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REVIEWMicroRNA detection by microarrayWei Li & Kangcheng RuanReceived: 31 October 2008 /Revised: 1 December 2008 /Accepted: 5 December 2008 /Published online: 9 January 2009# Springer-Verlag 2009Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs ∼22 nt in length that regulate gene expressionand play fundamental roles in multiple biological processes,including cell differentiation, proliferation and apoptosis aswell as disease processes. The study of miRNA has thusbecome a rapidly emerging field in life science. Thedetection of miRNA expression is a very important firststep in miRNA exploration. Several methodologies, includ-ing cloning, northern blotting, real-time RT-PCR, micro-RNA arrays and ISH (in situ hybridization), have beendeveloped and applied successfully in miRNA profiling.This review discusses the main existing microRNA detec-tion technologies, while emphasizing microRNA arrays.Keywords MicroRNA.MicroRNAdetection.MicroRNAmicroarray.MicroRNAlabelingIntroductionMicroRNAs are a class of ∼22 nt long noncoding RNAs.They are derived from the cleavage of hairpin precursors byDicer (a member of the RNAase III family), and areevolutionarily conserved [1–3]. The high conservation ofmicroRNA sequences highlights the significance of theirfunction. In animal cells, microRNAs inhibit the translationof target genes by binding with imperfect complementarityto multiple sites in the 3′ untranslated region (UTR) oftarget mRNAs [4–6]. A single microRNA can regulate theexpression of many target genes, and a target gene can alsobe regulated by several microRNAs [7, 8]. Early studiessuggested that microRNA genes account for about 1% ofthe genome in a species [9, 10]. However, according to thestudy early in 2005, the number of human microRNAs isgreater than 1000 [11], and over one-third of human genesappear to be conserved microRNA targets [12].At present, microRNAs are known to be involved inmany biological functions, including the timing of earlylarval development transitions [13, 14], left/right asymmetryof chemoreceptor expression in nematodes [15], cell proli-feration and apoptosis in insects [16], and hematopoieticdifferentiation in mammals [17], as well as leaf development[18], flowering transition timing [19], and flower develop-ment of Arabidopsis [20]. In addition, microRNAs areassociated with many major diseases in humans. Forexample, miR15 and miR16 are associated with human B-cell chronic lymphatic leukemia (B-CLL) [21], reducedexpression of let-7 in lung cancer leads to shortenedpostoperative survival [22], miR155 is associated with B-cell lymphomas [23], meanwhile miR-143 and miR-145display reduced expression levels in colorectal tumor cellscompared with normal colonic cells [24]. Moreover, miR-1is overexpressed in individuals with coronary artery disease[25], and overexpression of MiR-17-92 in the lymphocytesof mice results in lymphoproliferative disease and autoim-munity [26]. All of these findings indicate that microRNAexpression levels are closely associated with developmentalstages and physiological states as well as disease processes.From these findings, it has also been established thatmicroRNA expression detection and analysis is a basicand preliminary procedure in most miRNA studies. So far,several main techniques for detecting and analyzing miRNAexpression, such as northern blotting, real-time RT-PCR,Anal Bioanal Chem (2009) 394:1117–1124DOI 10.1007/s00216-008-2570-2W. Li:K. Ruan (*)StateKeyLaboratoryofMolecularBiology,Instituteof Biochemistryand Cell Biology, Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,320 Yue Yang Road,Shanghai 200031, Chinae-mail: kcruan@sibs.ac.cn