Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Hahn, Phillip ^a   Böse, Jens ^a   Edler, Stefanie ^a   Lengeling, Andreas ^a,b  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; DIOXYGENASE; JUMONJI C DOMAIN CONTAINING 6 PROTEIN; OXIDOREDUCTASE; CELL SURFACE RECEPTOR; ISOPROTEIN; JMJD6 PROTEIN, HUMAN;

AMINO TERMINAL SEQUENCE; ARTICLE; AUTOANALYSIS; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE DELETION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE STRUCTURE; GENETIC ORGANIZATION; GENETIC VARIABILITY; HUMAN; IN VIVO STUDY; KNOCKOUT MOUSE; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; C57BL MOUSE; CHEMICAL STRUCTURE; CHROMOSOME MAP; COMPARATIVE STUDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETICS; GENOMICS; METHODOLOGY; MOUSE; MOUSE MUTANT; NUCLEIC ACID DATABASE; PHYLOGENY; PROMOTER REGION; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL MODEL;

MAMMALIA; MUS;

AMINO ACID SEQUENCE; ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENOMICS; HUMANS; LIKELIHOOD FUNCTIONS; MICE; MICE, INBRED C57BL; MICE, KNOCKOUT; MODELS, MOLECULAR; PHYLOGENY; PROMOTER REGIONS (GENETICS); PROTEIN ISOFORMS; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, CELL SURFACE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

EID: 47249153638     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-293     Document Type: Article

References (108)

1. Takeuchi T Yamazaki Y Katoh-Fukui Y Tsuchiya R Kondo S Motoyama J Higashinakagawa T Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation Genes Dev 1995, 9:1211-1222. 10.1101/ gad.9.10.1211 7758946
2. Balciunas D Ronne H Evidence of domain swapping within the jumonji family of transcription factors Trends Biochem Sci 2000, 25:274-276. 10.1016/S0968-0004(00)01593-0 10838566
3. Clissold PM Ponting CP JmjC: Cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta Trends Biochem Sci 2001, 26:7-9. 10.1016/S0968-0004(00)01700-X 11165500
4. Klose RJ Kallin EM Zhang Y JmjC-domain-containing proteins and histone demethylation Nat Rev Genet 2006, 7:715-727. 10.1038/nrg1945 16983801
5. Takeuchi T Watanabe Y Takano-Shimizu T Kondo S Roles of jumonji and jumonji family genes in chromatin regulation and development Dev Dyn 2006, 235:2449-2459. 10.1002/dvdy.20851 16715513
6. Clifton IJ McDonough MA Ehrismann D Kershaw NJ Granatino N Schofield CJ Structural studies on 2-oxoglutarate oxygenases and related double-stranded beta-helix fold proteins J Inorg Biochem 2006, 100:644-669. 10.1016/j.jinorgbio.2006.01.024 16513174
7. Dunwell JM Culham A Carter CE Sosa-Aguirre CR Goodenough PW Evolution of functional diversity in the cupin superfamily Trends Biochem Sci 2001, 26:740-746. 10.1016/S0968-0004(01)01981-8 11738598
8. Schofield CJ Zhang Z Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes Curr Opin Struct Biol 1999, 9:722-731. 10.1016/S0959-440X(99)00036-6 10607676
9. Trewick SC McLaughlin PJ Allshire RC Methylation: Lost in hydroxylation? EMBO Rep 2005, 6:315-320. 1299289 15809658 10.1038/sj.embor.7400379
10. Lee Y Song AJ Baker R Micales B Conway SJ Lyons GE Jumonji, a nuclear protein that is necessary for normal heart development Circ Res 2000, 86:932-938. 10807864
11. Takeuchi T Kojima M Nakajima K Kondo S jumonji gene is essential for the neurulation and cardiac development of mouse embryos with a C3H/He background Mech Dev 1999, 86:29-38. 10.1016/S0925-4773(99)00100-8 10446263
12. Toyoda M Kojima M Takeuchi T Jumonji is a nuclear protein that participates in the negative regulation of cell growth Biochem Biophys Res Commun 2000, 274:332-336. 10.1006/bbrc.2000.3138 10913339
