Abstract
In less than 20 years, our appreciation for micro-RNA molecules (miRNAs) has grown from an original, curious observation in worms to their current status as incredibly important global regulators of gene expression that play key roles in many transformative biological processes. As our understanding of these small, non-coding transcripts continues to evolve, new approaches for their analysis are emerging. In this critical review we describe recent improvements to classical methods of detection as well as innovative new technologies that are poised to help shape the future landscape of miRNA analysis.
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References
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297
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(5):843–854
Poethig RS (2009) Small RNAs and developmental timing in plants. Curr Opin Genet Dev 19(4):374–378
Alvarez-Garcia I, Miska EA (2005) MicroRNA functions in animal development and human disease. Development 132(21):4653–4662
Fineberg SK, Kosik KS, Davidson BL (2009) MicroRNAs potentiate neural development. Neuron 64(3):303–309
Wang Y, Blelloch R (2009) Cell cycle regulation by MicroRNAs in embryonic stem cells. Cancer Res 69(10):4093–4096
Lin CH et al. (2009) Myc-regulated microRNAs attenuate embryonic stem cell differentiation. EMBO J 28(20):3157–3170
Chen CZ et al. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303(5654):83–86
Meola N, Gennarino VA, Banfi S (2009) MicroRNAs and genetic diseases. Pathogenetics 2(1):7
Tsai LM, Yu D (2010) MicroRNAs in common diseases and potential therapeutic applications. Clin Exp Pharmacol Physiol 37(1):102–107
Dennis PP, Omer A (2005) Small non-coding RNAs in Archaea. Curr Opin Microbiol 8(6):685–694
Masse E, Majdalani N, Gottesman S (2003) Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol 6(2):120–124
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
Pasquinelli AE et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808):86–89
Fire A et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811
Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30(4):460–471
Griffiths-Jones S et al. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158
Baek D et al. (2008) The impact of microRNAs on protein output. Nature 455(7209):64–71
Friedman RC et al. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1):92–105
Wu S et al. (2010) Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region. Oncogene 29(15):2302–2308
Cho WC (2010) MicroRNAs in cancer—from research to therapy. Biochim Biophys Acta 1805(2):209–217
Ruan K, Fang XG, Ouyang GL (2009) MicroRNAs: novel regulators in the hallmarks of human cancer. Cancer Lett 285(2):116–126
Eacker SM, Dawson TM, Dawson VL (2009) Understanding microRNAs in neurodegeneration. Nat Rev Neurosci 10(12):837–841
Kocerha J, Kauppinen S, Wahlestedt C (2009) MicroRNAs in CNS disorders. Neuromolecular Med 11(3):162–172
Pandey AK et al. (2009) MicroRNAs in diabetes: tiny players in big disease. Cell Physiol Biochem 23(4–6):221–232
Cai BZ, Pan ZW, Lu YJ (2010) The roles of microRNAs in heart diseases: a novel important regulator. Curr Med Chem 17(5):407–411
Saal S, Harvey SJ (2009) MicroRNAs and the kidney: coming of age. Curr Opin Nephrol Hypertens 18(4):317–323
Liang MY et al. (2009) MicroRNA: a new frontier in kidney and blood pressure research. Am J Physiol Ren Physiol 297(3):F553–F558
Chen XM (2009) MicroRNA signatures in liver diseases. World J Gastroenterol 15(14):1665–1672
O’Connell RM et al. (2010) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10(2):111–122
Tsitsiou E, Lindsay MA (2009) MicroRNAs and the immune response. Curr Opin Pharmacol 9(4):514–520
Li CS et al. (2009) Therapeutic microRNA strategies in human cancer. AAPS J 11(4):747–757
Roshan R et al. (2009) MicroRNAs: novel therapeutic targets in neurodegenerative diseases. Drug Discov Today 14(23–24):1123–1129
Arenz C (2006) MicroRNAs: future drug targets? Angew Chem Int Ed 45(31):5048–5050
Fabbri M (2010) miRNAs as molecular biomarkers of cancer. Expert Rev 10(4):435–444
Gilad S et al. (2008) Serum microRNAs are promising novel biomarkers. PLoS ONE 3(9):e3148
Mitchell PS et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105(30):10513–10518
Chen X et al. (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18(10):997–1006
Dai H et al. (2002) Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucl Acids Res 30(16):e86
Liu W-T, Mirzabekov AD, Stahl DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3(10):619–629
Dorris DR et al. (2003) Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnol 3:6
Urakawa H et al. (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol 69(5):2848–2856
Guschin D et al. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63(6):2397–2402
Mendes ND, Freitas AT, Sagot MF (2009) Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 37(8):2419–2433
Stark A et al. (2003) Identification of Drosophila microRNA targets. PLoS Biol 1(3):397–409
Brennecke J et al. (2005) Principles of microRNA–target recognition. PLoS Biol 3(3):404–418
Krek A et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37(5):495–500
Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1):15–20
Grun D et al. (2005) MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1(1):51–66
Chen K, Rajewsky N (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38(12):1452–1456
Friedman RC et al. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res e(1):92–105
Kiriakidou M et al. (2004) A combined computational–experimental approach predicts human microRNA targets. Genes Dev 18(10):1165–1178
Maragkakis M et al. (2009) DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 37:W273–W276
Alexiou P et al. (2010) The DIANA-mirExTra web server: from gene expression data to microRNA function. PLoS ONE 5(2):e9171
Rehmsmeier M et al. (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10(10):1507–1517
Hammell M et al. (2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Meth 5(9):813–819
John B et al. (2004) Human microRNA targets. PLoS Biol 2(11):1862–1879
Betel D et al. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149–D153
Long D et al. (2007) Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14(4):287–294
Lagos-Quintana M et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12(9):735–739
Landgraf P et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401–1414
Lau NC et al. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862
Cummins JM et al. (2006) The colorectal microRNAome. Proc Natl Acad Sci USA 103(10):3687–3692.
