An approach for the identification of microRNA with an application to Anopheles gambiae

Acta Biochimica Polonica

Volumn 53, Issue 2, 2006, Pages 303-309

  Chatterjee, Raghunath ^a   Chaudhuri, Keya ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Anopheles gambiae; microRNA; RNA folding

Indexed keywords

ANOPHELES GAMBIAE; DROSOPHILA MELANOGASTER; EUKARYOTA;

EID: 33745807260     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: 10.18388/abp.2006_3343     Document Type: Article

References (27)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132: 709-717.
3. Bartel DP (2004) MicroRNAs: genomics biogenesis mechanism and function. Cell 116: 281-297.
4. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101: 11511-11516.
5. Gautheret D, Lambert A (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 313: 1003-1011.
6. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32: D109-D111.
7. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
8. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets including a stress-induced miRNA. Mol Cell 14: 787-799.
9. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
10. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4: R42.
11. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
12. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
13. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 843-854.
14. Legendre M, Lambert A, Gautheret D (2005) Profile-based detection of microRNA precursors in animal genomes. Bioinformatics 21: 841-845.
15. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
16. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP (2003a) Vertebrate microRNA genes. Science 299: 1540.
17. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW et al. (2003b) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
18. Moss EG, Lee RC, Ambros V (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88: 637-646.
19. Moss EG, Poethig RS (2002) MicroRNAs: something new under the sun. Curr Biol 12: R688-R690.
20. Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB (2004) Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10: 1309-1322.
21. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
22. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
23. Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell 5: 659-669.
24. Wang X, Zhang J, Li F, Gu J, He T, Zhang X et al (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614.
25. Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana micro-RNAs and their mRNA targets. Genome Biol 5: R65.
26. Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272: 59-73.
27. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.