Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 17, 2006, Pages 6605-6610

  Rigoutsos, Isidore ^a   Huynh, Tien ^a   Miranda, Kevin ^a   Tsirigos, Aristotelis ^a   McHardy, Alice ^a   Platt, Daniel ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

Junk DNA; Pattern discovery; Posttranscriptional gene silencing; Pyknons; RNA interference

Indexed keywords

MICRORNA; NUCLEOTIDE; SPACER DNA;

3' UNTRANSLATED REGION; ARTICLE; CELL COMMUNICATION; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; HUMAN GENOME; INTRON; MOSAICISM; PRIORITY JOURNAL; RNA INTERFERENCE; RNA STRUCTURE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; UNTRANSLATED REGION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA; GENOME, HUMAN; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RNA INTERFERENCE; UNTRANSLATED REGIONS;

INVERTEBRATA; VERTEBRATA;

EID: 33646242293     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0601688103     Document Type: Article

References (44)

1. Mattick, J. S. (2004) Nat. Rev. Genet. 5, 316-323.
2. Ruvkun, G. (2001) Science 294, 797-799.
3. Ettwiller, L. M., Rung, J. & Birney, E. (2003) Genome Res. 13, 883-895.
4. Brazma, A., Jonassen, I., Vilo, J. & Ukkonen, E. (1998) Genome Res. 8, 1202-1215.
5. Lenhard, B., Sandelin, A., Mendoza, L., Engstrom, P., Jareborg, N. & Wasserman, W. W. (2003) J. Biol. 2, 13.
6. Sinha, S. & Tompa, M. (2002) Nucleic Acids Res. 30, 5549-5560.
7. Wasserman, W. W. & Sandelin, A. (2004) Nat. Rev. Genet. 5, 276-287.
8. Hobert, O. (2004) Trends Biochem. Sci. 29, 462-468.
9. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S. & Haussler, D. (2004) Science 304, 1321-1325.
10. Dubchak, I., Brudno, M., Loots, G. G., Pachter, L., Mayor, C., Ruhin, E. M. & Frazer, K. A. (2000) Genome Res. 10, 1304-1306.
11. Frazer, K. A., Sheehan, J. B., Stokowski, R. P., Chen, X., Hosseini, R., Cheng, J. F., Fodor, S. P., Cox, D. R. & Patil, N. (2001) Genome Res. 11, 1651-1659.
12. Jareborg, N., Birney, E. & Durbin, R. (1999) Genome Res. 9, 815-824.
13. Miziara, M. N., Riggs, P. K. & Amaral, M. E. (2004) Genet. Mol. Res. 3, 465-473.
14. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, D., Pachter, L. & Rubin, E. M. (2003) Science 299, 1391-1394.
15. Dermitzakis, E. T., Kirkness, E., Schwarz, S., Birney, E., Reymond, A. & Antonarakis, S. E. (2004) Genome Res. 14, 852-859.
16. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. (2003) Nature 423, 241-254.
17. Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W. & Lawrence, C. E. (2000) Nat. Genet. 26, 225-228.
18. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. & Cohen, S. M. (2003) Cell 113, 25-36.
19. Elbashir, S. M., Lendeckel, W. & Tuschl, T. (2001) Genes Dev. 15, 188-200.
20. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E. & Mello, C. C. (1998) Nature 391, 806-811.
21. Johnston, R. J. & Hobert, O. (2003) Nature 426, 845-849.
22. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. (2001) Science 294, 858-862.
23. Lee, R. C. & Ambros, V. (2001) Science 294, 862-864.
24. Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. & Bartel, D. P. (2003) Science 299, 1540.
25. Moss, E. G., Lee, R. C. & Ambros, V. (1997) Cell 88, 637-646.
26. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. & Ruvkun, G. (2000) Nature 403, 901-906.
27. Slack, F. J., Basson, M., Liu, Z., Ambros, V., Horvitz, H. R. & Ruvkun, G. (2000) Mol. Cell 5, 659-669.
28. Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. (2003) Curr. Biol. 13, 807-818.
29. Mattick, J. S. & Makunin, I. V. (2005) Hum. Mol. Genet. 14, R12L-RL32.
30. Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P. & Stoffel, M. (2004) Nature 432, 226-230.
31. Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., a al. (2005) PLoS Biol. 3, e7.
32. Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S. & Kellis, M. (2005) Nature 434, 338-345.
33. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. (2005) Science 308, 1149-1154.
34. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. & Eddy, S. R. (2003) Nucleic Acids Res. 31, 439-441.
35. Rigoutsos, I. & Floratos, A. (1998) Bioinformatics 14, 55-67.
36. Slabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M. & Birney, E. (2004) Genome Res. 14, 929-933.
37. Wootton, J. C. & Federhen, S. (1993) Comput. Chem. 17, 149-163.
38. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410.
39. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) Nat. Genet. 25, 25-29.
40. Hofacker, I. L., Fontana, W., Stadler, P., Bonhoeffer, L. S., Tacker, M. & Schuster, P. (1994) Monatsh. Chem. 125, 167-188.
41. Iwashita, S., Osada, N., Itoh, T., Sezaki, M., Oshima, K., Hashimoto, E., Kitagawa-Arita, Y., Takahashi, I., Masui, T., Hashimoto, K. & Makalowski, W. (2003) Mol. Biol. Evol. 20, 1556-1563.
42. Lev-Maor, G., Sorek, R., Shomron, N. & Ast, G. (2003) Science 300, 1288-1291.
43. Jiang, N., Bao, Z., Zhane, X., Eddy, S. R. & Wessler, S. R. (2004) Nature 431, 569-573.
44. Jorgensen, R. A. (2004) Cold Spring Harbor Symp. Quant. Biol. 69, 349-354.