Mattie M et al. (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5(1):24
Lagos-Quintana M et al. (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858
Sempere L et al. (2004) Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 5(3):R13
Calin GA et al. (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99(24):15524–15529.
Streit S et al. (2008) Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues. Nat Protocols 4(1):37–43
Fernyhough P (2001) Quantification of mRNA levels using northern blotting. In: Rush RA (ed) Neurotrophin protocols. Humana, Totowa, pp 53–63
Calin GA et al. (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99(24):15524–15529
Varallyay E, Burgyan J, Havelda Z (2008) MicroRNA detection by northern blotting using locked nucleic acid probes. Nat Protoc 3(2):190–196
Valoczi A et al. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32(22):e175
Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 8(1):1–7
Ramkissoon SH et al. (2006) Nonisotopic detection of microRNA using digoxigenin labeled RNA probes. Mol Cell Probes 20(1):1–4
Schmittgen TD et al. (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucl Acids Res 32(4):e43
Raymond CK et al. (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 11(11):1737–1744
Miska E et al. (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5(9):R68
Barad O et al. (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 14(12):2486–2494
Ohtsuka E et al. (1977) Joining of synthetic ribotrinucleotides with defined sequences catalyzed by T4 RNA ligase. Eur J Biochem 81(2):285–291
Mclaughlin LW et al. (1982) The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur J Biochem 125(3):639–643
Shi R, Chiang VL (2005) Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39(4):519–525
Andreasen D et al. (2010) Improved microRNA quantification in total RNA from clinical samples. Methods 50(4):S6–S9
Chen CF et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20):e179
Varkonyi-Gasic E et al. (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3:12
Li J et al. (2009) Real-time polymerase chain reaction microRNA detection based on enzymatic stem-loop probes ligation. Anal Chem 81(13):5446–5451
Lao KQ et al. (2006) Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Commun 343(1):85–89
Castoldi M et al. (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12(5):913–920
Wang H, Ach RA, Curry B (2007) Direct and sensitive miRNA profiling from low-input total RNA. RNA 13(1):151–159
Thomson JM et al. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat Meth 1(1):47–53
He L et al. (2005) A microRNA polycistron as a potential human oncogene. Nature 435(7043):828–833
Krichevsky AM et al. (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9(10):1274–1281
Goff LA et al. (2005) Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biol 2(3):93–100
Babak T et al. (2004) Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10(11):1813–1819
Wiegant JCAG et al. (1999) ULS: a versatile method of labeling nucleic acids for FISH based on a monofunctional reaction of cisplatin derivatives with guanine moieties. Cytogenet Genome Res 87(1–2):47–52
Liang RQ et al. (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res 33(2):e17
Nelson PT et al. (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Meth 1(2):155–161
Berezikov E et al. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 16(10):1289–1298
Nelson PT et al. (2006) RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA e(2):187–191
Yeung ML et al. (2005) Changes in microRNA expression profiles in HIV-1-transfected human cells. Retrovirology 2(1):81
Qavi AJ et al. (2009) Label-free technologies for quantitative multiparameter biological analysis. Anal Bioanal Chem 394:121–135
Egholm M et al. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules. Nature 365(6446):566–568
Nielsen PE et al. (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254(5037):1497–1500
Zhang G-J et al. (2009) Label-free direct detection of MiRNAs with silicon nanowire biosensors. Biosens Bioelectron 24(8):2504–2508
Zhang GJ et al. (2010) Silicon nanowire biosensor for highly sensitive and rapid detection of dengue virus. Sens Actuators B 146(1):138–144
Fan Y et al. (2007) Detection of microRNAs using target-guided formation of conducting polymer nanowires in nanogaps. J Am Chem Soc 129(17):5437–5443
Pohlmann C, Sprinzl M (2010) Electrochemical detection of microRNAs via gap hybridization assay. Anal Chem 82(11):4434–4440
