MicroRNA promoter element discovery in Arabidopsis

RNA

Volumn 12, Issue 9, 2006, Pages 1612-1619

  Megraw, Molly ^a   Baev, Vesselin ^d   Rusinov, Ventsislav ^d   Jensen, Shane T ^b   Kalantidis, Kriton ^d   Hatzigeorgiou, Artemis G ^a,c  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

Author keywords

MicroRNA; Position specific weight matrices; Promoter; Sequence scanning; Transcription factors

Indexed keywords

ARF PROTEIN; MICRORNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; BINDING SITE; COMPARATIVE STUDY; GENE SEQUENCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TATA BOX;

ARABIDOPSIS; BASE SEQUENCE; BINDING SITES; DATABASES, GENETIC; FEEDBACK, BIOCHEMICAL; GENES, PLANT; MICRORNAS; PROMOTER REGIONS (GENETICS); TATA BOX; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

ARABIDOPSIS;

EID: 33748132234     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.130506     Document Type: Article

References (33)

1. Bracht, J., Hunter, S., Eachus, R., Weeks, P., and Pasquinelli, A.E. 2004. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA 10: 1586-1594.
2. Busch, M.A., Bomblies, K., and Weigel, D. 1999. Activation of a floral homeotic gene in Arabidopsis. Science 285: 585-587.
3. Cai, X., Hagedorn, C.H., and Cullen, B.R. 2004. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957-1966.
4. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M., and Grotewold, E. 2003. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4: 25.
5. Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1999. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, UK.
6. Fazi, F., Rosa, A., Fatica, A., Gelmetti, V., De Marchis, M.L., Nervi, C., and Bozzoni, I. 2005. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPα regulates human granulopoiesis. Cell 123: 819-831.
7. 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.
8. Guarente, L. and Bermingham-McDonogh, O. 1992. Conservation and evolution of transcriptional mechanisms in eukaryotes. Trends Genet. 8: 27-32.
9. He, L. and Hannon, G.J. 2004. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5: 522-531.
10. Higo, K., Ugawa, Y., Iwamoto, M., and Korenaga, T. 1999. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27: 297-300.
11. Johnston Jr., R.J., Chang, S., Etchberger, J.F., Ortiz, C.O., and Hobert, O. 2005. MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl. Acad. Sci. 102: 12449-12454.
12. Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57: 19-53.
13. Lamb, R.S., Hill, T.A., Tan, Q.K., and Irish, V.F. 2002. Regulation of APETALA3 floral homeotic gene expression by meristem identity genes. Development 129: 2079-2086.
14. 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.
15. Lee, J.Y., Colinas, J., Wang, J.Y., Mace, D., Ohler, U., and Benfey, P.N. 2006. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl. Acad. Sci. 103: 6055-6060.
16. Lescot, M., Dehais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouze, P., and Rombauts, S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30: 325-327.
17. Li, X. and Carthew, R.W. 2005. A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye. Cell 123: 1267-1277.
18. Molina, C. and Grotewold, E. 2005. Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6: 25.
19. Ohler, U., Yekta, S., Lim, L.P., Bartel, D.P., and Burge, C.B. 2004. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10: 1309-1322.
20. Pandey, S.P. and Krishnamachari, A. 2006. Computational analysis of plant RNA Pol-II promoters. Biosystems 83: 38-50.
21. Parcy, F. 2005. Flowering: A time for integration. Int. J. Dev. Biol. 49: 585-593.
22. Parcy, F., Nilsson, O., Busch, M.A., Lee, I., and Weigel, D. 1998. A genetic framework for floral patterning. Nature 395: 561-566.
23. Rhee, S.Y., Beavis, W., Berardini, T.Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M., et al. 2003. The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31: 224-228.
24. Sethupathy, P., Megraw, M., Barrasa, M., and Hatzigeorgiou, A. 2005. Computational identification of regulatory factors involved in microRNA transcription. In Lecture notes in computer science pp. 457-468. Springer, Berlin/Heidelberg, Germany.
25. Sethupathy, P., Corda, B., and Hatzigeorgiou, A.G. 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12: 192-197.
26. Smale, S.T. 2001. Core promoters: Active contributors to combinatorial gene regulation. Genes & Dev. 15: 2503-2508.
27. Stormo, G.D. 2000. DNA binding sites: Representation and discovery. Bioinformatics 16: 16-23.
28. Sun, Y., Koo, S., White, N., Peralta, E., Esau, C., Dean, N.M., and Perera, R.J. 2004. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 32: e188.
29. Ulmasov, T., Hagen, G., and Guilfoyle, T.J. 1997a. ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865-1868.
30. Ulmasov, T., Murfett, J., Hagen, G., and Guilfoyle, T.J. 1997b. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9: 1963-1971.
31. Wagner, D., Sablowski, R.W., and Meyerowitz, E.M. 1999. Transcriptional activation of APETALA1 by LEAFY. Science 285: 582-584.
32. Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I., and Schacherer, F. 2000. TRANSFAC: An integrated system for gene expression regulation. Nucleic Acids Res. 28: 316-319.
33. Xie, Z., Allen, E., Fahlgren, N., Calamar, A., Givan, S.A., and Carrington, J.C. 2005. Expression of Arabidopsis miRNA genes. Plant Physiol. 138: 2145-2154.