Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Mead, Edward Andrew ^a   Tu, Zhijian ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LET 7; MICRORNA; MICRORNA 11; MICRORNA 12; MICRORNA 124; MICRORNA 14; MICRORNA 210; MICRORNA 276; MICRORNA 276A; MICRORNA 277; MICRORNA 281; MICRORNA 283; MICRORNA 2A; MICRORNA 304; MICRORNA 306; MICRORNA 317; MICRORNA 34; MICRORNA 375; MICRORNA 76; MICRORNA 8; MICRORNA 87; MICRORNA 9A; MICRORNA X1; MICRORNA X2; MICRORNA X3; MICRORNA X4; RNA DERIVATIVE;

AEDES AEGYPTI; ANOPHELES GAMBIAE; ANOPHELES STEPHENSI; APOPTOSIS; ARTICLE; CLUSTER ANALYSIS; DEVELOPMENTAL STAGE; DISEASE TRANSMISSION; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE LOSS; GENOME ANALYSIS; INTRON; LIFESPAN; LONGEVITY; MOLECULAR CLONING; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PATTERN RECOGNITION; REPRODUCTION; RIBONUCLEASE PROTECTION ASSAY; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; ANIMAL; ANOPHELES; FEEDING BEHAVIOR; GENE EXPRESSION REGULATION; GENETICS; MALE; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; OPEN READING FRAME; OVARY; PHYSIOLOGY; SEQUENCE HOMOLOGY; TIME;

AEDES AEGYPTI; ANOPHELES GAMBIAE; ANOPHELES STEPHENSI; DROSOPHILA MELANOGASTER;

ANIMALS; ANOPHELES; BASE SEQUENCE; BLOTTING, NORTHERN; CLONING, MOLECULAR; FEEDING BEHAVIOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; INTRONS; LONGEVITY; MALE; MICRORNAS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPEN READING FRAMES; OVARY; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS;

EID: 45749155980     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-244     Document Type: Article

References (47)

