A Phylogenetic Study of SPBP and RAI1: Evolutionary Conservation of Chromatin Binding Modules

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Darvekar, Sagar ^a   Rekdal, Cecilie ^a   Johansen, Terje ^a   Sjøttem, Eva ^a  

^a UNIVERSITY OF TROMSØ   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; RETINOIC ACID INDUCIBLE PROTEIN I; STROMELYSIN 1 PLATELET DERIVED GROWTH FACTOR RESPONSIVE ELEMENT BINDING PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE DUPLICATION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IN VITRO STUDY; NONHUMAN; NUCLEOSOME; PHYLOGENETIC TREE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROCESSING; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION REGULATION;

ANIMALS; CHROMATIN; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; ZINC FINGERS;

EID: 84885737397     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078907     Document Type: Article

References (41)

1. Kwon CS, Wagner D, (2007) Unwinding chromatin for development and growth: a few genes at a time. Trends Genet 23: 403-412. doi:10.1016/j.tig.2007.05.010. PubMed: 17566593.
2. Daniel JA, Grant PA, (2007) Multi-tasking on chromatin with the SAGA coactivator complexes. Mutat Res 618: 135-148. doi:10.1016/j.mrfmmm.2006.09.008. PubMed: 17337012.
3. Spiegelman BM, Heinrich R, (2004) Biological control through regulated transcriptional coactivators. Cell 119: 157-167. doi:10.1016/j.cell.2004.09.037. PubMed: 15479634.
4. Thorne JL, Campbell MJ, Turner BM, (2009) Transcription factors, chromatin and cancer. Int J Biochem Cell Biol 41: 164-175. doi:10.1016/j.biocel.2008.08.029. PubMed: 18804550.
5. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ, (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14: 1025-1040. doi:10.1038/nsmb1338. PubMed: 17984965.
6. Eustermann S, Yang JC, Law MJ, Amos R, Chapman LM, et al. (2011) Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nat Struct Mol Biol 18: 777-782. doi:10.1038/nsmb.2070. PubMed: 21666677.
7. Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, et al. (2010) Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 466: 258-262. doi:10.1038/nature09139. PubMed: 20613843.
8. Aravind L, Iyer LM, (2012) The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle 11: 119-131. doi:10.4161/cc.11.1.18475. PubMed: 22186017.
9. Arita K, Isogai S, Oda T, Unoki M, Sugita K, et al. (2012) Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. Proc Natl Acad Sci U S A 109: 12950-12955. doi:10.1073/pnas.1203701109. PubMed: 22837395.
10. Callebaut I, Mornon JP, (2012) The PWAPA cassette: Intimate association of a PHD-like finger and a winged-helix domain in proteins included in histone-modifying complexes. Biochimie 94: 2006-2012. doi:10.1016/j.biochi.2012.05.025. PubMed: 22664638.
11. Morra R, Lee BM, Shaw H, Tuma R, Mancini EJ, (2012) Concerted action of the PHD, chromo and motor domains regulates the human chromatin remodelling ATPase CHD4. FEBS Lett 586: 2513-2521. PubMed: 22749909.
12. Watson AA, Mahajan P, Mertens HD, Deery MJ, Zhang W, et al. (2012) The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4. J Mol Biol 422: 3-17. doi:10.1016/j.jmb.2012.04.031. PubMed: 22575888.
13. Kumar GS, Chang W, Xie T, Patel A, Zhang Y, et al. (2012) Sequence Requirements for Combinatorial Recognition of Histone H3 by the MRG15 and Pf1 Subunits of the Rpd3S/Sin3S Corepressor Complex. J Mol Biol 422: 519-531. doi:10.1016/j.jmb.2012.06.013. PubMed: 22728643.
14. Xie S, Jakoncic J, Qian C, (2012) UHRF1 double tudor domain and the adjacent PHD finger act together to recognize K9me3-containing histone H3 tail. J Mol Biol 415: 318-328. doi:10.1016/j.jmb.2011.11.012. PubMed: 22100450.
15. Oliver SS, Musselman CA, Srinivasan R, Svaren JP, Kutateladze TG, et al. (2012) Multivalent Recognition of Histone Tails by the PHD Fingers of CHD5. Biochemistry 51: 6534-6544. doi:10.1021/bi3006972. PubMed: 22834704.
16. Qiu Y, Liu L, Zhao C, Han C, Li F, et al. (2012) Combinatorial readout of unmodified H3R2 and acetylated H3K14 by the tandem PHD finger of MOZ reveals a regulatory mechanism for HOXA9 transcription. Genes Dev 26: 1376-1391. doi:10.1101/gad.188359.112. PubMed: 22713874.
17. Dhayalan A, Tamas R, Bock I, Tattermusch A, Dimitrova E, et al. (2011) The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. Hum Mol Genet 20: 2195-2203. doi:10.1093/hmg/ddr107. PubMed: 21421568.
18. Bi W, Ohyama T, Nakamura H, Yan J, Visvanathan J, et al. (2005) Inactivation of Rai1 in mice recapitulates phenotypes observed in chromosome engineered mouse models for Smith-Magenis syndrome. Hum Mol Genet 14: 983-995. doi:10.1093/hmg/ddi085. PubMed: 15746153.
