Home LiteratureArticle Details
PMID: 15496526 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Probing microRNAs with microarrays: tissue specificity and functional inference.

RNA (New York, N.Y.) ·Vol. 10 ·No. 11 ·2004-11-00 ·Pages 1813-9

Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR

Abstract

MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we describe a method to detect miRNAs using micro-arrays, in which the miRNAs are directly hybridized to the array. We used this method to analyze miRNA expression across 17 mouse organs and tissues. More than half of the 78 miRNAs detected were expressed in specific adult tissues, suggesting that miRNAs have widespread regulatory roles in adults. By comparing miRNA levels to mRNA levels determined in a parallel microarray analysis of the same tissues, we found that the expression of target mRNAs predicted on the basis of sequence complementarity is unrelated to the tissues in which the corresponding miRNA is expressed.

MeSH Terms
Animals Female Fluorescent Dyes Gene Expression Profiling Male Mice/genetics MicroRNAs/genetics,metabolism Oligonucleotide Array Sequence Analysis Organ Specificity RNA Processing, Post-Transcriptional RNA, Messenger/analysis Sensitivity and Specificity Sequence Analysis, DNA Tissue Distribution
Chemicals
Fluorescent Dyes MicroRNAs RNA, Messenger
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Babak Tomas
Banting and Best Department of Medical Research, 112 College St., University of Toronto, Toronto, Ontario M5G 1L6, Canada.
Zhang Wen
Morris Quaid
Blencowe Benjamin J
Hughes Timothy R
References (32)
32 references, click to expand
  1. Knowledge-based analysis of microarray gene expression data by using support vector machines.
    Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):262-7 PMID: 10618406
  2. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
    Cell. 1993 Dec 3;75(5):843-54 PMID: 8252621
  3. ULS: a versatile method of labeling nucleic acids for FISH based on a monofunctional reaction of cisplatin derivatives with guanine moieties.
    Cytogenet Cell Genet. 1999;87(1-2):47-52 PMID: 10640810
  4. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.
    Nature. 2000 Feb 24;403(6772):901-6 PMID: 10706289
  5. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  6. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.
    Nat Biotechnol. 2001 Apr;19(4):342-7 PMID: 11283592
  7. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.
    Science. 2001 Oct 26;294(5543):858-62 PMID: 11679671
  8. An extensive class of small RNAs in Caenorhabditis elegans.
    Science. 2001 Oct 26;294(5543):862-4 PMID: 11679672
  9. Role of HuD and other RNA-binding proteins in neural development and plasticity.
    J Neurosci Res. 2002 Apr 15;68(2):121-6 PMID: 11948657
  10. Identification of tissue-specific microRNAs from mouse.
    Curr Biol. 2002 Apr 30;12(9):735-9 PMID: 12007417
  11. Variance stabilization applied to microarray data calibration and to the quantification of differential expression.
    Bioinformatics. 2002;18 Suppl 1:S96-104 PMID: 12169536
  12. Regulation and function of local protein synthesis in neuronal dendrites.
    Trends Biochem Sci. 2002 Oct;27(10):506-13 PMID: 12368086
  13. New microRNAs from mouse and human.
    RNA. 2003 Feb;9(2):175-9 PMID: 12554859
  14. A uniform system for microRNA annotation.
    RNA. 2003 Mar;9(3):277-9 PMID: 12592000
  15. Vertebrate microRNA genes.
    Science. 2003 Mar 7;299(5612):1540 PMID: 12624257
  16. A panoramic view of yeast noncoding RNA processing.
    Cell. 2003 Jun 27;113(7):919-33 PMID: 12837249
  17. Embryonic stem cell-specific MicroRNAs.
    Dev Cell. 2003 Aug;5(2):351-8 PMID: 12919684
  18. A microRNA array reveals extensive regulation of microRNAs during brain development.
    RNA. 2003 Oct;9(10):1274-81 PMID: 13130141
  19. The nuclear RNase III Drosha initiates microRNA processing.
    Nature. 2003 Sep 25;425(6956):415-9 PMID: 14508493
  20. Prediction of mammalian microRNA targets.
    Cell. 2003 Dec 26;115(7):787-98 PMID: 14697198
  21. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs.
    Genes Dev. 2003 Dec 15;17(24):3011-6 PMID: 14681208
  22. Nuclear export of microRNA precursors.
    Science. 2004 Jan 2;303(5654):95-8 PMID: 14631048
  23. MicroRNA targets in Drosophila.
    Genome Biol. 2003;5(1):R1 PMID: 14709173
  24. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons.
    Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):360-5 PMID: 14691248
  25. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs.
    RNA. 2004 Feb;10(2):185-91 PMID: 14730017
  26. MicroRNAs: genomics, biogenesis, mechanism, and function.
    Cell. 2004 Jan 23;116(2):281-97 PMID: 14744438
  27. A high-throughput method to monitor the expression of microRNA precursors.
    Nucleic Acids Res. 2004;32(4):e43 PMID: 14985473
  28. 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(3):R13 PMID: 15003116
  29. Dicers at RISC; the mechanism of RNAi.
    Cell. 2004 Apr 2;117(1):1-3 PMID: 15066275
  30. MicroRNA-directed cleavage of HOXB8 mRNA.
    Science. 2004 Apr 23;304(5670):594-6 PMID: 15105502
  31. Quantitation of microRNAs using a modified Invader assay.
    RNA. 2004 Jul;10(7):1153-61 PMID: 15208450
  32. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues.
    Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9740-4 PMID: 15210942
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1355-8382
DOI
10.1261/rna.7119904
Published
2004-11-00
Pages
1813-9
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC1370668
Subset
IM
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1261/rna.7119904 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2