Mapping of transcription start sites of human retina expressed genes

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Roni, Valeria ^a   Carpio, Ronald ^a   Wissinger, Bernd ^a  

^a UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

5' UNTRANSLATED REGION; ADULT; ARTICLE; COMPUTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROMOTER REGION; RETINA; RNA SPLICING; TRANSCRIPTION INITIATION SITE; VALIDATION STUDY; ANIMAL; CHROMOSOME MAP; GENETICS; METABOLISM; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

COMPLEMENTARY DNA; MESSENGER RNA;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA, COMPLEMENTARY; EXONS; GENE EXPRESSION; HUMANS; MOLECULAR SEQUENCE DATA; RETINA; RNA SPLICING; RNA, MESSENGER; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EID: 33847257468     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-42     Document Type: Article

References (45)

1. Smale ST Kadonaga JT The RNA polymerase II core promoter Annu Rev Biochem 2003 72 449-479 10.1146/annurev.biochem.72.121801.161520 12651739
2. Hahn S Structure and mechanism of the RNA polymerase II transcription machinery Nat Struct Mol Biol 2004 11 5 394-403 1189732 15114340 10.1038/ nsmb763
3. Venter JC Adams MD Myers EW Li PW Mural RJ Sutton GG Smith HO Yandell M Evans CA Holt RA Gocayne JD Amanatides P Ballew RM Huson DH Wortman JR Zhang Q Kodira CD Zheng XH Chen L Skupski M Subramanian G Thomas PD Zhang J Gabor Miklos GL Nelson C Broder S Clark AG Nadeau J McKusick VA Zinder N Levine AJ Roberts RJ Simon M Slayman C Hunkapiller M Bolanos R Delcher A Dew I Fasulo D Flanigan M Florea L Halpern A Hannenhalli S Kravitz S Levy S Mobarry C Reinert K Remington K Abu-Threideh J Beasley E Biddick K Bonazzi V Brandon R Cargill M Chandramouliswaran I Charlab R Chaturvedi K Deng Z Di Francesco V Dunn P Eilbeck K Evangelista C Gabrielian AE Gan W Ge W Gong F Gu Z Guan P Heiman TJ Higgins ME Ji RR Ke Z Ketchum KA Lai Z Lei Y Li Z Li J Liang Y Lin X Lu F Merkulov GV Milshina N Moore HM Naik AK Narayan VA Neelam B Nusskern D Rusch DB Salzberg S Shao W Shue B Sun J Wang Z Wang A Wang X Wang J Wei M Wides R Xiao C The sequence of the human genome Science 2001 291 5507 1304-1351 10.1126/science.1058040 11181995
4. Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W Funke R Gage D Harris K Heaford A Howland J Kann L Lehoczky J LeVine R McEwan P McKernan K Meldrim J Mesirov JP Miranda C Morris W Naylor J Raymond C Rosetti M Santos R Sheridan A Sougnez C Stange-Thomann N Stojanovic N Subramanian A Wyman D Rogers J Sulston J Ainscough R Beck S Bentley D Burton J Clee C Carter N Coulson A Deadman R Deloukas P Dunham A Dunham I Durbin R French L Grafham D Gregory S Hubbard T Humphray S Hunt A Jones M Lloyd C McMurray A Matthews L Mercer S Milne S Mullikin JC Mungall A Plumb R Ross M Shownkeen R Sims S Waterston RH Wilson RK Hillier LW McPherson JD Marra MA Mardis ER Fulton LA Chinwalla AT Pepin KH Gish WR Chissoe SL Wendl MC Delehaunty KD Miner TL Delehaunty A Kramer JB Cook LL Fulton RS Johnson DL Minx PJ Clifton SW Hawkins T Branscomb E Predki P Richardson P Wenning S Slezak T Doggett N Cheng JF Olsen A Lucas S Elkin C Uberbacher E Initial sequencing and analysis of the human genome Nature 2001 409 6822 860-921 10.1038/35057062 11237011
5. 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
6. Davuluri RV Grosse I Zhang MQ Computational identification of promoters and first exons in the human genome Nat Genet 2001 29 4 412-417 10.1038/ ng780 11726928
7. Sonnenburg S Zien A Ratsch G ARTS: Accurate recognition of transcription starts in human Bioinformatics 2006 22 14 e472-80 10.1093/bioinformatics/ btl250 16873509
