Atypical transcription of microRNA gene fragments

Nucleic Acids Research

Volumn 38, Issue 9, 2010, Pages 2775-2787

  Gao, Jin Song ^a   Zhang, Yingjie ^a   Li, Ming ^a   Tucker, Lynne D ^a   Machan, Jason T ^a   Quesenberry, Peter ^a   Rigoutsos, Isidore ^b   Ramratnam, Bharat ^a  

^a BROWN UNIVERSITY   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; DNA FRAGMENT; MICRORNA; RNA POLYMERASE II; DNA; MIRN143 MICRORNA, HUMAN; RNA PRECURSOR;

ARTICLE; CELL STRAIN HCT116; CELL STRAIN HEK293; CONTROLLED STUDY; GENE EXPRESSION; GENETIC TRANSCRIPTION; HELA CELL; HUMAN; HUMAN CELL; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; PROMOTER REGION; BIOSYNTHESIS; CELL LINE; CHEMISTRY; GENETICS; METABOLISM;

CELL LINE; DNA; HUMANS; MICRORNAS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; RNA PRECURSORS; TRANSCRIPTION, GENETIC;

EID: 77953281988     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1242     Document Type: Article

References (25)

1. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A.O., Landthaler, M. et al. (2007) A mammalian micro RNA expression atlas based on small RNA library sequencing. Cell, 129, 1401-14.
2. Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Einav, U., Meiri, E. et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet., 37(7), 766-770.
3. Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H. and Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060.
4. Borchert, G.M., Lanier, W. and Davidson, B.L. (2006) RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol., 13, 1097-1101.
5. Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Rådmark, Y. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
6. Bernstein, E., Caudy, A.A., Hammond, S.M. and Hannon, G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363-366.
7. Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
8. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
9. Place, R.F., Li, L.C., Pookot, D., Noonan, E.J. and Dahiya, R. (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl Acad. Sci. USA, 105, 1608-1613. Epub 2008 Jan 28.
10. Fai, A.H.T. and Cornelius, P.L. (1996) Approximate F-tests of multiple degree of freedom hypotheses in generalized least squares analyses of unbalanced split-plot experiments. J. Stat. Comput. Simul., 54, 363-378.
11. Michael, M.Z., O' Connor, S.M., van Holst Pellekaan, N.G., Young, G.P., James, R.J. et al. (2003) Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res., 1, 882-891.
12. Chen, C.Z., Li, L., Lodish, H.F. and Bartel, D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83-86.
13. Esau, C., Kang, X., Peralta, E., Hanson, E., Marcusson, E.G., Ravichandran, L.V., Sun, Y., Koo, S., Perera, R.J., Jain, R. et al. (2004) MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem., 279, 52361-52365.
14. Corcoran, D.L., Pandit, D.L., Gordon, B., Bhattacharjee, A., Kaminski, N. and Benos, P.V. (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS ONE, 4, e5279.
15. Ozsolak, F., Poling, L.L., Wang, Z., Liu, H., Liu, X.S., Roeder, R.G., Zhang, X., Song, J.S., Fisher, D.E., Ozsolak, F. et al. (2008) Nucleic Acids Research, 2010, Vol. 38, No. 9 2787 Chromatin structure analyses identify miRNA promoters. Genes Dev., 22, 3172-3183.
16. Saini, H.K., Griffiths-Jones, S. and Enright, A.J. (2007) Genomic analysis of human microRNA transcripts. Proc. Natl Acad. Sci. USA, 104, 17719-17724.
17. Chen, H., Liu, X. and Patel, D.J. (1996) DNA bending and unwinding associated with actinomycin D antibiotics bound to partially overlapping sites on DNA. J. Mol. Biol., 258, 457-479.
18. Kenneth, N.S., Marshall, L. and White, R.J. (2008) Recruitment of RNA polymerase III in vivo. Nucleic Acids Res., 36, 3757-3764.
19. Chiu, H., Macmillan, J.B. and Chen, Z.J. (2009) RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell, 138, 576-591.
20. Kravchenko, J.E., Rogozin, J.E., Koonin, E.V., Chumakov, P.M. et al. (2005) Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature, 436, 735-739.
21. Beer, S., Bellovin, D.I., Lee, J.S., Komatsubara, S., Wang, L.S., Koh, H., Börner, K., Storm, T.A., Davis, C.R. et al. (2010) Low-level shRNA cytotoxicity can contribute to MYC-induced hepatocellular carcinoma in adult mice. Mol. Ther, 18, 161-70. Epub 2009 Oct 20.
22. Grimm, D., Streetz, K.L., Jopling, C.L., Storm, T.A., Pandey, K., Davis, C.R., Marion, P., Salazar, F. and Kay, M.A. (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature, 441, 537-541.
23. 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. et al. (2009) Tiny RNAs associated with transcription start sites in animals. Nat. Genet., 41, 572-578.
24. Langenberger, D., Bermudez-Santana, C., Hertel, J., Hoffmann, S., Khaitovich, P. and Stadler, P.F. (2009) Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics, 25, 2298-2301.
25. Boden, D., Pusch, O., Silbermann, R., Lee, F., Tucker, L. and Ramratnam, B. (2004) Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res., 32, 1154-1158.