13. Benevolenskaya EV Murray HL Branton P Young RA Kaelin WG Jr Binding of pRB to the PHD protein RBP2 promotes cellular differentiation Mol Cell 2005, 18:623-635. 10.1016/j.molcel.2005.05.012 15949438
14. Hsieh JC Sisk JM Jurutka PW Haussler CA Slater SA Haussler MR Thompson CC Physical and functional interaction between the vitamin D receptor and hairless corepressor, two proteins required for hair cycling J Biol Chem 2003, 278:38665-38674. 10.1074/jbc.M304886200 12847098
15. Moraitis: AN Giguere V Thompson CC Novel mechanism of nuclear receptor corepressor interaction dictated by activation function 2 helix determinants Mol Cell Biol 2002, 22:6831-6841. 134023 12215540 10.1128/ MCB.22.19.6831-6841.2002
16. Potter GB Beaudoin GM 3rd DeRenzo CL Zarach JM Chen SH Thompson CC The hairless gene mutated in congenital hair loss disorders encodes a novel nuclear receptor corepressor Genes Dev 2001, 15:2687-2701. 312820 11641275 10.1101/gad.916701
17. Ahmad W Faiyaz ul Haque M Brancolini V Tsou HC ul Haque S Lam H Aita VM Owen J deBlaquiere M Frank J Alopecia universalis associated with a mutation in the human hairless gene Science 1998, 279:720-724. 10.1126/ science.279.5351.720 9445480
18. Cichon S Anker M Vogt IR Rohleder H Putzstuck M Hillmer A Farooq SA Al-Dhafri KS Ahmad M Haque S Cloning, genomic organization, alternative transcripts and mutational analysis of the gene responsible for autosomal recessive universal congenital alopecia Hum Mol Genet 1998, 7:1671-1679. 10.1093/hmg/7.11.1671 9736769
19. Zarach JM Beaudoin GM 3rd Coulombe PA Thompson CC The co-repressor hairless has a role in epithelial cell differentiation in the skin Development 2004, 131:4189-4200. 10.1242/dev.01303 15280217
20. Martin C Zhang Y The diverse functions of histone lysine methylation Nat Rev Mol Cell Biol 2005, 6:838-849. 10.1038/nrm1761 16261189
21. Tsukada Y Fang J Erdjument-Bromage H Warren ME Borchers CH Tempst P Zhang Y Histone demethylation by a family of JmjC domain-containing proteins Nature 2006, 439:811-816. 10.1038/nature04433 16362057
22. Chen Z Zang J Whetstine J Hong X Davrazou F Kutateladze TG Simpson M Mao Q Pan CH Dai S Structural insights into histone demethylation by JMJD2 family members Cell 2006, 125:691-702. 10.1016/j.cell.2006.04.024 16677698
23. Whetstine JR Nottke A Lan F Huarte M Smolikov S Chen Z Spooner E Li E Zhang G Colaiacovo M Shi Y Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases Cell 2006, 125:467-481. 10.1016/ j.cell.2006.03.028 16603238
24. Klose RJ Gardner KE Liang G Erdjument-Bromage H Tempst P Zhang Y Demethylation of histone H3K36 and H3K9 by Rph1: A vestige of an H3K9 methylation system in Saccharomyces cerevisiae? Mol Cell Biol 2007, 27:3951-3961. 1900024 17371840 10.1128/MCB.02180-06
25. Tu S Bulloch EM Yang L Ren C Huang WC Hsu PH Chen CH Liao CL Yu HM Lo WS Identification of histone demethylases in Sacchromyces cerevisiae J Biol Chem 2007, 282:14262-14271. 10.1074/jbc.M609900200 17369256
26. Yamane K Tateishi K Klose RJ Fang J Fabrizio LA Erdjument-Bromage H Taylor-Papadimitriou J Tempst P Zhang Y PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation Mol Cell 2007, 25:801-812. 10.1016/j.molcel.2007.03.001 17363312
27. Cloos PA Christensen J Agger K Maiolica A Rappsilber J Antal T Hansen KH Helin K The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3 Nature 2006, 442:307-311. 10.1038/nature04837 16732293