1. Miska EA How microRNAs control cell division, differentiation and death Curr Opin Genet Dev 2005, 15(5):563-568. 10.1016/j.gde.2005.08.005 16099643
2. Du T Zamore PD Beginning to understand microRNA function Cell Research 2007, 17(8):661-663. 10.1038/cr.2007.67 17694094
3. Bartel DP MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5 14744438
4. Pasquinelli AE Hunter S Bracht J MicroRNAs: A developing story Curr Opin Genet Dev 2005, 15(2):200-205. 10.1016/j.gde.2005.01.002 15797203
5. Zhou X Ruan J Wang G Zhang W Characterization and identification of MicroRNA core promoters in four model species PLoS Comput Biol 2007, 3(3):e37. 1817659 17352530 10.1371/journal.pcbi.0030037
6. Lau NC Lim LP Weinstein EG Bartel DP An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans Science 2001, 294:858-862. 10.1126/science.1065062 11679671
7. Denli A Tops BBJ Plasterk RHA Ketting RF Hannon GJ Processing of primary microRNAs by the Microprocessor complex Nature 2004, 432:231-235. 10.1038/nature03049 15531879
8. Bushati N Cohen SM microRNA Functions Annual Review of Cell and Developmental Biology 2007, 23(1):175-205. 10.1146/ annurev.cellbio.23.090506.123406
9. Brennecke J Stark A Russell RB Cohen SM Principles of microRNA-target recognition PLoS Biol 2005, 3(3):e85. 1043860 15723116 10.1371/ journal.pbio.0030085
10. Grimson A Farh KK-H Johnston WK Garrett-Engele P Lim LP Bartel DP MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing Mol Cell 2007, 27:91-105. 10.1016/j.molcel.2007.06.017 17612493
11. Lai EC miRNAs: Whys and Wherefores of miRNA-Mediated Regulation Curr Biol 2005, 15(12):R458-R460. 10.1016/j.cub.2005.06.015 15964265
12. Du T Zamore PD microPrimer: The biogenesis and function of microRNA Development 2005, 132(21):4645-4652. 10.1242/dev.02070 16224044
13. Kim VN Small RNAs: Classification, Biogenesis, and Function Mol Cells 2005, 19(1):1-15. 10.1016/j.molcel.2005.05.026 15750334
14. Ambros V Chen X The regulation of genes and genomes by small RNAs Development 2007, 134(9):1635-1641. 10.1242/dev.002006 17409118
15. O'Connell RM Taganov KD Boldin MP Cheng G Baltimore D MicroRNA-155 is induced during the macrophage inflammatory response PNAS 2007, 104(5):1604-1609. 1780072 17242365 10.1073/pnas.0610731104
16. le Sage C Nagel R Egan DA Schrier M Mesman E Mangiola A Anile C Maira G Mercatelli N Ciafrè SA Regulation of the p27Kip1 tumor suppressor by miR-221 and miR-222 promotes cancer cell proliferation EMBO J 2007, 26:3699-3708. 10.1038/sj.emboj.7601790 17627278
17. Cullen BR Viruses and microRNAs Nature Genetics 2006, 38:S25-S30. 10.1038/ng1793 16736021
18. Nakahara K Kim K Sciulli C Dowd SR Minden JS Carthew RW Targets of microRNA regulation in the Drosophila oocyte proteome PNAS 2005, 102(34):12023-12028. 1189302 16099838 10.1073/pnas.0500053102
19. Lewis BP Burge CB Bartel DP Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets Cell 2005, 120(1):15-20. 10.1016/j.cell.2004.12.035 15652477
20. Lai E Tomancak P Williams R Rubin G Computational identification of Drosophila microRNA genes Genome Biology 2003, 4(7):R42. 193629 12844358 10.1186/gb-2003-4-7-r42
21. Aravin AA Lagos-Quintana M Yalcin A Zavolan M Marks D Snyder B Gaasterland T Meyer J Tuschl T The Small RNA Profile during Drosophila melanogaster Development Dev Cell 2003, 5(2):337-350. 10.1016/ S1534-5807(03)00228-4 12919683
22. Wang X Zhang J Li F Gu J He T Zhang X Li Y MicroRNA identification based on sequence and structure alignment Bioinformatics 2005, 21(18):3610-3614. 10.1093/bioinformatics/bti562 15994192
23. Chatterjee R Chaudhuri K An approach for the identification of microRNA with an application to Anopheles gambiae Acta Biochim Pol 2006, 53:303-309. 16770443
24. U.S. Centers for Disease Control http://www.cdc.gov/malaria/biology
25. The miRBase Registry http://microrna.sanger.ac.uk
26. Xu P Vernooy SY Guo M Hay BA The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism Curr Biol 2003, 13:790-795. 10.1016/S0960-9822(03)00250-1 12725740
27. Valoczi A Hornyik C Varga N Burgyan J Kauppinen S Havelda Z Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes Nucl Acids Res 2004, 32(22):e175. 545470 15598818 10.1093/nar/gnh171
28. miRscan Web Server http://genes.mit.edu/mirscan
29. Lim LP Lau NC Weinstein EG Abdelhakim A Yekta S Rhoades MW Burge CB Bartel DP The microRNAs of Caenorhabditis elegans Genes Dev 2003, 17:991-1008. 196042 12672692 10.1101/gad.1074403
30. Lim LP Glasner ME Yekta S Burge CB Bartel DP Vertebrate MicroRNA Genes Science 2003, 299:1540. 10.1126/science.1080372 12624257
31. Ambros V Bartel B Bartel DP Burge CB Carrington JC Chen X Dreyfuss G Eddy SR Griffiths-Jones SAM Marshall M Matzke M Ruvkun G Tuschl T A uniform system for microRNA annotation RNA 2003, 9:277-279. 1370393 12592000 10.1261/rna.2183803
32. Gu Z Eleswarapu S Jiang H Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland FEBS Lett 2007, 581:981-988. 10.1016/j.febslet.2007.01.081 17306260
33. Griffiths-Jones S The microRNA Registry Nucl Acids Res 2004, 32(suppl_1):D109-111. 10.1093/nar/gkh023
34. Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nucl Acids Res 2006, 34(suppl_1):D140-144. 10.1093/nar/gkj112
35. Smalheiser NA EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues Genome Biol 2003, 4(7):403. 193628 12844357 10.1186/ gb-2003-4-7-403
36. Kim YK Kim VN Processing of intronic microRNAs EMBO J 2007, 26(3):775-783. 1794378 17255951 10.1038/sj.emboj.7601512
37. Sempere LF Sokol NS Dubrovsky EB Berger EM Ambros V Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity Dev Biol 2003, 259(1):9-18. 10.1016/S0012-1606(03)00208-2 12812784
38. Berezikov E Cuppen E Plasterk RHA Approaches to microRNA discovery Nat Genet 2006, 38:52-57. 10.1038/ng1914
39. Krzywinski J Grushko OG Besansky NJ Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution Mol Phylogenet Evol 2006, 39(2):417-423. 10.1016/ j.ympev.2006.01.006 16473530
40. Ruby JG Stark A Johnston WK Kellis M Bartel DP Lai EC Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs Genome Res 2007, 17:1850-1864. 2099593 17989254 10.1101/gr.6597907
41. Stark A Kheradpour P Parts L Brennecke J Hodges E Hannon GJ Kellis M Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes Genome Res 2007, 17(12):1865-1879. 2099594 17989255 10.1101/gr.6593807
42. Winter F Edaye S Huttenhofer A Brunel C Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion Nucl Acids Res 2007, 35(20):6953-6962. 2175301 17933784 10.1093/nar/gkm686
43. Thompson JD Higgins DG Gibson TJ improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position- specific gap penalties and weight matrix choice Nucl Acids Res 1994, 22(22):4673-4680. 308517 7984417 10.1093/nar/22.22.4673
44. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucl Acids Res 1997, 25(17):3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
45. Ensembl http://www.ensembl.org
46. Vienna RNA Secondary Structure Prediction http://rna.tbi.univie.ac.at/ cgi-bin/RNAfold.cgi
47. Wienholds E Kloosterman WP Miska E Alvarez-Saavedra E Berezikov E de Bruijn E Horvitz HR Kauppinen S Plasterk RHA MicroRNA Expression in Zebrafish Embryonic Development Science 2005, 309:310-311. 10.1126/ science.1114519 15919954