Structural basis for molecular interactions involving MRG domains: Implications in chromatin biology

Structure

Volumn 20, Issue 1, 2012, Pages 151-160

  Xie, Tao ^a   Graveline, Richard ^b   Kumar, Ganesan Senthil ^a   Zhang, Yongbo ^a   Krishnan, Arvind ^a   David, Gregory ^b   Radhakrishnan, Ishwar ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE; PEPTIDES AND PROTEINS; PROTEIN PF1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MRG15; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CHROMATIN; COMPLEX FORMATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CHROMATIN; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SIN3 HISTONE DEACETYLASE AND COREPRESSOR COMPLEX; TRANSCRIPTION FACTORS;

EID: 84862972564     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.10.019     Document Type: Article

References (46)

1. A. Bax, and S. Grzesiek Methodological advances in protein NMR Acc. Chem. Res. 26 1993 131 138
2. M.J. Bertram, N.G. Bérubé, X. Hang-Swanson, Q. Ran, J.K. Leung, S. Bryce, K. Spurgers, R.J. Bick, A. Baldini, and Y. Ning Identification of a gene that reverses the immortal phenotype of a subset of cells and is a member of a novel family of transcription factor-like genes Mol. Cell. Biol. 19 1999 1479 1485 (Pubitemid 29046889)
3. B.R. Bowman, C.M. Moure, B.M. Kirtane, R.L. Welschhans, K. Tominaga, O.M. Pereira-Smith, and F.A. Quiocho Multipurpose MRG domain involved in cell senescence and proliferation exhibits structural homology to a DNA-interacting domain Structure 14 2006 151 158 (Pubitemid 43350082)
4. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
5. M.J. Carrozza, L. Florens, S.K. Swanson, W.J. Shia, S. Anderson, J. Yates, M.P. Washburn, and J.L. Workman Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex Biochim. Biophys. Acta 1731 2005 77 87 discussion 75-76 (Pubitemid 41712766)
6. M.J. Carrozza, B. Li, L. Florens, T. Suganuma, S.K. Swanson, K.K. Lee, W.J. Shia, S. Anderson, J. Yates, M.P. Washburn, and J.L. Workman Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription Cell 123 2005 581 592 (Pubitemid 41608462)
7. M. Chen, M. Takano-Maruyama, O.M. Pereira-Smith, G.O. Gaufo, and K. Tominaga MRG15, a component of HAT and HDAC complexes, is essential for proliferation and differentiation of neural precursor cells J. Neurosci. Res. 87 2009 1522 1531
8. M. Chen, K. Tominaga, and O.M. Pereira-Smith Emerging role of the MORF/MRG gene family in various biological processes, including aging Ann. N Y Acad. Sci. 1197 2010 134 141
9. M. Chen, O.M. Pereira-Smith, and K. Tominaga Loss of the chromatin regulator MRG15 limits neural stem/progenitor cell proliferation via increased expression of the p21 Cdk inhibitor Stem Cell Res. (Amst.) 7 2011 75 88
10. S.F. de Almeida, A.R. Grosso, F. Koch, R. Fenouil, S. Carvalho, J. Andrade, H. Levezinho, M. Gut, D. Eick, and I. Gut Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36 Nat. Struct. Mol. Biol. 18 2011 977 983
11. Y. Doyon, W. Selleck, W.S. Lane, S. Tan, and J. Côté Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans Mol. Cell. Biol. 24 2004 1884 1896 (Pubitemid 38248930)
12. A.E. Ferentz, and G. Wagner NMR spectroscopy: a multifaceted approach to macromolecular structure Q. Rev. Biophys. 33 2000 29 65
13. T.C. Fleischer, U.J. Yun, and D.E. Ayer Identification and characterization of three new components of the mSin3A corepressor complex Mol. Cell. Biol. 23 2003 3456 3467 (Pubitemid 36539178)
14. S. Fnu, E.A. Williamson, L.P. De Haro, M. Brenneman, J. Wray, M. Shaheen, K. Radhakrishnan, S.H. Lee, J.A. Nickoloff, and R. Hromas Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining Proc. Natl. Acad. Sci. USA 108 2011 540 545
15. S.N. Garcia, B.M. Kirtane, A.J. Podlutsky, O.M. Pereira-Smith, and K. Tominaga Mrg15 null and heterozygous mouse embryonic fibroblasts exhibit DNA-repair defects post exposure to gamma ionizing radiation FEBS Lett. 581 2007 5275 5281 (Pubitemid 350018755)
16. K.E. Gardner, C.D. Allis, and B.D. Strahl Operating on chromatin, a colorful language where context matters J. Mol. Biol. 409 2011 36 46
17. S.C. Gill, and P.H. von Hippel Calculation of protein extinction coefficients from amino acid sequence data Anal. Biochem. 182 1989 319 326 (Pubitemid 19277112)
18. Goddard, T.D., and Kneller, D.G. (2004). Sparky 3 (http://www.cgl.ucsf. edu/home/sparky/).
19. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723 (Pubitemid 28059943)
