Structures of microRNA precursors

Current Perspectives in microRNAs (miRNA)

Volumn , Issue , 2008, Pages 1-16

  Kozlowski, Piotr ^a   Starega Roslan, Julia ^a   Legacz, Marta ^a   Magnus, Marcin ^a   Krzyzosiak, Wlodzimierz J ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

Dicer; Drosha; miRNA biogenesis; pre miRNA structural motifs; pri miRNAs; RNA structure prediction

Indexed keywords

EID: 69549143874     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-8533-8_1     Document Type: Chapter

References (36)

1. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
2. Basyuk, E., Suavet, F., Doglio, A., Bordonne, R., and Bertrand, E. (2003). Human let-7 stemloop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 31, 6593-6597.
3. 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.
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. Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., and Hannon, G. J. (2004). Processing of primary microRNAs by the microprocessor complex. Nature 432, 231-235.
6. Gregory, R. I., Chendrimada, T. P., Cooch, N., and Shiekhattar, R. (2005). Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123, 631-640.
7. Gregory, R. I., Yan, K. P., Amuthan, G., Chendrimada, T., Doratotaj, B., Cooch, N., and Shiekhattar, R. (2004). The microprocessor complex mediates the genesis of microRNAs. Nature 432, 235-240.
8. Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A., and Enright, A. J. (2006). miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34, D140-D144.
9. Han, J., Lee, Y., Yeom, K. H., Nam, J. W., Heo, I., Rhee, J. K., Sohn, S. Y., Cho, Y., Zhang, B. T., and Kim, V. N. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887-901.
10. Huang, T. H., Fan, B., Rothschild, M. F., Hu, Z. L., Li, K., and Zhao, S. H. (2007). MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics 8, 341.
11. Jiang, P., Wu, H., Wang, W., Ma, W., Sun, X., and Lu, Z. (2007). MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 35, W339-W344.
12. Kim, V. N., and Nam, J. W. (2006). Genomics of microRNA. Trends Genet 22, 165-173.
13. Krol, J., Sobczak, K., Wilczynska, U., Drath, M., Jasinska, A., Kaczynska, D., and Krzyzosiak, W. J. (2004). Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 279, 42230-42239.
14. Krol, J., Starega-Roslan, J., Milanowska, K., Nowak, D., Kubiaczyk, E., Nowak, M., Majorek, K., Kaminska, K., and Krzyzosiak, W. J. (2006). Structural Features of microRNAs and Their Precursors, In microRNA: Biology, Function & Expression, N. Clarke, and P. Sanseau, eds. (DNA Press), Eagleville, PA, pp. 95-110.
15. Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003). Computational identification of Drosophila microRNA genes. Genome Biol 4, R42.
16. 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 microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414.
17. Landthaler, M., Yalcin, A., and Tuschl, T. (2004). The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14, 2162-2167.
18. Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S., and Kim, V. N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415-419.
19. 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.
20. Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.
21. Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B., and Bartel, D. P. (2003). Vertebrate micro- RNA genes. Science 299, 1540.
22. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2004). Nuclear export of microRNA precursors. Science 303, 95-98.
23. Macrae, I. J., Zhou, K., and Doudna, J. A. (2007). Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14, 934-940.
24. Macrae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., Adams, P. D., and Doudna, J. A. (2006). Structural basis for double-stranded RNA processing by Dicer. Science 311, 195-198.
25. Pillai, R. S., Bhattacharyya, S. N., Artus, C. G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., and Filipowicz, W. (2005). Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309, 1573-1576.
26. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B., and Radmark, O. (2002). Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J 21, 5864-5874.
27. Ritchie, W., Legendre, M., and Gautheret, D. (2007). RNA stem-loops: To be or not to be cleaved by RNAse III. RNA 13, 457-462.
28. Saetrom, P., Snove, O., Nedland, M., Grunfeld, T. B., Lin, Y., Bass, M. B., and Canon, J. R. (2006). Conserved microRNA characteristics in mammals. Oligonucleotides 16, 115-144.
29. Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E., and Zavolan, M. (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6, 267.
30. Sheng, Y., Engstrom, P. G., and Lenhard, B. (2007). Mammalian MicroRNA prediction through a support vector machine model of sequence and structure. PLoS ONE 2, e946.
31. Wang, X., Zhang, J., Li, F., Gu, J., He, T., Zhang, X., and Li, Y. (2005). MicroRNA identification based on sequence and structure alignment. Bioinformatics 21, 3610-3614.
32. Xue, C., Li, F., He, T., Liu, G. P., Li, Y., and Zhang, X. (2005). Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 6, 310.
33. Yekta, S., Shih, I. H., and Bartel, D. P. (2004). MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596.
34. Zhang, H., Kolb, F. A., Brondani, V., Billy, E., and Filipowicz, W. (2002). Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21, 5875-5885.
35. Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E., and Filipowicz, W. (2004). Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57-68.
36. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.