28. Fodor BD Kubicek S Yonezawa M O'Sullivan RJ Sengupta R Perez-Burgos L Opravil S Mechtler K Schotta G Jenuwein T Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells Genes Dev 2006, 20:1557-1562. 1482475 16738407 10.1101/gad.388206
29. Klose RJ Yamane K Bae Y Zhang D Erdjument-Bromage H Tempst P Wong J Zhang Y The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36 Nature 2006, 442:312-316. 10.1038/ nature04853 16732292
30. Wissmann M Yin N Muller JM Greschik H Fodor BD Jenuwein T Vogler C Schneider R Gunther T Buettner R Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression Nat Cell Biol 2007, 9:347-353. 10.1038/ncb1546 17277772
31. Christensen J Agger K Cloos PA Pasini D Rose S Sennels L Rappsilber J Hansen KH Salcini AE Helin K RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3 Cell 2007, 1281063-1076. 10.1016/j.cell.2007.02.003 17320161
32. Klose RJ Yan Q Tothova Z Yamane K Erdjument-Bromage H Tempst P Gilliland DG Zhang Y Kaelin WG Jr The retinoblastoma binding protein RBP2 is an H3K4 demethylase Cell 2007, 128:889-900. 10.1016/j.cell.2007.02.013 17320163
33. Iwase S Lan F Bayliss P de la Torre-Ubieta L Huarte M Qi HH Whetstine JR Bonni A Roberts TM Shi Y The X-linked mental retardation gene SMCX/ JARID1C defines a family of histone H3 lysine 4 demethylases Cell 2007, 128:1077-1088. 10.1016/j.cell.2007.02.017 17320160
34. Lee MG Norman J Shilatifard A Shiekhattar R Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein Cell 2007, 128:877-887. 10.1016/j.cell.2007.02.004 17320162
35. Liang G Klose RJ Gardner KE Zhang Y Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase Nat Struct Mol Biol 2007, 14:243-245. 10.1038/ nsmb1204 17310254
36. Seward DJ Cubberley G Kim S Schonewald M Zhang L Tripet B Bentley DL Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins Nat Struct Mol Biol 2007, 14:240-242. 10.1038/nsmb1200 17310255
37. Eissenberg JC Lee MG Schneider J Ilvarsonn A Shiekhattar R Shilatifard A The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase Nat Struct Mol Biol 2007, 14:344-346. 10.1038/nsmb1217 17351630
38. Lee N Zhang J Klose RJ Erdjument-Bromage H Tempst P Jones RS Zhang Y The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase Nat Struct Mol Biol 2007, 14:341-343. 10.1038/nsmb1216 17351631
39. Secombe J Li L Carlos L Eisenman RN The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth Genes Dev 2007, 21:537-551. 1820896 17311883 10.1101/gad.1523007
40. Huarte M Lan F Kim T Vaughn MW Zaratiegui M Martienssen RA Buratowski S Shi Y The fission yeast JMJ2 reverses histone H3 lysine 4 tri-methylation J Biol Chem 2007, 282:21662-21670. 10.1074/ jbc.M703897200 17550896
41. Agger K Cloos PA Christensen J Pasini D Rose S Rappsilber J Issaeva I Canaani E Salcini AE Helin K UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development Nature 2007, 449:731-734. 10.1038/nature06145 17713478
42. De Santa F Totaro MG Prosperini E Notarbartolo S Testa G Natoli G The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing Cell 2007, 130:1083-1094. 10.1016/ j.cell.2007.08.019 17825402
43. Lan F Bayliss PE Rinn JL Whetstine JR Wang JK Chen S Iwase S Alpatov R Issaeva I Canaani E A histone H3 lysine 27 demethylase regulates animal posterior development Nature 2007, 449:689-694. 10.1038/nature06192 17851529
44. Lee MG Villa R Trojer P Norman J Yan KP Reinberg D Di Croce L Shiekhattar R Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination Science 2007, 318:447-450. 10.1126/science.1149042 17761849