8. Suzuki Y Yamashita R Sugano S Nakai K DBTSS, DataBase of Transcriptional Start Sites: Progress report 2004 Nucleic Acids Res 2004 32 Database issue D78-81 308810 14681363 10.1093/nar/gkh076
9. Cheng J Kapranov P Drenkow J Dike S Brubaker S Patel S Long J Stern D Tammana H Helt G Sementchenko V Piccolboni A Bekiranov S Bailey DK Ganesh M Ghosh S Bell I Gerhard DS Gingeras TR Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution Science 2005 308 5725 1149-1154 10.1126/science.1108625 15790807
10. 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
11. Schulz HL Goetz T Kaschkoetoe J Weber BH The Retinome - defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium BMC Genomics 2004 5 1 50 512282 15283859 10.1186/ 1471-2164-5-50
12. Blackshaw S Harpavat S Trimarchi J Cai L Huang H Kuo WP Weber G Lee K Fraioli RE Cho SH Yung R Asch E Ohno-Machado L Wong WH Cepko CL Genomic analysis of mouse retinal development PLoS Biol 2004 2 9 E247 439783 15226823 10.1371/journal.pbio.0020247
13. Blackshaw S Fraioli RE Furukawa T Cepko CL Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes Cell 2001 107 5 579-589 10.1016/ S0092-8674(01)00574-8 11733058
14. Chowers I Gunatilaka TL Farkas RH Qian J Hackam AS Duh E Kageyama M Wang C Vora A Campochiaro PA Zack DJ Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray Invest Ophthalmol Vis Sci 2003 44 9 3732-3741 10.1167/ iovs.02-1080 12939286
15. Lord-Grignon J Tetreault N Mears AJ Swaroop A Bernier G Characterization of new transcripts enriched in the mouse retina and identification of candidate retinal disease genes Invest Ophthalmol Vis Sci 2004 45 9 3313-3319 10.1167/iovs.03-1350 15326156
16. Yu J Farjo R MacNee SP Baehr W Stambolian DE Swaroop A Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina Genome Biol 2003 4 10 R65 328454 14519200 10.1186/ gb-2003-4-10-r65
17. Schmid CD Perier R Praz V Bucher P EPD in its twentieth year: Towards complete promoter coverage of selected model organisms Nucleic Acids Res 2006 34 Database issue D82-5 1347508 16381980 10.1093/nar/gkj146
18. Wissinger B Gamer D Jagle H Giorda R Marx T Mayer S Tippmann S Broghammer M Jurklies B Rosenberg T Jacobson SG Sener EC Tatlipinar S Hoyng CB Castellan C Bitoun P Andreasson S Rudolph G Kellner U Lorenz B Wolff G Verellen-Dumoulin C Schwartz M Cremers FP Apfelstedt-Sylla E Zrenner E Salati R Sharpe LT Kohl S CNGA3 mutations in hereditary cone photoreceptor disorders Am J Hum Genet 2001 69 4 722-737 1226059 11536077 10.1086/323613
19. Haeseleer F Jang GF Imanishi Y Driessen CA Matsumura M Nelson PS Palczewski K Dual-substrate specificity short chain retinol dehydrogenases from the vertebrate retina J Biol Chem 2002 277 47 45537-45546 1435693 12226107 10.1074/jbc.M208882200
20. Janecke AR Thompson DA Utermann G Becker C Hubner CA Schmid E McHenry CL Nair AR Ruschendorf F Heckenlively J Wissinger B Nurnberg P Gal A Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy Nat Genet 2004 36 8 850-854 10.1038/ng1394 15258582
21. Perrault I Hanein S Gerber S Barbet F Ducroq D Dollfus H Hamel C Dufier JL Munnich A Kaplan J Rozet JM Retinal dehydrogenase 12 (RDH12) mutations in leber congenital amaurosis Am J Hum Genet 2004 75 4 639-646 1182050 15322982 10.1086/424889
22. Haeseleer F Huang J Lebioda L Saari JC Palczewski K Molecular characterization of a novel short-chain dehydrogenase/reductase that reduces all-trans-retinal J Biol Chem 1998 273 34 21790-21799 10.1074/ jbc.273.34.21790 9705317
23. Yoshida S Mears AJ Friedman JS Carter T He S Oh E Jing Y Farjo R Fleury G Barlow C Hero AO Swaroop A Expression profiling of the developing and mature Nrl-/- mouse retina: Identification of retinal disease candidates and transcriptional regulatory targets of Nrl Hum Mol Genet 2004 13 14 1487-1503 10.1093/hmg/ddh160 15163632