19. Sjottem E, Rekdal C, Svineng G, Johnsen SS, Klenow H, et al. (2007) The ePHD protein SPBP interacts with TopBP1 and together they co-operate to stimulate Ets1-mediated transcription. Nucleic Acids Res 35: 6648-6662.
20. Darvekar S, Johnsen SS, Eriksen AB, Johansen T, Sjøttem E, (2012) Identification of two independent nucleosome-binding domains in the transcriptional co-activator SPBP. Biochem J 442: 65-75. doi:10.1042/BJ20111230. PubMed: 22081970.
21. Rekdal C, Sjøttem E, Johansen T, (2000) The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators. J Biol Chem 275: 40288-40300. doi:10.1074/jbc.M006978200. PubMed: 10995766.
22. Sanz L, Moscat J, Diaz-Meco MT, (1995) Molecular characterization of a novel transcription factor that controls stromelysin expression. Mol Cell Biol 15: 3164-3170. PubMed: 7760812.
23. Elvenes J, Thomassen EI, Johnsen SS, Kaino K, Sjøttem E, et al. (2011) Pax6 Represses Androgen Receptor-Mediated Transactivation by Inhibiting Recruitment of the Coactivator SPBP. PLOS ONE 6: e24659. doi:10.1371/journal.pone.0024659. PubMed: 21935435.
24. Gburcik V, Bot N, Maggiolini M, Picard D, (2005) SPBP is a phosphoserine-specific repressor of estrogen receptor alpha. Mol Cell Biol 25: 3421-3430. doi:10.1128/MCB.25.9.3421-3430.2005. PubMed: 15831449.
25. Slager RE, Newton TL, Vlangos CN, Finucane B, Elsea SH, (2003) Mutations in RAI1 associated with Smith-Magenis syndrome. Nat Genet 33: 466-468. doi:10.1038/ng1126. PubMed: 12652298.
26. Potocki L, Bi W, Treadwell-Deering D, Carvalho CM, Eifert A, et al. (2007) Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 80: 633-649. doi:10.1086/512864. PubMed: 17357070.
27. Toulouse A, Rochefort D, Roussel J, Joober R, Rouleau GA, (2003) Molecular cloning and characterization of human RAI1, a gene associated with schizophrenia. Genomics 82: 162-171. doi:10.1016/S0888-7543(03)00101-0. PubMed: 12837267.
28. van der Zwaag B, Franke L, Poot M, Hochstenbach R, Spierenburg HA, et al. (2009) Gene-network analysis identifies susceptibility genes related to glycobiology in autism. PLOS ONE 4: e5324. doi:10.1371/journal.pone.0005324. PubMed: 19492091.
29. Hayes S, Turecki G, Brisebois K, Lopes-Cendes I, Gaspar C, et al. (2000) CAG repeat length in RAI1 is associated with age at onset variability in spinocerebellar ataxia type 2 (SCA2). Hum Mol Genet 9: 1753-1758. doi:10.1093/hmg/9.12.1753. PubMed: 10915763.
30. Lamark T, Perander M, Outzen H, Kristiansen K, Øvervatn A, et al. (2003) Interaction codes within the family of mammalian Phox and Bem1p domain-containing proteins. J Biol Chem 278: 34568-34581. doi:10.1074/jbc.M303221200. PubMed: 12813044.
31. Argentaro A, Yang JC, Chapman L, Kowalczyk MS, Gibbons RJ, et al. (2007) Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX. Proc Natl Acad Sci U S A 104: 11939-11944. doi:10.1073/pnas.0704057104. PubMed: 17609377.
32. Otani J, Nankumo T, Arita K, Inamoto S, Ariyoshi M, et al. (2009) Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep 10: 1235-1241. doi:10.1038/embor.2009.218. PubMed: 19834512.
33. Sanchez R, Zhou MM, (2011) The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36: 364-372. PubMed: 21514168.
34. Li Y, Li H, (2012) Many keys to push: diversifying the 'readership' of plant homeodomain fingers. Acta Biochim Biophys Sinica 44: 28-39. doi:10.1093/abbs/gmr117. PubMed: 22194011.
35. Kwan AH, Gell DA, Verger A, Crossley M, Matthews JM, et al. (2003) Engineering a protein scaffold from a PHD finger. Structure 11: 803-813. doi:10.1016/S0969-2126(03)00122-9. PubMed: 12842043.
36. Bi W, Saifi GM, Shaw CJ, Walz K, Fonseca P, et al. (2004) Mutations of RAI1, a PHD-containing protein, in nondeletion patients with Smith-Magenis syndrome. Hum Genet 115: 515-524. doi:10.1007/s00439-004-1187-6. PubMed: 15565467.
37. Iwase S, Xiang B, Ghosh S, Ren T, Lewis PW, et al. (2011) ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol 18: 769-776. doi:10.1038/nsmb.2062. PubMed: 21666679.
38. Lallous N, Legrand P, McEwen AG, Ramón-Maiques S, Samama JP, et al. (2011) The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers. PLOS ONE 6: e27599. doi:10.1371/journal.pone.0027599. PubMed: 22096602.
39. Girirajan S, Elsas LJ 2nd, Devriendt K, Elsea SH, (2005) RAI1 variations in Smith-Magenis syndrome patients without 17p11.2 deletions. J Med Genet 42: 820-828. doi:10.1136/jmg.2005.031211. PubMed: 15788730.
40. Vilboux T, Ciccone C, Blancato JK, Cox GF, Deshpande C, et al. (2011) Molecular analysis of the Retinoic Acid Induced 1 gene (RAI1) in patients with suspected Smith-Magenis syndrome without the 17p11.2 deletion. PLOS ONE 6: e22861. doi:10.1371/journal.pone.0022861. PubMed: 21857958.
41. Migliori V, Mapelli M, Guccione E, (2012) On WD40 proteins: Propelling our knowledge of transcriptional control? Epigenetics: official journal of the DNA Methylation Society 7: 815-22. PubMed: 22810296.