Bidirectional promoters in the transcription of mammalian genomes

Biochemistry (Moscow)

Volumn 78, Issue 4, 2013, Pages 335-341

  Orekhova, A S ^a   Rubtsov, P M ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

bidirectional promoters; CpG islands; divergent transcription; genome structure; promoter core elements; short noncoding RNAs; transcription factors; transcription initiation; transcriptome

Indexed keywords

EUKARYOTA; MAMMALIA;

RNA POLYMERASE II;

ANIMAL; GENETIC TRANSCRIPTION; GENETICS; GENOME; HUMAN; MAMMAL; METABOLISM; PROMOTER REGION;

ANIMALS; GENOME; HUMANS; MAMMALS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; TRANSCRIPTION, GENETIC;

EID: 84879445965     PISSN: 00062979     EISSN: 16083040     Source Type: Journal    
DOI: 10.1134/S0006297913040020     Document Type: Article

References (49)

1. Adachi, N., and Lieber, M. R. (2002) Cell, 109, 807-809. (Pubitemid 34785996)
2. Trinklein, N. D., Aldred, S. H., Hartman, S. J., Schroeder, D. I., Otillar, R. P., and Myers, R. M. (2004) Genome Res., 14, 62-66. (Pubitemid 38088526)
3. Collins, P. J., Kobayashi, Y., Nguyen, L., Trinklein, N. D., and Myers, R. M. (2007) PLoS Genet., 3, e208. (Pubitemid 350291584)
4. Koyanagi, K. O., Hagiwara, M., Itoh, T., Gojobori, T., and Imanishi, T. (2005) Gene, 353, 169-176. (Pubitemid 40942139)
5. Franck, E., Hulsen, T., Huynen, M. A., De Jong, W. W., Lubsen, N. H., and Madsen, O. (2008) Mol. Biol. Evol., 25, 1909-1921.
6. Yang, M. Q., and Elnitski, L. L. (2007) Lect. Notes Comput. Sci., 4463, 361-371.
7. Yang, M. Q., and Elnitski, L. L. (2008) BMC Genom., 9 (Suppl. 1), S2. (Pubitemid 351833875)
8. Piontkivska, H., Yang, M. Q., Larkin, D. M., Lewin, H. A., Reecy, J., and Elnitski, L. (2009) BMC Genom., 10, 189.
9. Engstrom, P. G., Suzuki, H., Ninomiya, N., Akalin, A., Sessa, L., Lavorgna, G., Brozzi, A., Lizi, L., Tan, S. L., Yang, L., Kunarso, G., Ng, E. L., Batalov, S., Wahlestedt, C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Wells, C., Bajic, V. B., Orlando, V., Reid, J. F., Lenhard, B., and Lipovich, L. (2006) PLoS Genet., 2, e47.
10. Yang, M. Q., and Elnitski, L. L. (2008) BMC Genom., 9(Suppl. 2), S3.
11. Smale, S. T., and Kadonaga, J. T. (2003) Annu. Rev. Biochem., 72, 449-479. (Pubitemid 36930452)
12. Kutach, A. K., and Kadonaga, J. T. (2000) Mol. Cell. Biol., 20, 4754-4764. (Pubitemid 30396122)
13. Lagrange, T., Kapanidis, A. N., Tang, H., Reinberg, D., and Ebright, R. H. (1998) Genes Dev., 12, 34-44.
14. Yang, C., Bolotin, E., Jiang, T., Sladek, F. M., and Martinez, E. (2007) Gene, 389, 52-65. (Pubitemid 46107776)
15. Javahery, R., Khachi, A., Lo, K., Zenzie-Gregory, B., and Smale, S. T. (1994) Mol. Cell. Biol., 14, 116-127.
16. Lin, J. M., Collins, P. J., Trinklein, N. D., Fu, Y., Xi, H., Myers, R. M., and Weng, Z. (2007) Genome Res., 17, 818-827. (Pubitemid 46919717)
17. Bird, A. P. (1986) Nature, 321, 209-213.
18. Gardiner-Garden, M., and Frommer, M. (1987) J. Mol. Biol., 196, 261-282.
19. Antequera, F. (2003) Cell. Mol. Life Sci., 60, 1647-1658. (Pubitemid 37041363)
20. Shu, J., Jelinek, J., Chang, H., Shen, L., Qin, T., Chung, W., Oki, Y., and Issa, J. P. (2006) Cancer Res., 66, 5077-5084. (Pubitemid 43844929)
21. Zanotto, E., Shah, Z. H., and Jacobs, H. T. (2007) Nucleic Acids Res., 35, 664-677. (Pubitemid 46232081)
22. Zanotto, E., Lehtonen, V., and Jacobs, H. T. (2008) Biochim. Biophys. Acta, 1783, 2352-2362.
