The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Lallous, Nada ^a,c   Legrand, Pierre ^b   McEwen, Alastair G ^a   Ramón Maiques, Santiago ^c   Samama, Jean Pierre ^b   Birck, Catherine ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b SYNCHROTRON SOLEIL   (France)

^c Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR PROTEIN; HISTONE H3; UBIQUITIN LIKE CONTAINING PHD AND RING FINGER DOMAIN 1 PROTEIN; UNCLASSIFIED DRUG; CCAAT ENHANCER BINDING PROTEIN; HISTONE; UHRF1 PROTEIN, HUMAN;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; GEL ELECTROPHORESIS; HISTONE METHYLATION; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR RECOGNITION; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; CALORIMETRY; CHEMISTRY; ELECTROPHORESIS; GENETICS; HUMAN; METABOLISM; METHYLATION; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; CALORIMETRY; CCAAT-ENHANCER-BINDING PROTEINS; ELECTROPHORESIS; HISTONES; HUMANS; METHYLATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 80855128817     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027599     Document Type: Article

References (40)

1. Bronner C, Achour M, Arima Y, Chataigneau T, Saya H, et al. (2007) The UHRF family: oncogenes that are drugable targets for cancer therapy in the near future? Pharmacol Ther 115: 419-434.
2. Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, et al. (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455: 826-829.
3. Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, et al. (2008) Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature 455: 822-825.
4. Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M, (2008) Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 455: 818-821.
5. Achour M, Jacq X, Ronde P, Alhosin M, Charlot C, et al. (2008) The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 27: 2187-2197.
6. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, et al. (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317: 1760-1764.
7. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, et al. (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450: 908-912.
8. Unoki M, Kelly JD, Neal DE, Ponder BA, Nakamura Y, et al. (2009) UHRF1 is a novel molecular marker for diagnosis and the prognosis of bladder cancer. Br J Cancer 101: 98-105.
9. Unoki M, Nishidate T, Nakamura Y, (2004) ICBP90, an E2F-1 target, recruits HDAC1 and binds to methyl-CpG through its SRA domain. Oncogene 23: 7601-7610.
10. Jeanblanc M, Mousli M, Hopfner R, Bathami K, Martinet N, et al. (2005) The retinoblastoma gene and its product are targeted by ICBP90: a key mechanism in the G1/S transition during the cell cycle. Oncogene 24: 7337-7345.
11. Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, et al. (2010) Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143: 470-484.
12. Karagianni P, Amazit L, Qin J, Wong J, (2008) ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol 28: 705-717.
13. Papait R, Pistore C, Negri D, Pecoraro D, Cantarini L, et al. (2007) Np95 is implicated in pericentromeric heterochromatin replication and in major satellite silencing. Mol Biol Cell 18: 1098-1106.
14. Papait R, Pistore C, Grazini U, Babbio F, Cogliati S, et al. (2008) The PHD domain of Np95 (mUHRF1) is involved in large-scale reorganization of pericentromeric heterochromatin. Mol Biol Cell 19: 3554-3563.
15. Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, et al. (2011) Recognition of Multivalent Histone States Associated with Heterochromatin by UHRF1 Protein. J Biol Chem 286: 24300-24311.
16. Rottach A, Frauer C, Pichler G, Bonapace IM, Spada F, et al. (2009) The multi-domain protein Np95 connects DNA methylation and histone modification. Nucleic Acids Res 38: 1796-1804.
17. Chignola F, Gaetani M, Rebane A, Org T, Mollica L, et al. (2009) The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation. Nucleic Acids Res 37: 2951-2961.
18. Chakravarty S, Zeng L, Zhou MM, (2009) Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator. Structure 17: 670-679.
19. van Ingen H, van Schaik FM, Wienk H, Ballering J, Rehmann H, et al. (2008) Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure 16: 1245-1256.
20. Ramon-Maiques S, Kuo AJ, Carney D, Matthews AG, Oettinger MA, et al. (2007) The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci U S A 104: 18993-18998.
21. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, et al. (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448: 718-722.
22. Li H, Ilin S, Wang W, Duncan EM, Wysocka J, et al. (2006) Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442: 91-95.
23. Wang Z, Song J, Milne TA, Wang GG, Li H, et al. (2010) Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression. Cell 141: 1183-1194.
24. Rajakumara E, Wang Z, Ma H, Hu L, Chen H, et al. (2011) PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 43: 275-284.
25. Hu L, Li Z, Wang P, Lin Y, Xu Y, (2011) Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2. Cell Res 21: 1374-1378.
26. Wang C, Shen J, Yang Z, Chen P, Zhao B, et al. (2011) Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger. Cell Res 21: 1379-1382.
27. Lallous N, Ramón-Maiques S, (2011) Chromatin recognition modules: the PHD finger. Encyclopedia of Life Sciences (ELS) John Wiley & Sons DOI: 10.1002/9780470015902.a0023176.
28. Li H, Ilin S, Wang W, Duncan EM, Wysocka J, et al. (2006) Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442: 91-95.
29. Palacios A, Muñoz IG, Pantoja-Uceda D, Marcaida MJ, Torres D, et al. (2008) Molecular basis of histone H3K4me3 recognition by ING4. J Biol Chem 283: 15956-15964.
30. Busso D, Delagoutte-Busso B, Moras D, (2005) Construction of a set Gateway-based destination vectors for high-throughput cloning and expression screening in Escherichia coli. Anal Biochem 343: 313-321.
31. Kabsch W, (2010) XDS. Acta Crystallogr D Biol Crystallogr 66: 125-132.
32. Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
33. Sheldrick GM, (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr 66: 479-485.
34. Terwilliger TC, Berendzen J, (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55: 849-861.
35. Terwilliger TC, (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 56: 965-972.
36. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
37. Murshudov GN, Vagin AA, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240-255.
38. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
39. Corpet F, (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881-10890.
40. Gouet P, Courcelle E, Stuart DI, Metoz F, (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.