Liên kết DNA nucleosome thúc đẩy sự nhận diện các nucleosome H3K36-methylated bởi miền PSIP1-PWWP
Tóm tắt
Từ khóa
#H3K36-methylated nucleosomes #PSIP1-PWWP domain #DNA-binding #histone modifications #structural biology.Tài liệu tham khảo
Fischle W, Wang Y, Allis CD: Histone and chromatin cross-talk. Curr Opin Cell Biol. 2003, 15: 172-183. 10.1016/S0955-0674(03)00013-9.
Kouzarides T: Chromatin modifications and their function. Cell. 2007, 128: 693-705. 10.1016/j.cell.2007.02.005.
Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell. 2007, 129: 823-837. 10.1016/j.cell.2007.05.009.
Wagner EJ, Carpenter PB: Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol. 2012, 13: 115-126. 10.1038/nrm3274.
Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M: Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010, 142: 967-980. 10.1016/j.cell.2010.08.020.
Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP: The Tudor domain ‘Royal Family’: tudor, plant agenet, chromo, PWWP and MBT domains. Trends Biochem Sci. 2003, 28: 69-74. 10.1016/S0968-0004(03)00004-5.
Hughes RM, Wiggins KR, Khorasanizadeh S, Waters ML: Recognition of trimethyl-lysine by a chromodomain is not driven by the hydrophobic effect. Proc Natl Acad Sci USA. 2007, 104: 11184-11188. 10.1073/pnas.0610850104.
Vezzoli A, Bonadies N, Allen MD, Freund SMV, Santiveri CM, Kvinlaug BT, Huntly BJP, Göttgens B, Bycroft M: Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat Struct Mol Biol. 2010, 17: 617-619. 10.1038/nsmb.1797.
Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J: Structural and histone-binding ability characterizations of human PWWP domains. PLoS One. 2011, 6: e18919-10.1371/journal.pone.0018919.
Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ: Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature. 2006, 442: 91-95.
Peña PV, Davrazou F, Shi X, Walter KL, Verkhusha VV, Gozani OP, Zhao R, Kutateladze TG: Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature. 2006, 442: 100-103.
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997, 389: 251-260. 10.1038/38444.
Lukasik SM, Cierpicki T, Borloz M, Grembecka J, Everett A, Bushweller JH: High resolution structure of the HDGF PWWP domain: a potential DNA-binding domain. Protein Sci. 2006, 15: 314-323. 10.1110/ps.051751706.
Laguri C, Duband-Goulet I, Friedrich N, Axt M, Belin P, Callebaut I, Gilquin B, Zinn-Justin S, Couprie J: Human mismatch repair protein MSH6 contains a PWWP domain that targets double-stranded DNA. Biochemistry. 2008, 47: 6199-6207. 10.1021/bi7024639.
Llano M, Vanegas M, Hutchins N, Thompson D, Delgado S, Poeschla EM: Identification and characterization of the chromatin-binding domains of the HIV-1 integrase interactor LEDGF/p75. J Mol Biol. 2006, 360: 760-773. 10.1016/j.jmb.2006.04.073.
Turlure F, Maertens G, Rahman S, Cherepanov P, Engelman A: A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo. Nucleic Acids Res. 2006, 34: 1653-1665. 10.1093/nar/gkl052.
Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA: Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet. 2012, 8: e1002717-10.1371/journal.pgen.1002717.
Ge H, Si Y, Roeder RG: Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation. EMBO J. 1998, 17: 6723-6729. 10.1093/emboj/17.22.6723.
Ferris AL, Wu X, Hughes CM, Stewart C, Smith SJ, Milne TA, Wang GG, Shun M-C, Allis CD, Engelman A, Hughes SH: Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration. Proc Natl Acad Sci USA. 2010, 107: 3135-3140. 10.1073/pnas.0914142107.
Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z: Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. J Biol Chem. 2011, 286: 41812-41825. 10.1074/jbc.M111.255711.
Yokoyama A, Cleary ML: Menin critically links MLL proteins with LEDGF on cancer-associated target genes. Cancer Cell. 2008, 14: 36-46. 10.1016/j.ccr.2008.05.003.
Daugaard M, Baude A, Fugger K, Povlsen LK, Beck H, Sørensen CS, Petersen NHT, Sorensen PHB, Lukas C, Bartek J, Lukas J, Rohde M, Jäättelä M: LEDGF (p75) promotes DNA-end resection and homologous recombination. Nat Struct Mol Biol. 2012, 19: 803-810. 10.1038/nsmb.2314.
Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M: Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res. 2013, 41: 3924-3936. 10.1093/nar/gkt074.
Vermeulen M, Mulder KW, Denissov S, Pijnappel WWMP, van Schaik FMA, Varier RA, Baltissen MPA, Stunnenberg HG, Mann M, Timmers HTM: Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell. 2007, 131: 58-69. 10.1016/j.cell.2007.08.016.
Singh DP, Kubo E, Takamura Y, Shinohara T, Kumar A, Chylack LT, Fatma N: DNA-binding domains and nuclear localization signal of LEDGF: contribution of two helix-turn-helix (HTH)-like domains and a stretch of 58 amino acids of the N-terminal to the trans-activation potential of LEDGF. J Mol Biol. 2006, 355: 379-394. 10.1016/j.jmb.2005.10.054.
Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM: The site-specific installation of methyl-lysine analogs into recombinant histones. Cell. 2007, 128: 1003-1012. 10.1016/j.cell.2006.12.041.
Hendrix J, Gijsbers R, De Rijck J, Voet A, Hotta J-I, McNeely M, Hofkens J, Debyser Z, Engelborghs Y: The transcriptional co-activator LEDGF/p75 displays a dynamic scan-and-lock mechanism for chromatin tethering. Nucleic Acids Res. 2011, 39: 1310-1325. 10.1093/nar/gkq933.
Kato H, van Ingen H, Zhou B-R, Feng H, Bustin M, Kay LE, Bai Y: Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proc Natl Acad Sci USA. 2011, 108: 12283-12288. 10.1073/pnas.1105848108.
Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE: Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc. 2003, 125: 10420-10428. 10.1021/ja030153x.
Jencks WP: On the attribution and additivity of binding energies. Proc Natl Acad Sci USA. 1981, 78: 4046-4050. 10.1073/pnas.78.7.4046.
Zhou H-X: Polymer models of protein stability, folding, and interactions. Biochemistry. 2004, 43: 2141-2154. 10.1021/bi036269n.
Rees DC, Congreve M, Murray CW, Carr R: Fragment-based lead discovery. Nat Rev Mol Cell Biol. 2004, 3: 660-672.
Dominguez C, Boelens R, Bonvin AMJJ: HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003, 125: 1731-1737. 10.1021/ja026939x.
Karaca E, Bonvin AMJJ: A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure. 2011, 19: 555-565. 10.1016/j.str.2011.01.014.
Tsutsui KM, Sano K, Hosoya O, Miyamoto T, Tsutsui K: Nuclear protein LEDGF/p75 recognizes supercoiled DNA by a novel DNA-binding domain. Nucleic Acids Res. 2011, 39: 5067-5081. 10.1093/nar/gkr088.
Shun M-C, Botbol Y, Li X, Di Nunzio F, Daigle JE, Yan N, Lieberman J, Lavigne M, Engelman A: Identification and characterization of PWWP domain residues critical for LEDGF/p75 chromatin binding and human immunodeficiency virus type 1 infectivity. J Virol. 2008, 82: 11555-11567. 10.1128/JVI.01561-08.
Kim D, Blus BJ, Chandra V, Huang P, Rastinejad F, Khorasanizadeh S: Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain. Nat Struct Mol Biol. 2010, 17: 1027-1029. 10.1038/nsmb.1856.
Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J: Solution structure of Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochem J. 2011, 442: 527-538.
van Ingen H, van Schaik FMA, Wienk H, Ballering J, Rehmann H, Dechesne AC, Kruijzer JAW, Liskamp RMJ, Timmers HTM, Boelens R: Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure. 2008, 16: 1245-1256. 10.1016/j.str.2008.04.015.
Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K: Reconstitution of nucleosome core particles from recombinant histones and DNA. Meth Enzymol. 2004, 375: 23-44.
Tighe A, Staples O, Taylor S: Mps1 kinase activity restrains anaphase during an unperturbed mitosis and targets Mad2 to kinetochores. J Cell Biol. 2008, 181: 893-901. 10.1083/jcb.200712028.
Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD: Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell. 2008, 134: 1066-1078. 10.1016/j.cell.2008.07.019.
de Graaf P, Mousson F, Geverts B, Scheer E, Tora L, Houtsmuller AB, Timmers HTM: Chromatin interaction of TATA-binding protein is dynamically regulated in human cells. J Cell Sci. 2010, 123: 2663-2671. 10.1242/jcs.064097.
Mokry M, Hatzis P, de Bruijn E, Koster J, Versteeg R, Schuijers J, van de Wetering M, Guryev V, Clevers H, Cuppen E: Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles. PLoS One. 2010, 5: e15092-10.1371/journal.pone.0015092.
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995, 6: 277-293.
Jung YS, Zweckstetter M: Mars - robust automatic backbone assignment of proteins. J Biomol NMR. 2004, 30: 11-23.
Shen Y, Delaglio F, Cornilescu G, Bax A: TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR. 2009, 44: 213-223. 10.1007/s10858-009-9333-z.
López-Méndez B, Güntert P: Automated protein structure determination from NMR spectra. J Am Chem Soc. 2006, 128: 13112-13122. 10.1021/ja061136l.
Herrmann T, Güntert P, Wüthrich K: Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002, 319: 209-227. 10.1016/S0022-2836(02)00241-3.
Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D: Biol Crystallogr. 1998, 54: 905-921.
Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ: RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. 2005, 59: 662-672. 10.1002/prot.20408.
Doreleijers JF, da Silva Sousa AW, Krieger E, Nabuurs SB, Spronk CAEM, Stevens TJ, Vranken WF, Vriend G, Vuister GW: CING: an integrated residue-based structure validation program suite. J Biomol NMR. 2012, 54: 267-283. 10.1007/s10858-012-9669-7.
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA: Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA. 2001, 98: 10037-10041. 10.1073/pnas.181342398.