The bromodomain interaction module

ε‐N‐acetylation of lysine residues (Kac) is one of the most abundant post‐translation modifications (PTMs) in the human proteome. In the nucleus, acetylation of histones has been linked to transcriptional activation of genes but the functional consequences of most acetylation events and proteins recruited to these sites remains largely unknown. Bromodomains (BRDs) are small helical interaction modules that specifically recognize acetylation sites in proteins. BRDs have recently emerged as interesting targets for the development of specific protein interaction inhibitors, enabling a novel exiting strategy for the development of new therapies. This review provides an overview over sequence requirements of BRDs, known substrates and the structural mechanisms of specific Kac recognition.

[1]  S. Robson,et al.  Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia , 2011, Nature.

[2]  Thomas A. Milne,et al.  Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions , 2011, Cell.

[3]  Ming-Ming Zhou,et al.  Brd4 Coactivates Transcriptional Activation of NF-κB via Specific Binding to Acetylated RelA , 2008, Molecular and Cellular Biology.

[4]  D. Patel,et al.  TRIM24 links a noncanonical histone signature to breast cancer , 2010, Nature.

[5]  P. Chambon,et al.  TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. , 1999, Oncogene.

[6]  D. Patel,et al.  A Poised Chromatin Platform for TGF-β Access to Master Regulators , 2011, Cell.

[7]  H. McDermid,et al.  Cecr2 mutations causing exencephaly trigger misregulation of mesenchymal/ectodermal transcription factors. , 2010, Birth defects research. Part A, Clinical and molecular teratology.

[8]  Xiangyuan Wang,et al.  The first bromodomain of Brdt, a testis-specific member of the BET sub-family of double-bromodomain-containing proteins, is essential for male germ cell differentiation , 2007, Development.

[9]  E. Salmon,et al.  The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[10]  J. Boeke,et al.  The Sirtuins Hst3 and Hst4p Preserve Genome Integrity by Controlling Histone H3 Lysine 56 Deacetylation , 2006, Current Biology.

[11]  S. Bhaumik,et al.  Mixed lineage leukemia: histone H3 lysine 4 methyltransferases from yeast to human , 2010, The FEBS journal.

[12]  P. Chambon,et al.  TIF1δ, a Novel HP1-interacting Member of the Transcriptional Intermediary Factor 1 (TIF1) Family Expressed by Elongating Spermatids* , 2004, Journal of Biological Chemistry.

[13]  Roman Osman,et al.  Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors. , 2011, Journal of the American Chemical Society.

[14]  Xin Cai,et al.  An acetylation switch in p53 mediates holo-TFIID recruitment. , 2007, Molecular cell.

[15]  P. Chambon,et al.  TIF1γ, a novel member of the transcriptional intermediary factor 1 family , 1999, Oncogene.

[16]  Zhenghe Wang,et al.  Differential binding modes of the bromodomains of CREB-binding protein (CBP) and p300 with acetylated MyoD. , 2008, Biochemical and biophysical research communications.

[17]  Yifan Cheng,et al.  The chromatin remodeler ACF acts as a dimeric motor to space nucleosomes , 2009, Nature.

[18]  Michael Boutros,et al.  Identification of JAK/STAT signalling components by genome-wide RNA interference , 2005, Nature.

[19]  P. Marks,et al.  Histone deacetylase inhibitors: molecular mechanisms of action , 2007, Oncogene.

[20]  T. Parmely,et al.  Identification of New Subunits of the Multiprotein Mammalian TRRAP/TIP60-containing Histone Acetyltransferase Complex* , 2003, Journal of Biological Chemistry.

[21]  Mahavir Singh,et al.  Structural Ramification for Acetyl‐Lysine Recognition by the Bromodomain of Human BRG1 Protein, a Central ATPase of the SWI/SNF Remodeling Complex , 2007, Chembiochem : a European journal of chemical biology.

[22]  Chao Xu,et al.  Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails. , 2007, Biochemistry.

[23]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[24]  Y. Kanno,et al.  Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. , 2004, Molecules and Cells.

[25]  Shigeyuki Yokoyama,et al.  Structural Basis for Acetylated Histone H4 Recognition by the Human BRD2 Bromodomain* , 2010, The Journal of Biological Chemistry.

[26]  B. Turner,et al.  Reading signals on the nucleosome with a new nomenclature for modified histones , 2005, Nature Structural &Molecular Biology.

[27]  Weiqun Shen,et al.  Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails , 2007, BMC Structural Biology.

[28]  D. Chaussabel,et al.  SP100 inhibits ETS1 activity in primary endothelial cells , 2005, Oncogene.

