Individual mRNA expression profiles reveal the effects of specific microRNAs

Genome Biology

Volumn 9, Issue 5, 2008, Pages

  Arora, Amit ^a   Simpson, David A C ^a  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; ARTICLE; CLONING; CORRELATION ANALYSIS; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE MAPPING; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DATABASE; HUMAN; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; NONHUMAN; NORTHERN BLOTTING; PREDICTION; RANK SUM TEST; RNA GENE; TISSUE DISTRIBUTION; TISSUE LEVEL; TISSUE MICROARRAY; ALGORITHM; ANIMAL; ANTIBODY SPECIFICITY; BIOLOGY; GENETICS; METABOLISM; MOUSE;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; MICE; MICRORNAS; ORGAN SPECIFICITY; RNA, MESSENGER;

EID: 47149088851     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-5-r82     Document Type: Article

References (53)

1. Bartel DP MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297 10.1016/S0092-8674(04)00045-5 14744438
2. Grimson A Farh KK 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
3. Maziere P Enright AJ Prediction of microRNA targets. Drug Discov Today 2007, 12:452-458 10.1016/j.drudis.2007.04.002 17532529
4. Lewis BP Burge CB Bartel DP Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20 10.1016/j.cell.2004.12.035 15652477
5. Lewis BP Shih IH Jones-Rhoades MW Bartel DP Burge CB Prediction of mammalian microRNA targets. Cell 2003, 115:787-798 10.1016/ S0092-8674(03)01018-3 14697198
6. Tang G Reinhart BJ Bartel DP Zamore PD A biochemical framework for RNA silencing in plants. Genes Dev 2003, 17:49-63 195971 12514099 10.1101/ gad.1048103
7. Llave C Xie Z Kasschau KD Carrington JC Cleavage of scarecrow-like mRNA targets directed by a class of arabidopsis miRNA. Science 2002, 297:2053-2056 10.1126/science.1076311 12242443
8. Pillai RS Bhattacharyya SN Filipowicz W Repression of protein synthesis by miRNAs: How many mechanisms? Trends Cell Biol 2007, 17:118-126 10.1016/j.tcb.2006.12.007 17197185
9. Yekta S Shih IH Bartel DP MicroRNA-directed cleavage of HOXB8 mRNA. Science 2004, 304:594-596 10.1126/science.1097434 15105502
10. Bagga S Bracht J Hunter S Massirer K Holtz J Eachus R Pasquinelli AE Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005, 122:553-563 10.1016/j.cell.2005.07.031 16122423
11. Lim LP Lau NC Garrett-Engele P Grimson A Schelter JM Castle J Bartel DP Linsley PS Johnson JM Microarray analysis shows that some microRNAs down-regulate large numbers of target mRNAs. Nature 2005, 433:769-773 10.1038/nature03315 15685193
12. Wang X Wang X Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res 2006, 34:1646-1652 1405822 16549876 10.1093/nar/gkl068
13. Krutzfeldt J Rajewsky N Braich R Rajeev KG Tuschl T Manoharan M Stoffel M Silencing of microRNAs in vivo with 'antagomirs'. Nature 2005, 438:685-689 10.1038/nature04303 16258535
14. Schmitter D Filkowski J Sewer A Pillai RS Oakeley EJ Zavolan M Svoboda P Filipowicz W Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res 2006, 34:4801-4815 1635286 16971455 10.1093/nar/gkl646
15. Rehwinkel J Natalin P Stark A Brennecke J Cohen SM Izaurralde E Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol 2006, 26:2965-2975 1446940 16581772 10.1128/MCB.26.8.2965-2975.2006
16. Sood P Krek A Zavolan M Macino G Rajewsky N Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci USA 2006, 103:2746-2751 1413820 16477010 10.1073/pnas.0511045103
17. Farh KK Grimson A Jan C Lewis BP Johnston WK Lim LP Burge CB Bartel DP The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 2005, 310:1817-1821 10.1126/science.1121158 16308420
18. MAQC Consortium Shi L Reid LH Jones WD Shippy R Warrington JA Baker SC Collins PJ de Longueville F Kawasaki ES Lee KY Luo Y Sun YA Willey JC Setterquist RA Fischer GM Tong W Dragan YP Dix DJ Frueh FW Goodsaid FM Herman D Jensen RV Johnson CD Lobenhofer EK Puri RK Schrf U Thierry-Mieg J Wang C Wilson M The MicroArray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161 10.1038/nbt1239 16964229
19. Kuo WP Liu F Trimarchi J Punzo C Lombardi M Sarang J Whipple ME Maysuria M Serikawa K Lee SY McCrann D Kang J Shearstone JR Burke J Park DJ Wang X Rector TL Ricciardi-Castagnoli P Perrin S Choi S Bumgarner R Kim JH Short GF 3rd Freeman MW Seed B Jensen R Church GM Hovig E Cepko CL Park P A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006, 24:832-840 10.1038/nbt1217 16823376
20. Barrett T Troup DB Wilhite SE Ledoux P Rudnev D Evangelista C Kim IF Soboleva A Tomashevsky M Edgar R NCBI GEO: Mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res 2007 35 D760 D765 1669752 17099226 10.1093/nar/gkl887
21. NCBI Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/projects/geo/