20. T. Hayakawa, F. Zhang, N. Hayakawa, Y. Ohtani, K. Shinmyozu, J. Nakayama, and P.R. Andreassen MRG15 binds directly to PALB2 and stimulates homology-directed repair of chromosomal breaks J. Cell Sci. 123 2010 1124 1130
21. P. Jelinic, J. Pellegrino, and G. David A novel mammalian complex containing Sin3B mitigates histone acetylation and RNA polymerase II progression within transcribed loci Mol. Cell. Biol. 31 2011 54 62
22. T. Jenuwein, and C.D. Allis Translating the histone code Science 293 2001 1074 1080 (Pubitemid 32758077)
23. A.A. Joshi, and K. Struhl Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation Mol. Cell 20 2005 971 978 (Pubitemid 41814885)
24. M.C. Keogh, S.K. Kurdistani, S.A. Morris, S.H. Ahn, V. Podolny, S.R. Collins, M. Schuldiner, K. Chin, T. Punna, and N.J. Thompson Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex Cell 123 2005 593 605 (Pubitemid 41608463)
25. G.S. Kumar, T. Xie, Y. Zhang, and I. Radhakrishnan Solution structure of the mSin3A PAH2-Pf1 SID1 complex: a Mad1/Mxd1-like interaction disrupted by MRG15 in the Rpd3S/Sin3S complex J. Mol. Biol. 408 2011 987 1000
26. C.D. Laherty, W.M. Yang, J.M. Sun, J.R. Davie, E. Seto, and R.N. Eisenman Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression Cell 89 1997 349 356 (Pubitemid 27220879)
27. R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486 (Pubitemid 126706801)
28. B. Li, M. Gogol, M. Carey, D. Lee, C. Seidel, and J.L. Workman Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin Science 316 2007 1050 1054 (Pubitemid 46799495)
29. J.P. Linge, M. Habeck, W. Rieping, and M. Nilges ARIA: automated NOE assignment and NMR structure calculation Bioinformatics 19 2003 315 316 (Pubitemid 36181930)
30. R.F. Luco, Q. Pan, K. Tominaga, B.J. Blencowe, O.M. Pereira-Smith, and T. Misteli Regulation of alternative splicing by histone modifications Science 327 2010 996 1000
31. E. Nicolas, T. Yamada, H.P. Cam, P.C. Fitzgerald, R. Kobayashi, and S.I. Grewal Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection Nat. Struct. Mol. Biol. 14 2007 372 380 (Pubitemid 46685888)
32. 1H]-NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions Q. Rev. Biophys. 23 1990 39 96
33. P.S. Pardo, J.K. Leung, J.C. Lucchesi, and O.M. Pereira-Smith MRG15, a novel chromodomain protein, is present in two distinct multiprotein complexes involved in transcriptional activation J. Biol. Chem. 277 2002 50860 50866 (Pubitemid 36042252)
34. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
35. M.J. Plevin, M.M. Mills, and M. Ikura The LxxLL motif: a multifunctional binding sequence in transcriptional regulation Trends Biochem. Sci. 30 2005 66 69 (Pubitemid 40187297)
36. W.J. Salerno, S.M. Seaver, B.R. Armstrong, and I. Radhakrishnan MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data Nucleic Acids Res. 32 Web Server issue 2004 W566 W568
37. Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
38. B. Sun, J. Hong, P. Zhang, X. Dong, X. Shen, D. Lin, and J. Ding Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36 J. Biol. Chem. 283 2008 36504 36512
39. K.A. Swanson, P.S. Knoepfler, K. Huang, R.S. Kang, S.M. Cowley, C.D. Laherty, R.N. Eisenman, and I. Radhakrishnan HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations Nat. Struct. Mol. Biol. 11 2004 738 746 (Pubitemid 39014499)
40. S.M. Sy, M.S. Huen, and J. Chen MRG15 is a novel PALB2-interacting factor involved in homologous recombination J. Biol. Chem. 284 2009 21127 21131
41. K. Tominaga, B. Kirtane, J.G. Jackson, Y. Ikeno, T. Ikeda, C. Hawks, J.R. Smith, M.M. Matzuk, and O.M. Pereira-Smith MRG15 regulates embryonic development and cell proliferation Mol. Cell. Biol. 25 2005 2924 2937
42. P.E. Wright, and H.J. Dyson Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm J. Mol. Biol. 293 1999 321 331 (Pubitemid 29516173)
43. C. Xu, G. Cui, M.V. Botuyan, and G. Mer Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S Structure 16 2008 1740 1750
44. G.S. Yochum, and D.E. Ayer Role for the mortality factors MORF4, MRGX, and MRG15 in transcriptional repression via associations with Pf1, mSin3A, and Transducin-Like Enhancer of Split Mol. Cell. Biol. 22 2002 7868 7876 (Pubitemid 35217297)
45. P. Zhang, J. Zhao, B. Wang, J. Du, Y. Lu, J. Chen, and J. Ding The MRG domain of human MRG15 uses a shallow hydrophobic pocket to interact with the N-terminal region of PAM14 Protein Sci. 15 2006 2423 2434 (Pubitemid 44496396)
46. Y. Zhang, Z.W. Sun, R. Iratni, H. Erdjument-Bromage, P. Tempst, M. Hampsey, and D. Reinberg SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex Mol. Cell 1 1998 1021 1031 (Pubitemid 128379263)