45. Yamane K Toumazou C Tsukada Y Erdjument-Bromage H Tempst P Wong J Zhang Y JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor Cell 2006, 125:483-495. 10.1016/ j.cell.2006.03.027 16603237
46. Zofall M Grewal SI Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats Mol Cell 2006, 22:681-692. 10.1016/j.molcel.2006.05.010 16762840
47. Huang Y Fang J Bedford MT Zhang Y Xu RM Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A Science 2006, 312:748-751. 10.1126/science.1125162 16601153
48. Dann CE 3rd Bruick RK Deisenhofer J Structure of factor-inhibiting hypoxia-inducible factor 1: An asparaginyl hydroxylase involved in the hypoxic response pathway Proc Natl Acad Sci USA 2002, 99:15351-15356. 137720 12432100 10.1073/pnas.202614999
49. Elkins JM Hewitson KS McNeill LA Seibel JF Schlemminger I Pugh CW Ratcliffe PJ Schofield CJ Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha J Biol Chem 2003, 278:1802-1806. 10.1074/ jbc.C200644200 12446723
50. Schofield CJ Ratcliffe PJ Oxygen sensing by HIF hydroxylases Nat Rev Mol Cell Biol 2004, 5:343-354. 10.1038/nrm1366 15122348
51. Falnes PO Johansen RF Seeberg E AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli Nature 2002, 419:178-182. 10.1038/nature01048 12226668
52. Trewick SC Henshaw TF Hausinger RP Lindahl T Sedgwick B Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage Nature 2002, 419:174-178. 10.1038/nature00908 12226667
53. Aravind L Koonin EV The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases Genome Biol 2001, 2. RESEARCH0007 30706 11276424 10.1186/ gb-2001-2-3-research0007
54. Böse J Gruber AD Helming L Schiebe S Wegener I Hafner M Beales M Kontgen F Lengeling A The phosphatidylserine receptor has essential functions during embryogenesis but not in apoptotic cell removal J Biol 2004, 3:15. 549712 15345036 10.1186/jbiol10
55. Schneider JE Böse J Bamforth SD Gruber AD Broadbent C Clarke K Neubauer S Lengeling A Bhattacharya S Identification of cardiac malformations in mice lacking Ptdsr using a novel high-throughput magnetic resonance imaging technique BMC Dev Biol 2004, 4:16. 545075 15615595 10.1186/1471-213X-4-16
56. Fadok VA Bratton DL Rose DM Pearson A Ezekewitz RA Henson PM A receptor for phosphatidylserine-specific clearance of apoptotic cells Nature 2000, 405:85-90. 10.1038/35011084 10811223
57. Cikala M Alexandrova O David CN Proschel M Stiening B Cramer P Böttger A The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity BMC Cell Biol 2004, 5:26. 442123 15193161 10.1186/1471-2121-5-26
58. Cui P Qin B Liu N Pan G Pei D Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals Exp Cell Res 2004, 293:154-163. 10.1016/j.yexcr.2003.09.023 14729065
59. Krieser RJ Moore FE Dresnek D Pellock BJ Patel R Huang A Brachmann C White K The Drosophila homolog of the putative phosphatidylserine receptor functions to inhibit apoptosis Development 2007, 134:2407-2414. 10.1242/dev.02860 17522160
60. Mitchell JE Cvetanovic M Tibrewal N Patel V Colamonici OR Li MO Flavell RA Levine JS Birge RB Ucker DS The presumptive phosphatidylserine receptor is dispensable for innate anti-inflammatory recognition and clearance of apoptotic cells J Biol Chem 2006, 281:5718-5725. 10.1074/ jbc.M509775200 16317002
61. Tibrewal N Liu T Li H Birge RB Characterization of the biochemical and biophysical properties of the phosphatidylserine receptor (PS-R) gene product Mol Cell Biochem 2007, 304:119-125. 10.1007/s11010-007-9492-8 17534701
62. Li MO Sarkisian MR Mehal WZ Rakic P Flavell RA Phosphatidylserine receptor is required for clearance of apoptotic cells Science 2003, 302:1560-1563. 10.1126/science.1087621 14645847
