Direct isolation and identification of promoters in the human genome

Genome Research

Volumn 15, Issue 6, 2005, Pages 830-839

  Tae, Hoon Kim ^a   Barrera, Leah O ^a   Qu, Chunxu ^a   Van Calcar, Sara ^a   Trinklein, Nathan D ^c   Cooper, Sara J ^c   Luna, Rosa M ^b   Glass, Christopher K ^b   Rosenfeld, Michael G ^a   Myers, Richard M ^c   Ren, Bing ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; GENE PRODUCT;

ARTICLE; CELL LINE; COMPLEX FORMATION; CONTROLLED STUDY; DNA FLANKING REGION; DNA MICROARRAY; DNA PROTEIN COMPLEX; DNA SEQUENCE; GENE IDENTIFICATION; GENE ISOLATION; GENE STRUCTURE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN GENOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN STRUCTURE; RNA ISOLATION;

CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; DNA, COMPLEMENTARY; GENOME, HUMAN; HELA CELLS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

ANIMALIA;

EID: 22344435841     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3430605     Document Type: Article

References (44)

1. Adachi, N. and Lieber, M.R. 2002. Bidirectional gene organization: A common architectural feature of the human genome. Cell 109: 807-809.
2. Ashurst, J.L. and Collins, J.E. 2003. Gene annotation: Prediction and testing. Annu. Rev. Genomics Hum. Genet. 4: 69-88.
3. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. 2003. GenBank. Nucleic Acids Res. 31: 23-27.
5. Brivanlou, A.H. and Darnell Jr., J.E. 2002. Signal transduction and the control of gene expression. Science 295: 813-818.
6. Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
7. The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
8. Espinosa, J.M., Verdun, R.E., and Emerson, B.M. 2003. p53 functions through stress- and promoter-specific recruitment of transcription initiation components before and after DNA damage. Mol. Cell 12: 1015-1027.
9. Euskirchen, G., Royce, T.E., Bertone, P., Martone, R., Rinn, J.L., Nelson, F.K., Sayward, F., Luscombe, N.M., Miller, P., Gerstein, M., et al. 2004. CREB binds to multiple loci on human chromosome 22. Mol. Cell. Biol. 24: 3804-3814.
10. Fischle, W., Wang, Y., and Allis, C.D. 2003. Binary switches and modification cassettes in histone biology and beyond. Nature 425: 475-479.
11. Hahn, S. 2004. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11: 394-403.
12. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J., et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
13. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., et al. 2004. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2: 856-875.
14. International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
15. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
16. Jenuwein, T. and Allis, C.D. 2001. Translating the histone code. Science 293: 1074-1080.
17. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., et al. 2004. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14: 331-342.
18. Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P., and Gingeras, T.R. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
19. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. 2003. The UCSC Genome Browser Database. Nucleic Acids Res. 31: 51-54.
20. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
21. Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Q., and Ren, B. 2003. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. 100: 8164-8169.
22. Liang, G., Lin, J.C., Wei, V., Yoo, C., Cheng, J.C., Nguyen, C.T., Weisenberger, D.J., Egger, G., Takai, D., Gonzales, F.A., et al. 2004. Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc. Natl. Acad. Sci. 101: 7357-7362.
23. Martone, R., Euskirchen, G., Bertone, P., Hartman, S., Royce, T.E., Luscombe, N.M., Rinn, J.L., Nelson, F.K., Miller, P., Gerstein, M., et al. 2003. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. 100: 12247-12252.
24. Maruyama, K. and Sugano, S. 1994. Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138: 171-174.
25. The MGC Project Team. 2004. The Status, quality and expansion of the NIH full-length cDNA project: The Mammalian Genome Collection (MGC). Genome Res. 14: 2121-2127.
26. Odom, D.T., Zizlsperger, N., Gordon, D.B., Bell, G.W., Rinaldi, N.J., Murray, H.L., Volkert, T.L., Schreiber, J., Rolfe, P.A., Gifford, D.K., et al. 2004. Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381.
27. Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. 2004. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet. 36: 40-45.
28. Pruitt, K.D., Tatusova, T., and Maglott, D.R. 2003. NCBI Reference Sequence project: Update and current status. Nucleic Acids Res. 31: 34-37.
29. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
30. Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880.
31. Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
32. Ruppert, S., Wang, E.H., and Tjian, R. 1993. Cloning and expression of human TAFII250: A TBP-associated factor implicated in cell-cycle regulation. Nature 362: 175-179.
33. Schneider, R., Bannister, A.J., Myers, F.A., Thorne, A.W., Crane-Robinson, C., and Kouzarides, T. 2004. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell. Biol. 6: 73-77.
34. Schubeler, D., MacAlpine, D.M., Scalzo, D., Wirbelauer, C., Kooperberg, C., Van Leeuwen, F., Gottschling, D.E., O'Neill, L.P., Turner, B.M., Delrow, J., et al. 2004. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes & Dev. 18: 1263-1271.
35. Siepel, A. and Haussler, D. 2003. Combining phylogenetic and hidden Markov models in biosequence analysis. In Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB 2003), pp. 277-286.
36. Sims III, R.J., Mandal, S.S., and Reinberg, D. 2004. Recent highlights of RNA-polymerase-II-mediated transcription. Curr. Opin. Cell. Biol. 16: 263-271.
37. Smale, S.T. and Kadonaga, J.T. 2003. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72: 449-479.
38. Suzuki, Y., Yamashita, R., Sugano, S., and Nakai, K. 2004. DBTSS, DataBase of transcriptional start sites: Progress report 2004. Nucleic Acids Res. 32: D78-D81.
39. Thompson, N.E., Steinberg, T.H., Aronson, D.B., and Burgess, R.R. 1989. Inhibition of in vivo and in vitro transcription by monoclonal antibodies prepared against wheat germ RNA polymerase II that react with the heptapeptide repeat of eukaryotic RNA polymerase II. J. Biol. Chem. 264: 11511-11520.
40. Trinklein, N.D., Aldred, S.J., Saldanha, A.J., and Myers, R.M. 2003. Identification and functional analysis of human transcriptional promoters. Genome Res. 13: 308-312.
41. Trinklein, N.D., Aldred, S.F., Hartman, S.J., Schroeder, D.I., Otillar, R.P., and Myers, R.M. 2004. An abundance of bidirectional promoters in the human genome. Genome Res. 14: 62-66.
42. Zhang, M.Q. 2003. Prediction, annotation, and analysis of human promoters. Cold Spring Harbor Symp. Quant. Biol. 68: 217-225.
43. http://genome.ucsc.edu/; the UCSC Genome Browser.
44. http://www.genome.gov/10506161; The ENCODE Project Consortium 2004.