22. Parkinson H Kapushesky M Shojatalab M Abeygunawardena N Coulson R Farne A Holloway E Kolesnykov N Lilja P Lukk M Mani R Rayner T Sharma A William E Sarkans U Brazma A ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007, 35:D747-D750 1716725 17132828 10.1093/nar/gkl995
23. Yu Z Jian Z Shen SH Purisima E Wang E Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and drosophila tissues than in the embryos. Nucleic Acids Res 2007, 35:152-164 1802562 17158157 10.1093/nar/gkl1032
24. Didiano D Hobert O Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 2006, 13:849-851 10.1038/nsmb1138 16921378
25. Saetrom P Heale BS Snove O Jr Aagaard L Alluin J Rossi JJ Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res 2007, 35:2333-2342 1874663 17389647 10.1093/nar/gkm133
26. Hon LS Zhang Z The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol 2007, 8:R166 2374997 17697356 10.1186/gb-2007-8-8-r166
27. TargetScan: Prediction of MicroRNA Targets http://www.targetscan.org/
28. Lagos-Quintana M Rauhut R Yalcin A Meyer J Lendeckel W Tuschl T Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12:735-739 10.1016/S0960-9822(02)00809-6 12007417
29. Sempere LF Freemantle S Pitha-Rowe I Moss E Dmitrovsky E Ambros V Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 2004, 5:R13 395763 15003116 10.1186/gb-2004-5-3-r13
30. Ason B Darnell DK Wittbrodt B Berezikov E Kloosterman WP Wittbrodt J Antin PB Plasterk RH Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA 2006, 103:14385-14389 1599972 16983084 10.1073/ pnas.0603529103
31. Cui Q Yu Z Purisima EO Wang E MicroRNA regulation and interspecific variation of gene expression. Trends Genet 2007, 23:372-375 10.1016/ j.tig.2007.04.003 17482307
32. Matthews BW Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975, 405:442-451 1180967
33. Thomson JM Parker J Perou CM Hammond SM A custom microarray platform for analysis of microRNA gene expression. Nat Methods 2004, 1:47-53 10.1038/ nmeth704 15782152
34. Liang Y Ridzon D Wong L Chen C Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 2007, 8:166 1904203 17565689 10.1186/1471-2164-8-166
35. Jing Q Huang S Guth S Zarubin T Motoyama A Chen J Di Padova F Lin SC Gram H Han J Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 2005, 120:623-634 10.1016/j.cell.2004.12.038 15766526
36. John B Enright AJ Aravin A Tuschl T Sander C Marks DS Human microRNA targets. PLoS Biol 2004, 2:e363 521178 15502875 10.1371/ journal.pbio.0020363
37. Human MicroRNA Targets http://www.microrna.org/
38. Rehmsmeier M Steffen P Hochsmann M Giegerich R Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10:1507-1517 1370637 15383676 10.1261/rna.5248604
39. RNAhybrid Web Tool on the Bielefeld Bioinformatics Server http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
40. Lytle JR Yario TA Steitz JA Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci USA 2007 104 9667 9672 1887587 17535905 10.1073/ pnas.0703820104
41. Jackson RJ Standart N How do microRNAs regulate gene expression? Sci STKE 2007, 2007:rE1 10.1126/stke.3672007re1 17200520
42. Giraldez AJ Mishima Y Rihel J Grocock RJ Van Dongen S Inoue K Enright AJ Schier AF Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79 10.1126/science.1122689 16484454
43. The Comprehensive R Archive Network http://cran.r-project.org/
44. Edgar R Domrachev M Lash AE Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210 99122 11752295 10.1093/nar/30.1.207
45. The Biomart Project http://www.biomart.org/
46. miRBase Targets http://microrna.sanger.ac.uk/targets/
47. Gu J He T Pei Y Li F Wang X Zhang J Zhang X Li Y Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mamm Genome 2006, 17:1033-1041 10.1007/ s00335-006-0007-9 17019647
48. Naraba H Iwai N Assessment of the microRNA system in salt-sensitive hypertension. Hypertens Res 2005, 28:819-826 10.1291/hypres.28.819 16471176
49. Zhao Y Samal E Srivastava D Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436:214-220 10.1038/nature03817 15951802
50. Lagos-Quintana M Rauhut R Lendeckel W Tuschl T Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858 10.1126/ science.1064921 11679670
51. Lagos-Quintana M Rauhut R Meyer J Borkhardt A Tuschl T New microRNAs from mouse and human. RNA 2003, 9:175-179 1370382 12554859 10.1261/ rna.2146903
52. Hayashita Y Osada H Tatematsu Y Yamada H Yanagisawa K Tomida S Yatabe Y Kawahara K Sekido Y Takahashi T A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 2005, 65:9628-9632 10.1158/ 0008-5472.CAN-05-2352 16266980
53. Yu Z Raabe T Hecht NB MicroRNA Mirn122a reduces expression of the posttranscriptionally regulated germ cell transition protein 2 (Tnp2) messenger RNA (mRNA) by mRNA cleavage. Biol Reprod 2005, 73:427-433 10.1095/biolreprod.105.040998 15901636