23. Hakkinen, A., Healy, S., Jacobs, H. T., and Ribeiro, A. S. (2011) J. Theor. Biol., 281, 74-83.
24. Anno, Y.-N., Myslinski, E., Ngondo-Mbongo, R. P., Krol, A., Poch, O., Lecompte, O., and Carbon, P. (2011) Nucleic Acids Res., 39, 3116-3127.
25. Schuster, C., Myslinski, E., Krol, A., and Carbon, P. (1995) EMBO J., 14, 3777-3787.
26. Schaub, M., Myslinski, E., Schuster, C., Krol, A., and Carbon, P. (1997) EMBO J., 16, 173-181. (Pubitemid 27032860)
27. Myslinski, E., Krol, A., and Carbon, P. (1998) J. Biol. Chem., 273, 21998-22006. (Pubitemid 28405380)
28. Schaub, M., Krol, A., and Carbon, P. (1999) J. Biol. Chem., 274, 24241-24249. (Pubitemid 29390360)
29. Myslinski, E., Gerard, M. A., Krol, A., and Carbon, P. (2006) J. Biol. Chem., 281, 39953-39962. (Pubitemid 46041799)
30. Ame, J.-C., Schreiber, V., Fraulob, V., Dolle, P., de Murcia, G., and Niedergang, C. P. (2001) J. Biol. Chem., 276, 11092-11099. (Pubitemid 38089292)
31. Hung, C. F., Cheng, T. L., Wu, R. H., Teng, C. F., and Chang, W. T. (2006) Biochem. Biophys. Res. Commun., 339, 1035-1042. (Pubitemid 41790568)
32. Orekhova, A. S., Sverdlova, P. S., Spirin, P. V., Leonova, O. G., Popenko, V. I., Prasolov, V. S., and Rubtsov, P. M. (2011) Mol. Biol. (Moscow), 45, 486-495.
33. The ENCODE Project Consortium (2007) Nature, 447, 799-816. (Pubitemid 46920138)
34. Jacquier, A. (2009) Nat. Rev. Genet., 10, 833-844.
35. Carninci, P. (2010) DNA Res., 17, 51-59.
36. Wei, W., Pelechano, V., Jarvelin, A. I., and Steinmetz, L. M. (2011) Tends Genet., 27, 267-276.
37. Seila, A. C., Calabrese, J. M., Levine, S. S., Yeo, G. W., Rahl, P. B., Flynn, R. A., Young, R. A., and Sharp, P. A. (2008) Science, 322, 1849-1851.
38. Seila, A. C., Core, L. J., Lis, J. T., and Sharp, P. A. (2009) Cell. Cycle, 8, 2557-2564.
39. Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermuller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., and Gingeras, T. R. (2007) Science, 316, 1484-1488. (Pubitemid 46906616)
40. Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., and Gingeras, T. R. (2009) Nature, 457, 1028-1032.
41. Core, L. J., Waterfall, J. J., and Lis, J. T. (2008) Science, 322, 1845-1848.
42. Taft, R. J., Glazov, E. A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G. J., Lassmann, T., Forrest, A. R., Grimmond, S. M., Schroder, K., Irvine, K., Arakawa, T., Nakamura, M., Kubosaki, A., Hayashida, K., Kawazu, C., Murata, M., Nishiyori, H., Fukuda, S., Kawai, J., Daub, C. O., Hume, D. A., Suzuki, H., Orlando, V., Carninci, P., Hayashizaki, Y., and Mattick, J. S. (2009) Nat. Genet., 41, 572-578.
43. Preker, P., Nielsen, J., Kammler, S., Lykke-Andersen, S., Christensen, M. S., Mapendano, C. K., Schierup, M. H., and Jensen, T. H. (2008) Science, 322, 1851-1854.
44. Preker, P., Nielsen, J., Schierup, M. H., and Jensen, T. H. (2009) Cell. Cycle, 8, 1106-1107.
45. Preker, P., Almvig, K., Christensen, M. S., Valen, E., Mapendano, C. K., Sandelin, A., and Jensen, T. H. (2011) Nucleic Acids Res., 39, 7179-7193.
46. The ENCODE Project Consortium (2012) Nature, 489, 57-74.
47. Sanyal, A., Lajoie, B. R., Jain, G., and Dekker, J. (2012) Nature, 489, 109-113.
48. Yip, K. I., Cheng, C., Bhardwaj, N., Brown, J. B., Leng, J., Kundaje, A., Rozowsky, J., Birney, E., Bickel, P., Snyder, M., and Gerstein, M. (2012) Genome Biol., 13,R48, 1-22.
49. Tan-Wong, S. M., Zaugg, J. B., Camblong, J., Xu, Z., Zhang, D. W., Mischo, H. E., Ansari, A. Z., Luscombe, N. M., Steinmetz, L. M., and Proudfoot, N. J. (2012) Science, 338, 671-675.