63. Kunisaki Y Masuko S Noda M Inayoshi A Sanui T Harada M Sasazuki T Fukui Y Defective fetal liver erythropoiesis and T lymphopoiesis in mice lacking the phosphatidylserine receptor Blood 2004, 103:3362-3364. 10.1182/blood-2003-09-3245 14715629
64. Fackelmayer FO Protein arginine methyltransferases: Guardians of the Arg? Trends Biochem Sci 2005, 30:666-671. 16257219
65. Bermingham JR Jr Arden KC Naumova AK Sapienza C Viars CS Fu XD Khotz J Manley JL Rosenfeld MG Chromosomal localization of mouse and human genes encoding the splicing factors ASF/SF2 (SFRS1) and SC-35 (SFRS2) Genomics 1995, 29:70-79. 10.1006/geno.1995.1216 8530103
66. Schwartz S Zhang Z Frazer KA Smit A Riemer C Bouck J Gibbs R Hardison R Miller W PipMaker - a web server for aligning two genomic DNA sequences Genome Res 2000, 10:577-586. 310868 10779500 10.1101/gr.10.4.577
67. Krüger J Sczyrba A Kurtz S Giegerich R e2g: An interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences Nucleic Acids Res 2004, 32:W301-304. 441616 15215398 10.1093/nar/gkh478
68. Florea L Hartzell G Zhang Z Rubin GM Miller W A computer program for aligning a cDNA sequence with a genomic DNA sequence Genome Res 1998, 8:967-974. 310774 9750195
69. Fadok VA Xue D Henson P If phosphatidylserine is the death knell, a new phosphatidylserine-specific receptor is the bellringer Cell Death Differ 2001, 8:582-587. 10.1038/sj.cdd.4400856 11536008
70. Huntley MA Golding GB Selection and slippage creating serine homopolymers Mol Biol Evol 2006, 23:2017-2025. 10.1093/molbev/msl073 16877497
71. Amrani N Sachs MS Jacobson A Early nonsense: mRNA decay solves a translational problem Nat Rev Mol Cell Biol 2006, 7:415-425. 10.1038/ nrm1942 16723977
72. Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997, 278:631-637. 10.1126/science.278.5338.631 9381173
73. Hubbard TJ Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Ensembl 2007 Nucleic Acids Res 2007, 35:D610-617. 1761443 17148474 10.1093/nar/gkl996
74. Söding J Protein homology detection by HMM-HMM comparison Bioinformatics 2005, 21:951-960. 10.1093/bioinformatics/bti125 15531603
75. Sali A Blundell TL Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 1993, 234:779-815. 10.1006/jmbi.1993.1626 8254673
76. Britsch L Dedio J Saedler H Forkmann G Molecular characterization of flavanone 3 beta-hydroxylases. Consensus sequence, comparison with related enzymes and the role of conserved histidine residues Eur J Biochem 1993, 217:745-754. 10.1111/j.1432-1033.1993.tb18301.x 8223617
77. Hogan DA Smith SR Saari EA McCracken J Hausinger RP Site-directed mutagenesis of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding J Biol Chem 2000, 275:12400-12409. 10.1074/jbc.275.17.12400 10777523
78. Lee DH Jin SG Cai S Chen Y Pfeifer GP O'Connor TR Repair of methylation damage in DNA and RNA by mammalian AlkB homologues J Biol Chem 2005, 280:39448-39459. 10.1074/jbc.M509881200 16174769
79. Yu B Edstrom WC Benach J Hamuro Y Weber PC Gibney BR Hunt JF Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB Nature 2006, 439:879-884. 10.1038/nature04561 16482161
80. Klose RJ Zhang Y Regulation of histone methylation by demethylimination and demethylation Nat Rev Mol Cell Biol 2007, 8:307-318. 10.1038/nrm2143 17342184
81. Ozer A Bruick RK Non-heme dioxygenases: Cellular sensors and regulators jelly rolled into one? Nat Chem Biol 2007, 3:144-153. 10.1038/ nchembio863 17301803
82. Weitzman JB The curious world of apoptotic cell clearance J Biol 2004, 3:13. 10.1186/jbiol13
