Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Bellora, Nicolás ^a,b   Farré, Domènec ^b   Mar, M Mar ^a,c,d  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^c INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 1; HEPATOCYTE NUCLEAR FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR RFX; TRANSCRIPTION FACTOR YY1; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; BINDING SITE; GENE EXPRESSION; GENE SEQUENCE; HOUSEKEEPING GENE; MOUSE; NONHUMAN; PREDICTION; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; TISSUE SPECIFICITY; TRANSCRIPTION REGULATION; ANIMAL; ANTIBODY SPECIFICITY; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NUCLEIC ACID DATABASE;

MAMMALIA;

ANIMALS; DATABASES, NUCLEIC ACID; GENE EXPRESSION REGULATION; MICE; ORGAN SPECIFICITY; PROMOTER REGIONS (GENETICS); SOFTWARE; TRANSCRIPTION FACTORS;

EID: 39749150501     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-459     Document Type: Article

References (45)

1. Maston GA Evans SK Green MR Transcriptional Regulatory Elements in the Human Genome Annu Rev Genomics Hum Genet 2006, 7:29-59 10.1146/ annurev.genom.7.080505.115623 16719718
2. Trinklein ND Aldred SJ Saldanha AJ Myers RM Identification and functional analysis of human transcriptional promoters Genome Res 2003, 13(2):308-312 420378 12566409 10.1101/gr.794803
3. Berendzen KW Stuber K Harter K Wanke D Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves BMC Bioinformatics 2006, 7:522 1698937 17137509 10.1186/1471-2105-7-522
4. Sharov AA Dudekula DB Ko MS CisView: A browser and database of cis-regulatory modules predicted in the mouse genome DNA Res 2006, 13(3):123-134 10.1093/dnares/dsl005 16980320
5. Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals Nature 2005, 434(7031):338-345 10.1038/nature03441 15735639
6. FitzGerald PC Shlyakhtenko A Mir AA Vinson C Clustering of DNA sequences in human promoters Genome Res 2004, 14(8):1562-1574 509265 15256515 10.1101/gr.1953904
7. Marino-Ramirez L Spouge JL Kanga GC Landsman D Statistical analysis of over-represented words in human promoter sequences Nucleic Acids Res 2004, 32(3):949-958 373387 14963262 10.1093/nar/gkh246
8. Wray GA Hahn MW Abouheif E Balhoff JP Pizer M Rockman MV Romano LA The evolution of transcriptional regulation in eukaryotes Mol Biol Evol 2003, 20(9):1377-1419 10.1093/molbev/msg140 12777501
9. Smith B Fang H Pan Y Walker PR Famili AF Sikorska M Evolution of motif variants and positional bias of the cyclic-AMP response element BMC Evol Biol 2007, 7(Suppl 1):S15 1796609 17288573 10.1186/1471-2148-7-S1-S15
10. Roepcke S Zhi D Vingron M Arndt PF Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters Gene 2006, 365:48-56 10.1016/j.gene.2005.09.033 16343812
11. Krivan W Wasserman WW A predictive model for regulatory sequences directing liver-specific transcription Genome Res 2001, 11(9):1559-1566 311083 11544200 10.1101/gr.180601
12. Howard ML Davidson EH cis-Regulatory control circuits in development Dev Biol 2004, 271(1):109-118 10.1016/j.ydbio.2004.03.031 15196954
13. Ambrosini G Praz V Jagannathan V Bucher P Signal search analysis server Nucleic Acids Res 2003, 31(13):3618-3620 169017 12824379 10.1093/nar/ gkg611
14. Bellora N Farre D Mar Alba M PEAKS: Identification of regulatory motifs by their position in DNA sequences Bioinformatics 2007, 23(2):243-244 10.1093/bioinformatics/btl568 17098773
15. PEAKS http://genomics.imim.es/peaks/
16. Zhang W Morris QD Chang R Shai O Bakowski MA Mitsakakis N Mohammad N Robinson MD Zirngibl R Somogyi E Laurin N Eftekharpour E Sat E Grigull J Pan Q Peng WT Krogan N Greenblatt J Fehlings M van der Kooy D Aubin J Bruneau BG Rossant J Blencowe BJ Frey BJ Hughes TR The functional landscape of mouse gene expression J Biol 2004, 3(5):21 549719 15588312 10.1186/jbiol16
17. Karolchik D Baertsch R Diekhans M Furey TS Hinrichs A Lu YT Roskin KM Schwartz M Sugnet CW Thomas DJ Weber RJ Haussler D Kent WJ The UCSC Genome Browser Database Nucleic Acids Res 2003, 31(1):51-54 165576 12519945 10.1093/nar/gkg129
18. Matys V Fricke E Geffers R Gossling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV Kloos DU Land S Lewicki-Potapov B Michael H Munch R Reuter I Rotert S Saxel H Scheer M Thiele S Wingender E TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31(1):374-378 165555 12520026 10.1093/nar/gkg108
19. Vlieghe D Sandelin A De Bleser PJ Vleminckx K Wasserman WW van Roy F Lenhard B A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Nucleic Acids Res 2006, 34(Database issue):D95-7 1347477 16381983 10.1093/nar/gkj115
20. Sharrocks AD The ETS-domain transcription factor family Nat Rev Mol Cell Biol 2001, 2(11):827-837 10.1038/35099076 11715049
21. Rowland BD Bernards R Re-evaluating cell-cycle regulation by E2Fs Cell 2006, 127(5):871-874 10.1016/j.cell.2006.11.019 17129771
