molecular Cell Biology.

[38]  Or Gozani,et al.  The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3 , 2006, Molecular and Cellular Biology.

[39]  Thomas A Milne,et al.  Regulation of MLL1 H3K4 methyltransferase activity by its core components , 2006, Nature Structural &Molecular Biology.

[40]  Paul Tempst,et al.  The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36 , 2006, Nature.

[41]  Jean-François Couture,et al.  Molecular recognition of histone H3 by the WD40 protein WDR5 , 2006, Nature Structural &Molecular Biology.

[42]  D. Patel,et al.  Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF , 2006, Nature.

[43]  Anjanabha Saha,et al.  ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression , 2006, Nature.

[44]  Thomas A. Milne,et al.  A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling , 2006, Nature.

[45]  V. Verkhusha,et al.  Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 , 2006, Nature.

[46]  D. Patel,et al.  Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex , 2006, Nature Structural &Molecular Biology.

[47]  T. Pawson,et al.  Reading protein modifications with interaction domains , 2006, Nature Reviews Molecular Cell Biology.

[48]  A. Baldwin,et al.  The Kinases MSK1 and MSK2 Are Required for Epidermal Growth Factor-induced, but Not Tumor Necrosis Factor-induced, Histone H3 Ser10 Phosphorylation* , 2006, Journal of Biological Chemistry.

[49]  Yi Zhang,et al.  Recognition of Histone H3 Lysine-4 Methylation by the Double Tudor Domain of JMJD2A , 2006, Science.

[50]  Yang Shi,et al.  Reversal of Histone Lysine Trimethylation by the JMJD2 Family of Histone Demethylases , 2006, Cell.

[51]  M. Bottomley,et al.  Structure and functional analysis of the MYND domain. , 2006, Journal of molecular biology.

[52]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[53]  Xing Wang Deng,et al.  Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. , 2006, Molecular cell.

[54]  Yi Zhang,et al.  Tudor, MBT and chromo domains gauge the degree of lysine methylation , 2006, EMBO reports.

[55]  M. Pazin,et al.  Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions , 2006, Science.

[56]  Song Tan,et al.  ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. , 2006, Molecular cell.

[57]  B. Garcia,et al.  Expression Patterns and Post-translational Modifications Associated with Mammalian Histone H3 Variants* , 2006, Journal of Biological Chemistry.

[58]  M. Bienz.  The PHD finger, a nuclear protein-interaction domain. , 2006, Trends in biochemical sciences.

[59]  M. Yaffe,et al.  MDC1 Directly Binds Phosphorylated Histone H2AX to Regulate Cellular Responses to DNA Double-Strand Breaks , 2008, Cell.

[60]  Danny Reinberg,et al.  Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains* , 2005, Journal of Biological Chemistry.

[61]  Kevin Struhl,et al.  Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. , 2005, Molecular cell.

[62]  S. Khorasanizadeh,et al.  Double chromodomains cooperate to recognize the methylated histone H3 tail , 2005, Nature.

[63]  Jesse J. Lipp,et al.  Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin , 2005, Nature.

[64]  Benjamin A. Garcia,et al.  Regulation of HP1–chromatin binding by histone H3 methylation and phosphorylation , 2005, Nature.

[65]  Bing Li,et al.  Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription , 2005, Cell.

[66]  Cyrus Martin,et al.  The diverse functions of histone lysine methylation , 2005, Nature Reviews Molecular Cell Biology.

[67]  G. Orphanides,et al.  Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. , 2005, Molecular cell.

[68]  J. Glover,et al.  Structure of the BRCT Repeat Domain of MDC1 and Its Specificity for the Free COOH-terminal End of the γ-H2AX Histone Tail* , 2005, Journal of Biological Chemistry.

[69]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[70]  Thomas A. Milne,et al.  WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development , 2005, Cell.

[71]  Robert E Collins,et al.  Structural and sequence motifs of protein (histone) methylation enzymes. , 2005, Annual review of biophysics and biomolecular structure.

[72]  John R. Yates,et al.  Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation , 2005, Nature.

[73]  Sung-Hee Ahn,et al.  Sterile 20 Kinase Phosphorylates Histone H2B at Serine 10 during Hydrogen Peroxide-Induced Apoptosis in S. cerevisiae , 2005, Cell.

[74]  J. T. Kadonaga,et al.  Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly , 2005, Nature Structural &Molecular Biology.

[75]  Yang Shi,et al.  Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1 , 2004, Cell.

[76]  J. Mata,et al.  Methylation of Histone H4 Lysine 20 Controls Recruitment of Crb2 to Sites of DNA Damage , 2004, Cell.