83. Williamson P Schlegel RA Hide and seek: The secret identity of the phosphatidylserine receptor J Biol 2004, 3:14. 549716 15453906 10.1186/ jbiol14
84. Wolf A Schmitz C Bottger A Changing story of the receptor for phosphatidylserine-dependent clearance of apoptotic cells EMBO Rep 2007, 8:465-469. 1866200 17471263 10.1038/sj.embor.7400956
85. Aravind L Landsman D AT-hook motifs identified in a wide variety of DNA-binding proteins Nucleic Acids Res 1998, 26:4413-4421. 147871 9742243 10.1093/nar/26.19.4413
86. Chang B Chen Y Zhao Y Bruick RK JMJD6 is a histone arginine demethylase Science 2007, 318:444-447. 10.1126/science.1145801 17947579
87. Guccione E Bassi C Casadio F Martinato F Cesaroni M Schuchlautz H Luscher B Amati B Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive Nature 2007, 449:933-937. 10.1038/ nature06166 17898714
88. Kirmizis A Santos-Rosa H Penkett CJ Singer MA Vermeulen M Mann M Bahler J Green RD Kouzarides T Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation Nature 2007, 449:928-932. 10.1038/ nature06160 17898715
89. Ng SS Kavanagh KL McDonough MA Butler D Pilka ES Lienard BM Bray JE Savitsky P Gileadi O von Delft F Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity Nature 2007, 448:87-91. 10.1038/nature05971 17589501
90. Kim J Daniel J Espejo A Lake A Krishna M Xia L Zhang Y Bedford MT Tudor, MBT and chromo domains gauge the degree of lysine methylation EMBO Rep 2006, 7:397-403. 1456902 16415788
91. 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. 10.1038/nature05020 16728978
92. Pena PV Davrazou F Shi X Walter KL Verkhusha VV Gozani O Zhao R Kutateladze TG Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 Nature 2006, 442:100-103. 16728977
93. Shi X Hong T Walter KL Ewalt M Michishita E Hung T Carney D Pena P Lan F Kaadige MR ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression Nature 2006, 442:96-99. 10.1038/nature05140 16728974
94. Wysocka J Swigut T Xiao H Milne TA Kwon SY Landry J Kauer M Tackett AJ Chait BT Badenhorst P A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling Nature 2006, 442:86-90. 16728976
95. Hong JR Lin GH Lin CJ Wang WP Lee CC Lin TL Wu JL Phosphatidylserine receptor is required for the engulfment of dead apoptotic cells and for normal embryonic development in zebrafish Development 2004, 131:5417-5427. 10.1242/dev.01409 15469976
96. Wang X Wu YC Fadok VA Lee MC Gengyo-Ando K Cheng LC Ledwich D Hsu PK Chen JY Chou BK Cell corpse engulfment mediated by C. elegans phosphatidylserine receptor through CED-5 and CED-12 Science 2003, 302:1563-1566. 10.1126/science.1087641 14645848
97. RepeatMasker http://www.repeatmasker.org
98. NCBI-BLAST http://www.ncbi.nlm.nih.gov/BLAST
99. SMART http://smart.embl-heidelberg.de
100. Beitz E TEXshade: Shading and labeling of multiple sequence alignments using LATEX2 epsilon Bioinformatics 2000, 16:135-139. 10.1093/ bioinformatics/16.2.135 10842735
101. Biegert A Mayer C Remmert M Soding J Lupas AN The MPI Bioinformatics Toolkit for protein sequence analysis Nucleic Acids Res 2006, 34:W335-339. 1538786 16845021 10.1093/nar/gkl217
102. Swiss-Pdb-Viewer http://expasy.org/spdbv
103. PyMOL http://pymol.sourceforge.net/
104. PHYLIP http://evolution.genetics.washington.edu/phylip.html
105. SUMOplot http://www.abgent.com.cn/doc/sumoplot/login.asp
106. NetNES http://www.cbs.dtu.dk/services/NetNES
107. Jpred-3 http://www.compbio.dundee.ac.uk/~www-jpred
108. NCBI-Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/