Intrinsic promoter activities of primary DNA sequences in the human genome

DNA Research

Volumn 14, Issue 2, 2007, Pages 71-77

  Sakakibara, Yuta ^a,b   Irie, Takuma ^a   Suzuki, Yutaka ^a   Yamashita, Riu ^a   Wakaguri, Hiroyuki ^a   Kanai, Akinori ^a   Chiba, Joe ^b   Takagi, Toshihisa ^a   Mizushima Sugano, Junko ^a,c   Hashimoto, Shin Ichi ^d   Nakai, Kenta ^a   Sugano, Sumio ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b TOKYO UNIVERSITY OF SCIENCE   (Japan)

^c KITASATO UNIVERSITY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

Human genome; Promoter; Transcriptional start site

Indexed keywords

COMPLEMENTARY DNA; DNA; LUCIFERASE; UNTRANSLATED RNA;

ARTICLE; CELL LINE; CLASSIFICATION; CPG ISLAND; DNA BASE COMPOSITION; GENETIC TRANSCRIPTION; GENETICS; GENOME; HUMAN; PROMOTER REGION; REPORTER GENE; TATA BOX;

BASE COMPOSITION; CELL LINE; CPG ISLANDS; DNA; DNA, COMPLEMENTARY; GENES, REPORTER; GENOME, HUMAN; HUMANS; LUCIFERASES; PROMOTER REGIONS (GENETICS); RNA, UNTRANSLATED; TATA BOX; TRANSCRIPTION, GENETIC;

EID: 34548461287     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsm006     Document Type: Article

References (28)

1. International Human Genome Sequencing Consortium. 2004, Finishing the euchromatic sequence of the human genome, Nature, 431, 931-945.
2. Zhang, Q. H., Ye, M., Wu, X. Y., Ren, S. X., Zhao, M., Zhao, C. J., Fu, G., Shen, Y., Fan, H. Y., Lu, G., et al. 2000, Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells, Genome Res., 10, 1546-1560.
3. Wiemann, S., Weil, B., Wellenreuther, R., Gassenhuber, J., Glassl, S., Ansorge, W., Bocher, M., Blocker, H., Bauersachs, S., Blum, H., et al. 2001, Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs, Genome Res., 11, 422-435.
4. Strausberg, R. L., Feingold, E. A., Grouse, L. H., Derge, J. G., Klausner, R. D., Collins, F. S., Wagner, L., Shenmen, C. M., Schuler, G. D., Altschul, S. F., et al. 2002, Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences, Proc. Natl. Acad. Sci. USA, 99, 16899-16903.
5. 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.
6. 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, pE162.
7. Fraser, A. G. and Marcotte, E. M. 2004, A probabilistic view of gene function, Nat. Genet., 36, 559-564.
8. Khodursky, A. B. and Bernstein, J. A. 2003, Life after transcription - revisiting the fate of messenger RNA, Trends Genet., 19, 113-115.
9. Roeder, R. G. 1996, The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci., 21, 327-335.
10. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E., Kel-Margoulis, O. V., et al. 2003, TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.
11. Suzuki, Y. and Sugano, S. 2003, Construction of a fulllength enriched and a 5′-end enriched cDNA library using the oligo-capping method, Methods Mol. Biol., 221, 73-91.
12. Yamashita, R., Suzuki, Y., Wakaguri, H., Tsuritani, K., Nakai, K. and Sugano, S. 2006, DBTSS: DataBase of Human Transcription Start Sites, progress report 2006, Nucleic Acids Res., 34, D86-D89.
13. Suzuki, Y., Tsunoda, T., Sese, J., Taira, H., Mizushima-Sugano, J., Hata, H., Ota, T., Isogai, T., Tanaka, T., Nakamura, Y., et al. 2001, Identification and characterization of the potential promoter regions of 1031 kinds of human genes, Genome Res., 11, 677-684.
14. 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.
15. Versteeg, R., van Schaik, B. D., van Batenburg, M. F., Roos, M., Monajemi, R., Caron, H., Bussemaker, H. J. and van Kampen, A. H. 2003, The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes, Genome Res., 13, 1998-2004.
16. Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., Hayashizaki, Y. and Tomita, M. 2003, Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection, Genome Res., 13, 1301-1306.
17. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al. 2002, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563-573.
18. Willingham, A. T. and Gingeras, T. R. 2006, TUF love for "junk" DNA, Cell, 125, 1215-1220.
19. Wang, J., Zhang, J., Zheng, H., Li, J., Liu, D., Li, H., Samudrala, R., Yu, J. and Wong, G. K. 2004, Mouse tran-scriptome: neutral evolution of 'non-coding' complementary DNAs, Nature, 431, 757.
20. Nobrega, M. A., Zhu, Y., Plajzer-Frick, I., Afzal, V. and Rubin, E. M. 2004, Megabase deletions of gene deserts result in viable mice, Nature, 431, 988-993.
21. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., et al. 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559-1563.
22. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. 2005, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, 308, 1149-1154.
23. Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T. A., Wu, Y., Green, R. D. and Ren, B. 2005, A high-resolution map of active promoters in the human genome, Nature, 436, 876-880.
24. Kimura, K., Wakamatsu, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine, M., Tsuritani, K., Wakaguri, H., et al. 2006, Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes, Genome Res., 16, 55-65.
25. Landry, J. R., Mager, D. L. and Wilhelm, B. T. 2003, Complex controls: the role of alternative promoters in mammalian genomes, Trends Genet., 19, 640-648.
26. Modrek, B. and Lee, C. J. 2003, Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss, Nat. Genet., 34, 177-180.
27. Rockman, M. V. and Wray, G. A. 2002, Abundant raw material for cis-regulatory evolution in humans, Mol. Biol. Evol., 19, 1991-2004.
28. Bajic, V. B., Tan, S. L., Suzuki, Y. and Sugano, S. 2004, Promoter prediction analysis on the whole human genome, Nat. Biotechnol., 22, 1467-1473.