[77]  Tom J. Petty,et al.  Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks , 2004, Nature.

[78]  Jef D Boeke,et al.  Regulated nucleosome mobility and the histone code , 2004, Nature Structural &Molecular Biology.

[79]  Danny Reinberg,et al.  Elongation by RNA polymerase II: the short and long of it. , 2004, Genes & development.

[80]  Steven Clarke,et al.  Human PAD4 Regulates Histone Arginine Methylation Levels via Demethylimination , 2004, Science.

[81]  Paul Tempst,et al.  Histone Deimination Antagonizes Arginine Methylation , 2004, Cell.

[82]  W. Herr,et al.  Leukemia Proto-Oncoprotein MLL Forms a SET1-Like Histone Methyltransferase Complex with Menin To Regulate Hox Gene Expression , 2004, Molecular and Cellular Biology.

[83]  R. Roeder,et al.  Ordered Cooperative Functions of PRMT1, p300, and CARM1 in Transcriptional Activation by p53 , 2004, Cell.

[84]  Drew M. Lowery,et al.  Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer , 2004, Nature Structural &Molecular Biology.

[85]  D. Morrison,et al.  Unlocking the code of 14-3-3 , 2004, Journal of Cell Science.

[86]  Victor G Corces,et al.  Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation. , 2004, Trends in genetics : TIG.

[87]  H. Szerlong,et al.  Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 , 2004, The EMBO journal.

[88]  Wolfgang Fischle,et al.  Binary switches and modification cassettes in histone biology and beyond , 2003, Nature.

[89]  J. Min,et al.  Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. , 2003, Genes & development.

[90]  Youngchang Kim,et al.  Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. , 2003, Genes & development.

[91]  D. Patel,et al.  Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets. , 2003, Structure.

[92]  Geng Wu,et al.  Structure of a -TrCP1-Skp1--Catenin Complex , 2003 .

[93]  Stuart Thomson,et al.  MSK2 and MSK1 mediate the mitogen‐ and stress‐induced phosphorylation of histone H3 and HMG‐14 , 2003, The EMBO journal.

[94]  P. Boccuni,et al.  The Human L(3)MBT Polycomb Group Protein Is a Transcriptional Repressor and Interacts Physically and Functionally with TEL (ETV6)* , 2003, The Journal of Biological Chemistry.

[95]  Michael Sattler,et al.  High-resolution X-ray and NMR structures of the SMN Tudor domain: conformational variation in the binding site for symmetrically dimethylated arginine residues. , 2003, Journal of molecular biology.

[96]  Phang-lang Chen,et al.  NFBD1, Like 53BP1, Is an Early and Redundant Transducer Mediating Chk2 Phosphorylation in Response to DNA Damage* , 2003, The Journal of Biological Chemistry.

[97]  Sebastian Maurer-Stroh,et al.  The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. , 2003, Trends in biochemical sciences.

[98]  Geng Wu,et al.  Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. , 2003, Molecular cell.

[99]  Stuart L. Schreiber,et al.  Active genes are tri-methylated at K4 of histone H3 , 2002, Nature.

[100]  R. Shiekhattar,et al.  A core–BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[101]  Alexey G. Murzin,et al.  Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9 , 2002, Nature.

[102]  S. Jacobs,et al.  Structure of HP1 Chromodomain Bound to a Lysine 9-Methylated Histone H3 Tail , 2002, Science.

[103]  Ming-Ming Zhou,et al.  Bromodomain: an acetyl‐lysine binding domain , 2002, FEBS letters.

[104]  T. Bestor,et al.  Dnmt3L and the Establishment of Maternal Genomic Imprints , 2001, Science.

[105]  Michael M. Murphy,et al.  ATM Phosphorylates Histone H2AX in Response to DNA Double-strand Breaks* , 2001, The Journal of Biological Chemistry.

[106]  N. Brown.  Faculty Opinions recommendation of Crystal structure of the extracellular segment of integrin alpha Vbeta3. , 2001 .

[107]  Sean D. Taverna,et al.  Specificity of the HP1 chromo domain for the methylated N‐terminus of histone H3 , 2001, The EMBO journal.

[108]  Thilo Stehle,et al.  Crystal Structure of the Extracellular Segment of Integrin αVβ3 , 2001, Science.

[109]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[110]  Brian D. Strahl,et al.  Methylation of histone H4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator PRMT1 , 2001, Current Biology.

[111]  C. Allis,et al.  Methylation of Histone H4 at Arginine 3 Facilitating Transcriptional Activation by Nuclear Hormone Receptor , 2001, Science.