22. Suske G The Sp-family of transcription factors Gene 1999, 238(2):291-300 10.1016/S0378-1119(99)00357-1 10570957
23. Smale ST Baltimore D The "initiator" as a transcription control element Cell 1989, 57(1):103-113 10.1016/0092-8674(89)90176-1 2467742
24. Le Cam L Lacroix M Ciemerych MA Sardet C Sicinski P The E4F protein is required for mitotic progression during embryonic cell cycles Mol Cell Biol 2004, 24(14):6467-6475 434264 15226446 10.1128/ MCB.24.14.6467-6475.2004
25. Vinogradov AE Dualism of gene GC content and CpG pattern in regard to expression in the human genome: Magnitude versus breadth Trends Genet 2005, 21(12):639-643 10.1016/j.tig.2005.09.002 16202472
26. Yamashita R Suzuki Y Sugano S Nakai K Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity Gene 2005, 350(2):129-136 10.1016/j.gene.2005.01.012 15784181
27. Odom DT Zizlsperger N Gordon DB Bell GW Rinaldi NJ Murray HL Volkert TL Schreiber J Rolfe PA Gifford DK Fraenkel E Bell GI Young RA Control of pancreas and liver gene expression by HNF transcription factors Science 2004, 303(5662):1378-1381 10.1126/science.1089769 14988562
28. Mahapatra NR Mahata M Ghosh S Gayen JR O'Connor DT Mahata SK Molecular basis of neuroendocrine cell type-specific expression of the chromogranin B gene: Crucial role of the transcription factors CREB, AP-2, Egr-1 and Sp1 J Neurochem 2006, 99(1):119-133 10.1111/ j.1471-4159.2006.04128.x 16987240
29. Wolfe SA van Wert J Grimes SR Transcription factor RFX2 is abundant in rat testis and enriched in nuclei of primary spermatocytes where it appears to be required for transcription of the testis-specific histone H1t gene J Cell Biochem 2006, 99(3):735-746 10.1002/jcb.20959 16676351
30. Thomas MD Kremer CS Ravichandran KS Rajewsky K Bender TP c-Myb is critical for B cell development and maintenance of follicular B cells Immunity 2005, 23(3):275-286 10.1016/j.immuni.2005.08.005 16169500
31. van Deursen D Botma GJ Jansen H Verhoeven AJ Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes BMC Genomics 2007, 8:99 1853088 17428321 10.1186/1471-2164-8-99
32. Bajic VB Choudhary V Hock CK Content analysis of the core promoter region of human genes In Silico Biol 2004, 4(2):109-125 15089758
33. Chowdhary R Ali RA Albig W Doenecke D Bajic VB Promoter modeling: The case study of mammalian histone promoters Bioinformatics 2005, 21(11):2623-2628 10.1093/bioinformatics/bti387 15769833
34. Carninci P Sandelin A Lenhard B Katayama S Shimokawa K Ponjavic J Semple CA Taylor MS Engstrom PG Frith MC Forrest AR Alkema WB Tan SL Plessy C Kodzius R Ravasi T Kasukawa T Fukuda S Kanamori-Katayama M Kitazume Y Kawaji H Kai C Nakamura M Konno H Nakano K Mottagui-Tabar S Arner P Chesi A Gustincich S Persichetti F Suzuki H Grimmond SM Wells CA Orlando V Wahlestedt C Liu ET Harbers M Kawai J Bajic VB Hume DA Hayashizaki Y Genome-wide analysis of mammalian promoter architecture and evolution Nat Genet 2006, 16645617
35. Bajic VB Tan SL Christoffels A Schonbach C Lipovich L Yang L Hofmann O Kruger A Hide W Kai C Kawai J Hume DA Carninci P Hayashizaki Y Mice and men: Their promoter properties PLoS Genet 2006, 2(4):e54 1449896 16683032 10.1371/journal.pgen.0020054
36. Lee JS Galvin KM Shi Y Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1 Proc Natl Acad Sci U S A 1993, 90(13):6145-6149 46884 8327494 10.1073/pnas.90.13.6145
37. Karlseder J Rotheneder H Wintersberger E Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F Mol Cell Biol 1996, 16(4):1659-1667 231152 8657141
38. Frontini M Imbriano C diSilvio A Bell B Bogni A Romier C Moras D Tora L Davidson I Mantovani R NF-Y recruitment of TFIID, multiple interactions with histone fold TAF(II)s J Biol Chem 2002, 277(8):5841-5848 10.1074/ jbc.M103651200 11689552
39. Smith AD Sumazin P Xuan Z Zhang MQ DNA motifs in human and mouse proximal promoters predict tissue-specific expression Proc Natl Acad Sci U S A 2006, 103(16):6275-6280 1458868 16606849 10.1073/pnas.0508169103
40. Smith AD Sumazin P Zhang MQ Tissue-specific regulatory elements in mammalian promoters Mol Syst Biol 2007, 3:73 1800356 17224917
41. Xie X Mikkelsen TS Gnirke A Lindblad-Toh K Kellis M Lander ES Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites Proc Natl Acad Sci U S A 2007, 104(17):7145-7150 1852749 17442748 10.1073/pnas.0701811104
42. Nelander S Larsson E Kristiansson E Mansson R Nerman O Sigvardsson M Mostad P Lindahl P Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals BMC Genomics 2005, 6(1):68 1134656 15882449 10.1186/1471-2164-6-68
43. Farre D Bellora N Mularoni L Messeguer X Alba MM Housekeeping genes tend to show reduced upstream sequence conservation Genome Biol 2007, 8(7):R140 10.1186/gb-2007-8-7-r140 17626644
44. Quandt K Frech K Karas H Wingender E Werner T MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data Nucleic Acids Res 1995, 23(23):4878-4884 307478 8532532 10.1093/nar/23.23.4878
45. R Project http://www.r-project.org/