[29]  Jeroen Krijgsveld,et al.  Cooperative binding of two acetylation marks on a histone tail by a single bromodomain , 2009, Nature.

[30]  D. Wassarman,et al.  TAF(II)250: a transcription toolbox. , 2001, Journal of cell science.

[31]  K. Jones,et al.  The multi-tasking P-TEFb complex. , 2008, Current opinion in cell biology.

[32]  L. Kedes,et al.  Acetylation of MyoD directed by PCAF is necessary for the execution of the muscle program. , 1999, Molecular cell.

[33]  Shetal Patel,et al.  Mammalian ASH1L Is a Histone Methyltransferase That Occupies the Transcribed Region of Active Genes , 2007, Molecular and Cellular Biology.

[34]  H. Dyson,et al.  Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. , 2000, Journal of molecular biology.

[35]  Roberto Sanchez,et al.  Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. , 2004, Molecular cell.

[36]  Tom Misteli,et al.  The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[37]  D. Bowden,et al.  Identification and characterization of PRKCBP1, a candidate RACK-like protein , 2000, Mammalian Genome.

[38]  F. Mustafa,et al.  Selective recognition of acetylated histones by bromodomains in transcriptional co-activators. , 2007, The Biochemical journal.

[39]  Stefan Knapp,et al.  Bromodomains as therapeutic targets , 2011, Expert Reviews in Molecular Medicine.

[40]  P. Munster,et al.  Rational therapeutic combinations with histone deacetylase inhibitors for the treatment of cancer. , 2011, Future oncology.

[41]  J. Manfredi,et al.  Target structure-based discovery of small molecules that block human p53 and CREB binding protein association. , 2006, Chemistry & biology.

[42]  Ming-Ming Zhou,et al.  A small molecule binding to the coactivator CREB-binding protein blocks apoptosis in cardiomyocytes. , 2011, Chemistry & biology.

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

[44]  C. Rice,et al.  Suppression of inflammation by a synthetic histone mimic , 2010, Nature.

[45]  M. Thompson,et al.  Polybromo-1-bromodomains bind histone H3 at specific acetyl-lysine positions. , 2007, Biochemical and biophysical research communications.

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

[47]  K. Garber HDAC inhibitors overcome first hurdle , 2007, Nature Biotechnology.

[48]  J. Yates,et al.  BRD7, a Novel PBAF-specific SWI/SNF Subunit, Is Required for Target Gene Activation and Repression in Embryonic Stem Cells* , 2008, Journal of Biological Chemistry.

[49]  D. Wassarman,et al.  TAFII250: a transcription toolbox , 2001 .

[50]  A. El-Osta,et al.  Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing , 2005, Nature Genetics.

[51]  Y. Doyon,et al.  Molecular Architecture of Quartet MOZ/MORF Histone Acetyltransferase Complexes , 2008, Molecular and Cellular Biology.

[52]  Zhike Lu,et al.  Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.

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

[54]  K. Marushige Activation of chromatin by acetylation of histone side chains. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[55]  I. Grummt,et al.  Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing , 2009, Nature Cell Biology.

[56]  R. Hardison,et al.  Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes , 2011, Proceedings of the National Academy of Sciences of the United States of America.

[57]  L. Zon,et al.  TIF1γ Controls Erythroid Cell Fate by Regulating Transcription Elongation , 2010, Cell.

[58]  Hongbin Sun,et al.  Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4. , 2007, Biochemical and biophysical research communications.

[59]  J. Kushner,et al.  Identification of a WD40 Repeat-Containing Isoform of PHIP as a Novel Regulator of β-Cell Growth and Survival , 2007, Molecular and Cellular Biology.

[60]  B. Howard,et al.  A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A , 1996, Nature.

[61]  Y. Liu,et al.  Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails. , 2008, Biochemistry.

[62]  S. Knapp,et al.  3,5-Dimethylisoxazoles Act As Acetyl-lysine-mimetic Bromodomain Ligands , 2011, Journal of medicinal chemistry.

[63]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[64]  Helen M. Rowe,et al.  KAP1 controls endogenous retroviruses in embryonic stem cells , 2010, Nature.

[65]  T. Archer,et al.  The BRG1 transcriptional coregulator , 2008, Nuclear receptor signaling.

[66]  P. Tucker,et al.  Regulation of matrix attachment region‐dependent, lymphocyte‐restricted transcription through differential localization within promyelocytic leukemia nuclear bodies , 2000, The EMBO journal.

[67]  R. Young,et al.  BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc , 2011, Cell.

[68]  J. Nezu,et al.  A novel family of bromodomain genes. , 2000, Genomics.

[69]  W. Greene,et al.  Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF‐κB , 2002, The EMBO journal.