Yang H et al. (2009) Direct, electronic microRNA detection for the rapid determination of differential expression profiles. Angew Chem Int Ed 48(45):8461–8464
Soleymani L et al. (2009) Nanostructuring of patterned microelectrodes to enhance the sensitivity of electrochemical nucleic acids detection. Angew Chem Int Ed 48(45):8457–8460
Lusi EA et al. (2009) Innovative electrochemical approach for an early detection of microRNAs. Anal Chem 81(7):2819–2822
Yang WJ et al. (2008) Quantification of microRNA by gold nanoparticle probes. Anal Biochem 376(2):183–188
Gao ZQ, Yang ZC (2006) Detection of microRNAs using electrocatalytic nanoparticle tags. Anal Chem 78(5):1470–1477
Gao ZQ, Yu YH (2007) Direct labeling microRNA with an electrocatalytic moiety and its application in ultrasensitive microRNA assays. Biosens Bioelectron 22(6):933–940
Gao ZQ, Yu YH (2007) A microRNA biosensor based on direct chemical ligation and electrochemically amplified detection. Sens Actuators B 121(2):552–559
Li JS et al. (2009) Detection of microRNA by fluorescence amplification based on cation exchange in nanocrystals. Anal Chem 81(23):9723–9729
Neely LA et al. (2006) A single-molecule method for the quantitation of microRNA gene expression. Nat Meth 3(1):41–46
Cissell KA et al. (2008) Bioluminescence-based detection of microRNA, miR21 in breast cancer cells. Anal Chem 80(7):2319–2325
Cho H et al. (2009) Label-free and highly sensitive biomolecular detection using SERS and electrokinetic preconcentration. Lab Chip 9(23):3360–3363
Huh YS et al. (2009) Enhanced on-chip SERS based biomolecular detection using electrokinetically active microwells. Lab Chip 9(3):433–439
Hudson SD, Chumanov G (2009) Bioanalytical applications of SERS (surface-enhanced Raman spectroscopy). Anal Bioanal Chem 394(3):679–686
Driskell JD et al. (2008) Rapid microRNA (miRNA) detection and classification via surface-enhanced Raman spectroscopy (SERS). Biosens Bioelectron 24(4):917–922
Nelson BP et al. (2000) Surface plasmon resonance imaging measurements of DNA and RNA hybridization adsorption onto DNA microarrays. Anal Chem 73(1):1–7
Wegner GJ, Lee HJ, Corn RM (2002) Characterization and optimization of peptide arrays for the study of epitope–antibody interactions using surface plasmon resonance imaging. Anal Chem 74(20):5161–5168
Smith EA et al. (2003) Surface plasmon resonance imaging studies of protein–carbohydrate interactions. J Am Chem Soc 125(20):6140–6148
Wegner GJ et al. (2004) Real-time surface plasmon resonance imaging measurements for the multiplexed determination of protein adsorption/desorption kinetics and surface enzymatic reactions on peptide microarrays. Anal Chem 76(19):5677–5684
Fang S et al. (2006) Attomole microarray detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. J Am Chem Soc 128(43):14044–14046
Washburn AL, Gunn LC, Bailey RC (2009) Label-free quantitation of a cancer biomarker in complex media using silicon photonic microring resonators. Anal Chem 81(22):9499–9506
Washburn AL et al. (2010) Quantitative, label-free detection of five protein biomarkers using multiplexed arrays of silicon photonic microring resonators. Anal Chem 82(1):69–72
Luchansky MS, Bailey RC (2010) Silicon photonic microring resonators for quantitative cytokine detection and T-cell secretion analysis. Anal Chem 82(5):1975–1981
Qavi AJ, Bailey RC (2010) Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators. Angew Chem Int Ed 49(27):4608–4611
Acknowledgements
We gratefully acknowledge financial support for our own efforts in developing a quantitative, multiparameter miRNA analysis platform from the National Institutes of Health (NIH) Director’s New Innovator Award Program, part of the NIH Roadmap for Medical Research, through grant number 1-DP2-OD002190-01; the Camille and Henry Dreyfus Foundation, through a New Faculty Award; and the Eastman Chemical Company (fellowship to AJQ).
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Published in the special issue on Focus on Bioanalysis with Guest Editors Antje J. Baeumner, Günter Gauglitz, and Frieder W. Scheller.
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Qavi, A.J., Kindt, J.T. & Bailey, R.C. Sizing up the future of microRNA analysis. Anal Bioanal Chem 398, 2535–2549 (2010). https://doi.org/10.1007/s00216-010-4018-8
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DOI: https://doi.org/10.1007/s00216-010-4018-8