24. Barragan I Marcos I Borrego S Antinolo G Mutation screening of three candidate genes, ELOVL5, SMAP1 and GLULD1 in autosomal recessive retinitis pigmentosa Int J Mol Med 2005 16 6 1163-1167 16273301
25. Hoang E Bost-Usinger L Burnside B Characterization of a novel C-kinesin (KIFC3) abundantly expressed in vertebrate retina and RPE Exp Eye Res 1999 69 1 57-68 10.1006/exer.1999.0671 10375449
26. Maeda A Ohguro H Maeda T Wada I Sato N Kuroki Y Nakagawa T Aberrant expression of photoreceptor-specific calcium-binding protein (recoverin) in cancer cell lines Cancer Res 2000 60 7 1914-1920 10766180
27. Wiechmann A Howard E Functional analysis of the human recoverin gene promoter Curr Eye Res 2003 26 1 25-32 10.1076/ceyr.26.1.25.14249 12789533
28. Li XF Kraev AS Lytton J Molecular cloning of a fourth member of the potassium-dependent sodium-calcium exchanger gene family, NCKX4 J Biol Chem 2002 277 50 48410-48417 10.1074/jbc.M210011200 12379639
29. Sharon D Yamamoto H McGee TL Rabe V Szerencsei RT Winkfein RJ Prinsen CF Barnes CS Andreasson S Fishman GA Schnetkamp PP Berson EL Dryja TP Mutated alleles of the rod and cone Na-Ca+K-exchanger genes in patients with retinal diseases Invest Ophthalmol Vis Sci 2002 43 6 1971-1979 12037007
30. Frith MC Ponjavic J Fredman D Kai C Kawai J Carninci P Hayashizaki Y Sandelin A Evolutionary turnover of mammalian transcription start sites Genome Res 2006 16 6 713 722 1473182 16687732 10.1101/gr.5031006
31. King DC Taylor J Elnitski L Chiaromonte F Miller W Hardison RC Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences Genome Res 2005 15 8 1051-1060 1182217 16024817 10.1101/gr.3642605
32. Dike S Balija VS Nascimento LU Xuan Z Ou J Zutavern T Palmer LE Hannon G Zhang MQ McCombie WR The mouse genome: Experimental examination of gene predictions and transcriptional start sites Genome Res 2004 14 12 2424-2429 534666 15574821 10.1101/gr.3158304
33. Oyama M Itagaki C Hata H Suzuki Y Izumi T Natsume T Isobe T Sugano S Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs Genome Res 2004 14 10B 2048-2052 528919 15489325 10.1101/gr.2384604
34. Rogozin IB Kochetov AV Kondrashov FA Koonin EV Milanesi L Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon Bioinformatics 2001 17 10 890-900 10.1093/bioinformatics/17.10.890 11673233
35. Sachs MS Geballe AP Downstream control of upstream open reading frames Genes Dev 2006 20 8 915-921 10.1101/gad.1427006 16618802
36. Hochheimer A Tjian R Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression Genes Dev 2003 17 11 1309-1320 10.1101/gad.1099903 12782648
37. Zhang T Haws P Wu Q Multiple variable first exons: A mechanism for cell- and tissue-specific gene regulation Genome Res 2004 14 1 79-89 314283 14672974 10.1101/gr.1225204
38. Bortoluzzi S Coppe A Bisognin A Pizzi C Danieli GA A multistep bioinformatic approach detects putative regulatory elements in gene promoters BMC Bioinformatics 2005 6 121 1173081 15904489 10.1186/ 1471-2105-6-121
39. Halees AS Leyfer D Weng Z PromoSer: A large-scale mammalian promoter and transcription start site identification service Nucleic Acids Res 2003 31 13 3554-3559 168956 12824364 10.1093/nar/gkg549
40. Eukaryotic Promoter Database Current Release 87 http://www.epd.isb-sib.ch
41. DBTSS http://dbtss.hgc.jp
42. Kent WJ BLAT - the BLAST-like alignment tool Genome Res 2002 12 4 656-664 187518 11932250 10.1101/gr.229202. Article published online before March 2002
43. AceView http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
44. BioEdit pairwise and multiple alignments http://www.mbio.ncsu.edu/ BioEdit/bioedit.html
45. Primer3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi