Characteristics of the CArG-SRF binding context in mammalian genomes

Mammalian Genome

Volumn 21, Issue 1-2, 2010, Pages 104-113

  Wu, Wenwu ^a   Shen, Xia ^a   Tao, Shiheng ^a  

^a NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; PROTEIN CARG; REPRESSOR PROTEIN; SERUM RESPONSE FACTOR; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER SIMULATION; DNA FLANKING REGION; GENOME ANALYSIS; INTRON; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; CPG ISLANDS; GENOME; GENOME, HUMAN; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN GROUP A-B; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SERUM RESPONSE FACTOR;

MAMMALIA;

EID: 77949271497     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-009-9238-x     Document Type: Article

References (52)

1. S Alberti SM Krause O Kretz U Philippar T Lemberger, et al. 2005 Neuronal migration in the murine rostral migratory stream requires serum response factor Proc Natl Acad Sci USA 102 6148 6153 10.1073/pnas.0501191102 1:CAS:528:DC%2BD2MXkt1Cls7g%3D 15837932 (Pubitemid 40594270)
2. F Antequera 2003 Structure, function and evolution of CpG island promoters Cell Mol Life Sci 60 1647 1658 10.1007/s00018-003-3088-6 1:CAS:528:DC%2BD3sXnsFynurY%3D 14504655 (Pubitemid 37041363)
3. S Arsenian B Weinhold M Oelgeschlager U Ruther A Nordheim 1998 Serum response factor is essential for mesoderm formation during mouse embryogenesis EMBO J 17 6289 6299 10.1093/emboj/17.21.6289 1:CAS:528:DyaK1cXnsVKht7c%3D 9799237 (Pubitemid 28497801)
4. RD Bell R Deane N Chow X Long A Sagare, et al. 2009 SRF and myocardin regulate LRP-mediated amyloid-beta clearance in brain vascular cells Nat Cell Biol 11 143 153 10.1038/ncb1819 1:CAS:528:DC%2BD1MXht1Oqt7g%3D 19098903
5. AP Bird 1980 DNA methylation and the frequency of CpG in animal DNA Nucleic Acids Res 8 1499 1504 10.1093/nar/8.7.1499 1:CAS:528:DyaL3cXktVantb8%3D 6253938
6. B Cen A Selvaraj R Prywes 2004 Myocardin/MKL family of SRF coactivators: key regulators of immediate early and muscle specific gene expression J Cell Biochem 93 74 82 10.1002/jcb.20199 1:CAS:528:DC%2BD2cXns1Siur4%3D 15352164
7. J Chai AS Tarnawski 2002 Serum response factor: discovery, biochemistry, biological roles and implications for tissue injury healing J Physiol Pharmacol 53 147 157 1:CAS:528:DC%2BD38XlvVKgtb8%3D 12120892
8. SJ Cooper ND Trinklein L Nguyen RM Myers 2007 Serum response factor binding sites differ in three human cell types Genome Res 17 136 144 10.1101/gr.5875007 1:CAS:528:DC%2BD2sXhsFKisr8%3D 17200232 (Pubitemid 46220758)
9. C Coulondre JH Miller PJ Farabaugh W Gilbert 1978 Molecular basis of base substitution hotspots in Escherichia coli Nature 274 775 780 10.1038/274775a0 1:CAS:528:DyaE1MXpvFylsA%3D%3D 355893
10. S De Folter GC Angenent 2006 trans meets cis in MADS science Trends Plant Sci 11 224 231 10.1016/j.tplants.2006.03.008 16616581 (Pubitemid 43674087)
11. M Ehrlich RY Wang 1981 5-Methylcytosine in eukaryotic DNA Science 212 1350 1357 10.1126/science.6262918 1:CAS:528:DyaL3MXktlOhtrk%3D 6262918
12. A Fleige S Alberti L Grobe U Frischmann R Geffers, et al. 2007 Serum response factor contributes selectively to lymphocyte development J Biol Chem 282 24320 24328 10.1074/jbc.M703119200 1:CAS:528:DC%2BD2sXoslOnu7w%3D 17591768 (Pubitemid 47328050)
13. JA Hendrix BR Wamhoff OG McDonald S Sinha T Yoshida, et al. 2005 5′ CArG degeneracy in smooth muscle alpha-actin is required for injury-induced gene suppression in vivo J Clin Invest 115 418 427 1:CAS:528: DC%2BD2MXhtFyjsbk%3D 15690088
14. A Huet A Parlakian MC Arnaud JM Glandieres P Valat, et al. 2005 Mechanism of binding of serum response factor to serum response element FEBS J 272 3105 3119 10.1111/j.1742-4658.2005.04724.x 1:CAS:528:DC%2BD2MXlslCiu7o%3D 15955069 (Pubitemid 40904697)
15. D Iyer D Chang J Marx L Wei EN Olson, et al. 2006 Serum response factor MADS box serine-162 phosphorylation switches proliferation and myogenic gene programs Proc Natl Acad Sci USA 103 4516 4521 10.1073/pnas.0505338103 1:CAS:528:DC%2BD28XjtlKjtb0%3D 16537394
16. K Jabbari G Bernardi 2004 Cytosine methylation and CpG, TpG (CpA) and TpA frequencies Gene 333 143 149 10.1016/j.gene.2004.02.043 1:CAS:528: DC%2BD2cXksFOmtrc%3D 15177689 (Pubitemid 38737360)
17. V Joliot M Demma R Prywes 1995 Interaction with RAP74 subunit of TFIIF is required for transcriptional activation by serum response factor Nature 373 632 635 10.1038/373632a0 1:CAS:528:DyaK2MXjsl2mtr0%3D 7854423
18. PR Kemp JC Metcalfe 2000 Four isoforms of serum response factor that increase or inhibit smooth-muscle-specific promoter activity Biochem J 345 Pt 3 445 451 10.1042/0264-6021:3450445 1:CAS:528:DC%2BD3cXisFOlsLY%3D 10642500 (Pubitemid 30099071)
19. H Koegel L von Tobel M Schafer S Alberti E Kremmer, et al. 2009 Loss of serum response factor in keratinocytes results in hyperproliferative skin disease in mice J Clin Invest 119 899 910 10.1172/JCI37771 1:CAS:528: DC%2BD1MXktlSnt70%3D 19307725
20. S Leung NG Miyamoto 1989 Point mutational analysis of the human c-fos serum response factor binding site Nucleic Acids Res 17 1177 1195 10.1093/nar/17.3.1177 1:CAS:528:DyaL1MXhvVOjtLs%3D 2493627
21. X Long EE Creemers DZ Wang EN Olson JM Miano 2007 Myocardin is a bifunctional switch for smooth versus skeletal muscle differentiation Proc Natl Acad Sci USA 104 16570 16575 10.1073/pnas.0708253104 1:CAS:528: DC%2BD2sXht1Wgsr3L 17940050 (Pubitemid 350211059)
22. CP Mack MM Thompson S Lawrenz-Smith GK Owens 2000 Smooth muscle alpha-actin CArG elements coordinate formation of a smooth muscle cell-selective, serum response factor-containing activation complex Circ Res 86 221 232 1:CAS:528:DC%2BD3cXht1Cktrg%3D 10666419
23. OG McDonald BR Wamhoff MH Hoofnagle GK Owens 2006 Control of SRF binding to CArG box chromatin regulates smooth muscle gene expression in vivo J Clin Invest 116 36 48 10.1172/JCI26505 1:CAS:528:DC%2BD28XjslOitg%3D%3D 16395403 (Pubitemid 43121789)
24. JM Miano 2003 Serum response factor: toggling between disparate programs of gene expression J Mol Cell Cardiol 35 577 593 10.1016/S0022-2828(03)00110-X 1:CAS:528:DC%2BD3sXkt1GktLo%3D 12788374 (Pubitemid 36681543)
25. JM Miano 2008 Deck of CArGs Circ Res 103 13 15 10.1161/CIRCRESAHA.108. 179978 1:CAS:528:DC%2BD1cXhtVCiu7rP 18596263
26. JM Miano N Ramanan MA Georger KL de Mesy Bentley RL Emerson, et al. 2004 Restricted inactivation of serum response factor to the cardiovascular system Proc Natl Acad Sci USA 101 17132 17137 10.1073/pnas.0406041101 1:CAS:528:DC%2BD2cXhtFagu7bP 15569937 (Pubitemid 39627786)
27. JM Miano X Long K Fujiwara 2007 Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus Am J Physiol Cell Physiol 292 C70 C81 10.1152/ajpcell.00386.2006 1:CAS:528:DC%2BD2sXisFCrtLY%3D 16928770 (Pubitemid 46115122)
28. MW Nachman SL Crowell 2000 Estimate of the mutation rate per nucleotide in humans Genetics 156 297 304 1:CAS:528:DC%2BD3cXntVylt74%3D 10978293
29. Z Niu W Yu SX Zhang M Barron NS Belaguli, et al. 2005 Conditional mutagenesis of the murine serum response factor gene blocks cardiogenesis and the transcription of downstream gene targets J Biol Chem 280 32531 32538 10.1074/jbc.M501372200 1:CAS:528:DC%2BD2MXpvVyqu7g%3D 15929941 (Pubitemid 41361867)
30. A Parlakian C Charvet B Escoubet M Mericskay JD Molkentin, et al. 2005 Temporally controlled onset of dilated cardiomyopathy through disruption of the SRF gene in adult heart Circulation 112 2930 2939 1:CAS:528:DC%2BD2MXhtFKqtrjI 16260633
31. LC Patten NS Belaguli MJ Baek SP Fagan SS Awad, et al. 2004 Serum response factor is alternatively spliced in human colon cancer J Surg Res 121 92 100 10.1016/j.jss.2004.02.031 1:CAS:528:DC%2BD2cXmslalsrY%3D 15313381 (Pubitemid 39094101)
32. L Pellegrini S Tan TJ Richmond 1995 Structure of serum response factor core bound to DNA Nature 376 490 498 10.1038/376490a0 1:CAS:528: DyaK2MXnsVCrs7Y%3D 7637780
33. MM Petit H Lindskog E Larsson P Wasteson E Athley, et al. 2008 Smooth muscle expression of lipoma preferred partner is mediated by an alternative intronic promoter that is regulated by serum response factor/myocardin Circ Res 103 61 69 10.1161/CIRCRESAHA.108.177436 1:CAS:528:DC%2BD1cXnsFOmtLY%3D 18511849
34. R Prywes RG Roeder 1987 Purification of the c-fos enhancer-binding protein Mol Cell Biol 7 3482 3489 1:CAS:528:DyaL1cXltFCqtg%3D%3D 3316979
35. SS Rensen PM Niessen X Long PA Doevendans JM Miano, et al. 2006 Contribution of serum response factor and myocardin to transcriptional regulation of smoothelins Cardiovasc Res 70 136 145 10.1016/j.cardiores.2005.12. 018 1:CAS:528:DC%2BD28XivVejsbY%3D 16451796
36. JM Rozenberg A Shlyakhtenko K Glass V Rishi MV Myakishev, et al. 2008 All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues BMC Genomics 9 67 10.1186/1471-2164-9-67 18252004 (Pubitemid 351359712)
37. PE Shaw H Schroter A Nordheim 1989 The ability of a ternary complex to form over the serum response element correlates with serum inducibility of the human c-fos promoter Cell 56 563 572 10.1016/0092-8674(89)90579-5 1:CAS:528:DyaL1MXhs1Oht7g%3D 2492906 (Pubitemid 19065528)