[70]  L. Thompson,et al.  Therapeutic application of histone deacetylase inhibitors for central nervous system disorders , 2008, Nature Reviews Drug Discovery.

[71]  J. Lippincott-Schwartz,et al.  A Bromodomain Protein, MCAP, Associates with Mitotic Chromosomes and Affects G2-to-M Transition , 2000, Molecular and Cellular Biology.

[72]  Yixue Li,et al.  Regulation of Cellular Metabolism by Protein Lysine Acetylation , 2010, Science.

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

[74]  Thomas A. Milne,et al.  Pro Isomerization in MLL1 PHD3-Bromo Cassette Connects H3K4me Readout to CyP33 and HDAC-Mediated Repression , 2010, Cell.

[75]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[76]  Ming-Ming Zhou,et al.  Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. , 2008, Structure.

[77]  K. Helin,et al.  ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. , 2009, Cancer research.

[78]  A. Revenko,et al.  Chromatin Loading of E2F-MLL Complex by Cancer-Associated Coregulator ANCCA via Reading a Specific Histone Mark , 2010, Molecular and Cellular Biology.

[79]  Thomas C. Kaufman,et al.  brahma: A regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2 SWI2 , 1992, Cell.

[80]  R Holliday,et al.  The inheritance of epigenetic defects. , 1987, Science.

[81]  S. Knapp,et al.  Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family , 2012, Bioorganic & medicinal chemistry.

[82]  He Huang,et al.  Expression of the Wdr9 gene and protein products during mouse development , 2003, Developmental dynamics : an official publication of the American Association of Anatomists.

[83]  S. Berger,et al.  Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. , 2000, Molecular cell.

[84]  Thomas A. Milne,et al.  Physical Association and Coordinate Function of the H3 K4 Methyltransferase MLL1 and the H4 K16 Acetyltransferase MOF , 2005, Cell.

[85]  I. Talianidis,et al.  Histone modifications defining active genes persist after transcriptional and mitotic inactivation , 2005, The EMBO journal.

[86]  E. Verdin,et al.  Two-pronged Binding with Bromodomain-containing Protein 4 Liberates Positive Transcription Elongation Factor b from Inactive Ribonucleoprotein Complexes* , 2011, The Journal of Biological Chemistry.

[87]  A. Harel-Bellan,et al.  Interaction between Acetylated MyoD and the Bromodomain of CBP and / or p 300 , 2001 .

[88]  Eric Verdin,et al.  Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. , 2002, Molecular cell.

[89]  E. Kalkhoven,et al.  CBP and p300: HATs for different occasions. , 2004, Biochemical pharmacology.

[90]  C. Waddington Preliminary Notes on the Development of the Wings in Normal and Mutant Strains of Drosophila. , 1939, Proceedings of the National Academy of Sciences of the United States of America.

[91]  A. Gingras,et al.  Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family , 2012, Cell.

[92]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[93]  S. J. Flint,et al.  The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. , 2008, Molecular cell.

[94]  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.

[95]  Patrik Asp,et al.  The WSTF-SNF2h Chromatin Remodeling Complex Interacts with Several Nuclear Proteins in Transcription* , 2006, Journal of Biological Chemistry.

[96]  Ming-Ming Zhou,et al.  Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2 , 2010, Cell Research.

[97]  Jessica E. Bolden,et al.  Anticancer activities of histone deacetylase inhibitors , 2006, Nature Reviews Drug Discovery.

[98]  Tony Kouzarides,et al.  Acetylation: a regulatory modification to rival phosphorylation? , 2000, The EMBO journal.

[99]  J. Chiche,et al.  Sp110 Localizes to the PML-Sp100 Nuclear Body and May Function as a Nuclear Hormone Receptor Transcriptional Coactivator , 2000, Molecular and Cellular Biology.

[100]  Joel P. Mackay,et al.  Structural Basis and Specificity of Acetylated Transcription Factor GATA1 Recognition by BET Family Bromodomain Protein Brd3 , 2011, Molecular and Cellular Biology.

[101]  M. Geyer,et al.  Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains. , 2010, Angewandte Chemie.

[102]  M. Thompson,et al.  Kinetic analysis of acetylation-dependent Pb1 bromodomain-histone interactions. , 2008, Biophysical chemistry.

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

[104]  E. Brambilla,et al.  Functional characterization of ATAD2 as a new cancer/testis factor and a predictor of poor prognosis in breast and lung cancers , 2010, Oncogene.

[105]  C. Kimmel,et al.  The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity , 2008, Development.

[106]  D. Page,et al.  Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. , 2002, Human molecular genetics.

[107]  R. Bernards,et al.  The adenovirus E1A binding protein BS69 is a corepressor of transcription through recruitment of N-CoR , 2000, Oncogene.

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