[112]  P. Chambon,et al.  Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. , 2001, Molecular cell.

[113]  Karl Mechtler,et al.  Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins , 2001, Nature.

[114]  Andrew J. Bannister,et al.  Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain , 2001, Nature.

[115]  R. Shiekhattar,et al.  A Human BRCA2 Complex Containing a Structural DNA Binding Component Influences Cell Cycle Progression , 2001, Cell.

[116]  G. Stier,et al.  SMN Tudor domain structure and its interaction with the Sm proteins , 2001, Nature Structural Biology.

[117]  P. Evans,et al.  The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p , 2000, The EMBO journal.

[118]  C. Allis,et al.  Signaling to Chromatin through Histone Modifications , 2000, Cell.

[119]  C. Allis,et al.  Heterochromatin protein 1 binds to nucleosomes and DNA in vitro. , 2000, The Journal of biological chemistry.

[120]  Zu-Wen Sun,et al.  Mitotic Phosphorylation of Histone H3 Is Governed by Ipl1/aurora Kinase and Glc7/PP1 Phosphatase in Budding Yeast and Nematodes , 2000, Cell.

[121]  C. Allis,et al.  Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. , 2000, Molecular cell.

[122]  R. Tjian,et al.  Structure and function of a human TAFII250 double bromodomain module. , 2000, Science.

[123]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[124]  M. J. Barratt,et al.  The nucleosomal response associated with immediate‐early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG‐14 kinase , 1999, The EMBO journal.

[125]  H. Saya,et al.  A human homolog of Drosophila lethal(3)malignant brain tumor (l(3)mbt) protein associates with condensed mitotic chromosomes , 1999, Oncogene.

[126]  Lei Zeng,et al.  Structure and ligand of a histone acetyltransferase bromodomain , 1999, Nature.

[127]  A. Wolffe,et al.  Chromatin disruption and modification. , 1999, Nucleic acids research.

[128]  E. Li,et al.  Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases , 1998, Nature Genetics.

[129]  E. Rogakou,et al.  DNA Double-stranded Breaks Induce Histone H2AX Phosphorylation on Serine 139* , 1998, The Journal of Biological Chemistry.

[130]  Bruce Stillman,et al.  Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase , 1998, Current Biology.

[131]  M. Yaffe,et al.  The Structural Basis for 14-3-3:Phosphopeptide Binding Specificity , 1997, Cell.

[132]  G. Mizuguchi,et al.  Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. , 1997, Molecular cell.

[133]  D. A. Dougherty,et al.  The Cationminus signpi Interaction. , 1997, Chemical reviews.

[134]  V. Pirrotta,et al.  Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. , 1997, Trends in genetics : TIG.

[135]  A. Wolffe,et al.  Histone acetylation: influence on transcription, nucleosome mobility and positioning, and linker histone‐dependent transcriptional repression , 1997, The EMBO journal.

[136]  C. Allis,et al.  Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines , 1996, Nature.

[137]  D. Edmondson,et al.  Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. , 1996, Genes & development.

[138]  S. Schreiber,et al.  A Mammalian Histone Deacetylase Related to the Yeast Transcriptional Regulator Rpd3p , 1996, Science.

[139]  C. Allis,et al.  Tetrahymena Histone Acetyltransferase A: A Homolog to Yeast Gcn5p Linking Histone Acetylation to Gene Activation , 1996, Cell.

[140]  P. Allen,et al.  Interaction of 14-3-3 with Signaling Proteins Is Mediated by the Recognition of Phosphoserine , 1996, Cell.

[141]  Carl Wu,et al.  Purification and properties of an ATP-dependent nucleosome remodeling factor , 1995, Cell.

[142]  S. Sprang,et al.  The structure of the G protein heterotrimer Giα1 β 1 γ 2 , 1995, Cell.

[143]  S. Sprang,et al.  The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. , 1995, Cell.

[144]  R. Paro,et al.  The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[145]  G. Petsko,et al.  Weakly polar interactions in proteins. , 1988, Advances in protein chemistry.

[146]  V. Ingram,et al.  Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[147]  A. Razin,et al.  Substrate and sequence specificity of a eukaryotic DNA methylase , 1982, Nature.

[148]  C. Allis,et al.  Proteolytic processing of histone H3 in chromatin: a physiologically regulated event in tetrahymena micronuclei , 1980, Cell.

[149]  R. Smith,et al.  Occurrence and distribution of acid-labile histone phosphates in regenerating rat liver. , 1974, Biochemistry.

[150]  A. Mirsky,et al.  ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[151]  N. Young.  The Short and the Long of it , 1955 .