A common ancestry for BAP1 and Uch37 regulators

Bioinformatics

Volumn 28, Issue 15, 2012, Pages 1953-1956

  Sanchez pulido, Luis ^a   Kong, Lesheng ^a   Ponting, Chris P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADRM1 PROTEIN, HUMAN; ASXL1 PROTEIN, HUMAN; BAP1 PROTEIN, HUMAN; CARBOXYPEPTIDASE; DNA BINDING PROTEIN; MEMBRANE PROTEIN; NFRKB PROTEIN, HUMAN; REPRESSOR PROTEIN; TUMOR SUPPRESSOR PROTEIN; UBIQUITIN THIOLESTERASE; UCHL5 PROTEIN, HUMAN;

ANIMAL; ARTICLE; BIOLOGY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALS; CARBOXYPEPTIDASES; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; HUMANS; MEMBRANE GLYCOPROTEINS; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; TUMOR SUPPRESSOR PROTEINS; UBIQUITIN THIOLESTERASE;

EID: 84865149961     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts319     Document Type: Article

References (46)

1. Aravind,L. and Iyer,L.M. (2012) The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle, 11, 119-131.
2. Bejar,R. et al. (2011) Clinical effect of point mutations in myelodysplastic syndromes. N. Engl. J. Med., 364, 2496-2506.
3. Bell,D. et al. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 609-615.
4. Bott,M. et al. (2011) The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat. Genet., 43, 668-672.
5. Boultwood,J. et al. (2010) Frequent mutation of the polycomb-associated gene ASXL1 in the myelodysplastic syndromes and in acute myeloid leukemia. Leukemia, 24, 1062-1065.
6. Boura,E. et al. (2010) Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA. Acta Crystallogr. D Biol. Crystallogr., 66, 1351-1357.
7. Bratzel,F. et al. (2010) Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination. Curr. Biol., 20, 1853-1859.
8. Breen,T.R. and Duncan,I.M. (1986) Maternal expression of genes that regulate the bithorax complex of Drosophila melanogaster. Dev. Biol., 118, 442-456.
9. Brent,M.M. et al. (2008) Structural basis for DNA recognition by FoxO1 and its regulation by posttranslational modification. Structure, 16, 1407-1416.
10. Carbuccia,N. et al. (2009) Mutations of ASXL1 gene in myeloproliferative neoplasms. Leukemia, 23, 2183-2186.
11. Chen,X. et al. (2010) Structure of proteasome ubiquitin receptor hRpn13 and its activation by the scaffolding protein hRpn2. Mol. Cell, 38, 404-415.
12. Chen,Y. et al. (2011) Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding. EMBO Rep., 12, 797-803.
13. Cho,Y.S. et al. (2006) Additional sex comb-like 1 (ASXL1), in cooperation with SRC- 1, acts as a ligand-dependent coactivator for retinoic acid receptor. J. Biol. Chem., 281, 17588-17598.
14. Clark,K.L. et al. (1993) Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature, 364, 412-420.
15. Conaway,R.C. and Conaway,J.W. (2009) The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem. Sci., 34, 71-77.
16. Finn,R.D. et al. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
17. Fisher,C.L. et al. (2003) A human homolog of additional sex combs, ADDITIONAL SEX COMBS-LIKE 1, maps to chromosome 20q11. Gene, 306, 115-126.
18. Fisher,C.L. et al. (2006) Characterization of Asxl1, a murine homolog of additional sex combs, and analysis of the Asx-like gene family. Gene, 369, 109-118.
19. Fisher,C.L. et al. (2010a) Loss-of-function additional sex combs like 1mutations disrupt hematopoiesis but do not cause severe myelodysplasia or leukemia. Blood, 115, 38-46.
20. Fisher,C.L. et al. (2010b) Additional sex combs-like 1 belongs to the enhancer of trithorax and polycomb group and genetically interacts with Cbx2 in mice. Dev. Biol., 337, 9-15.
21. Gelsi-Boyer,V. et al. (2009) Mutations of polycomb-associated gene ASXL1 in myelodysplastic syndromes and chronic myelomonocytic leukaemia. Br. J. Haematol., 145, 788-800.
22. Hamazaki,J. et al. (2006) A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J., 25, 4524-4536.
23. Hellström-Lindberg,E. (2010) Significance of JAK2 and TET2 mutations in myelodysplastic syndromes. Blood Rev., 24, 83-90.
24. Hoischen,A. et al. (2011) De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome. Nat. Genet., 43, 729-731.
25. Katoh,M. and Katoh,M. (2003) Identification and characterization of ASXL2 gene in silico. Int. J. Oncol., 23, 845-850.
26. Katoh,M. and Katoh,M. (2004) Identification and characterization of ASXL3 gene in silico. Int. J. Oncol., 24, 1617-1622.
27. Komander,D. et al. (2009) Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol., 10, 550-563.
28. Lee,S.W. et al. (2010) ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1. J. Biol. Chem., 285, 18-29.
29. Manfield,I.W. et al. (2007) Conservation, convergence, and divergence of lightresponsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol., 143, 941-958.
30. McLendon,R. et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
31. Milne,T.A. et al. (1999) The additional sex combs gene of Drosophila is required for activation and repression of homeotic loci, and interacts specifically with Polycomb and super sex combs. Mol. Gen. Genet., 261, 753-761.
32. Misaghi,S. et al. (2009) Association of C-terminal ubiquitin hydrolase BRCA1- associated protein 1 with cell cycle regulator host cell factor 1. Mol. Cell Biol., 29, 2181-2192.
33. Papamichos-Chronakis,M. et al. (2011) Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell, 144, 200-213.
34. Park,U.H. et al. (2011) Additional sex comb-like (ASXL) proteins 1 and 2 play opposite roles in adipogenesis via reciprocal regulation of peroxisome proliferator-activated receptor {gamma}. J. Biol. Chem., 286, 1354-1363.
35. Qiu,X.B. et al. (2006) hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J., 25, 5742-5753.
36. Sanchez-Pulido,L. et al. (2008) RAWUL: a new ubiquitin-like domain in PRC1 ring finger proteins that unveils putative plant and worm PRC1 orthologs. BMC Genomics, 9, 308.
37. Sarvan,S. et al. (2011) Crystal structure of the trithorax group protein ASH2L reveals a forkhead-like DNA binding domain. Nat. Struct. Mol. Biol., 18, 857-859.
38. Scheuermann,J.C. et al. (2010). Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature, 465, 243-247.
39. Scotto,L. et al. (2008) Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression. Genes Chromosomes Cancer, 47, 755-765.
40. Sinclair,D.A. et al. (1992) Genetic analysis of the additional sex combs locus of Drosophila melanogaster. Genetics, 130, 817-825.
41. Soding,J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, 244-248.
42. Stroud,J.C. et al. (2006) Structure of the forkhead domain of FOXP2 bound to DNA. Structure, 14, 159-166.
43. Tsai,K.L. et al. (2006) Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins. J. Biol. Chem., 281, 17400-17409.
44. Williams,D.S. et al. (2010) Nonsense mediated decay resistant mutations are a source of expressed mutant proteins in colon cancer cell lines with microsatellite instability. PLoS One, 5, e16012.
45. Yao,T. et al. (2006) Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat. Cell. Biol., 8, 994-1002.
46. Yao,T. et al. (2008) Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Mol. Cell, 31, 909-917