38. X Shen B Walsh JJ Li HX Pang WJ Wang, et al. 2009 The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus Genome 52 217 221 10.1139/G08-117 1:CAS:528:DC%2BD1MXit1agtrw%3D 19234549
39. V Shepelev A Fedorov 2006 Advances in the Exon-Intron Database (EID) Brief Bioinform 7 178 185 10.1093/bib/bbl003 1:CAS:528:DC%2BD28Xot1CgtLY%3D 16772261 (Pubitemid 44404884)
40. P Shore AD Sharrocks 1995 The MADS-box family of transcription factors Eur J Biochem 229 1 13 10.1111/j.1432-1033.1995.tb20430.x 1:CAS:528: DyaK2MXltFSgtbo%3D 7744019
41. J Stepanek M Vincent PY Turpin D Paulin S Fermandjian, et al. 2007 C → G base mutations in the CArG box of c-fos serum response element alter its bending flexibility. Consequences for core-SRF recognition FEBS J 274 2333 2348 10.1111/j.1742-4658.2007.05768.x 1:CAS:528:DC%2BD2sXlt1Oqu70%3D 17403043 (Pubitemid 46633460)
42. Q Sun G Chen JW Streb X Long Y Yang, et al. 2006 Defining the mammalian CArGome Genome Res 16 197 207 10.1101/gr.4108706 1:CAS:528:DC%2BD28XhsFahsb0%3D 16365378 (Pubitemid 43200268)
43. R Treisman 1986 Identification of a protein-binding site that mediates transcriptional response of the c-fos gene to serum factors Cell 46 567 574 10.1016/0092-8674(86)90882-2 1:CAS:528:DyaL28Xlt1yksb0%3D 3524858
44. R Treisman 1987 Identification and purification of a polypeptide that binds to the c-fos serum response element EMBO J 6 2711 2717 1:CAS:528:DyaL2sXmtlWku7w%3D 3119326
45. R Treisman 1992 The serum response element Trends Biochem Sci 17 423 426 10.1016/0968-0004(92)90013-Y 1:CAS:528:DyaK38Xmt1Oiu74%3D 1455511
46. A Verger M Duterque-Coquillaud 2002 When Ets transcription factors meet their partners Bioessays 24 362 370 10.1002/bies.10068 1:CAS:528: DC%2BD38XjsFWjt70%3D 11948622 (Pubitemid 34305691)
47. H Wakaguri R Yamashita Y Suzuki S Sugano K Nakai 2008 DBTSS: database of transcription start sites, progress report 2008 Nucleic Acids Res 36 D97 D101 10.1093/nar/gkm901 1:CAS:528:DC%2BD1cXhtVSrsrg%3D 17942421 (Pubitemid 351149703)
48. JC Walser L Ponger AV Furano 2008 CpG dinucleotides and the mutation rate of non-CpG DNA Genome Res 18 1403 1414 10.1101/gr.076455.108 1:CAS:528:DC%2BD1cXhtV2qsrzE 18550801
49. CT Workman Y Yin DL Corcoran T Ideker GD Stormo, et al. 2005 enoLOGOS: a versatile web tool for energy normalized sequence logos Nucleic Acids Res 33 W389 W392 10.1093/nar/gki439 1:CAS:528:DC%2BD2MXlslyqsbw%3D 15980495 (Pubitemid 44529949)
50. 2 test J R Stat Soc 1 217 235
51. SX Zhang E Garcia-Gras DR Wycuff SJ Marriot N Kadeer, et al. 2005 Identification of direct serum-response factor gene targets during Me2SO-induced P19 cardiac cell differentiation J Biol Chem 280 19115 19126 10.1074/jbc.M413793200 1:CAS:528:DC%2BD2MXjvFers78%3D 15699019 (Pubitemid 41379618)
52. H Zhu V Joliot R Prywes 1994 Role of transcription factor TFIIF in serum response factor-activated transcription J Biol Chem 269 3489 3497 1:CAS:528:DyaK2cXhvVCmtLk%3D 8106390