Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×

Online ordering will be unavailable from 17:00 GMT on Friday, April 25 until 17:00 GMT on Sunday, April 27 due to maintenance. We apologise for the inconvenience.

Hostname: page-component-669899f699-tzmfd Total loading time: 0 Render date: 2025-04-27T15:25:36.268Z Has data issue: false hasContentIssue false

17 - Detection and analysis of microRNAs using LNA (locked nucleic acid)-modified probes

from IV - Detection and quantitation of microRNAs

Published online by Cambridge University Press:  22 August 2009

By
Sakari Kauppinen
Edited by
Krishnarao Appasani
Foreword by
Sidney Altman  and
Victor R. Ambros
Sakari Kauppinen
Affiliation:
Wilhelm Johannsen Centre for Functional Genome Research Institute of Medical Biochemistry and Genetics University of Copenhagen Blegdamsvej 3 DK-2200 Copenhagen NorthDenmark; Santaris Pharma Boge Alle 3 Horshol DK-2970 Denmark
Get access

Summary

Introduction

MicroRNAs (miRNAs) are an abundant class of short endogenous RNAs that act as post-transcriptional regulators of gene expression by base-pairing with their target mRNAs. To date more than 3500 microRNAs have been annotated in vertebrates, invertebrates and plants according to the miRBase microRNA database release 8.0 in February 2006 (Griffiths-Jones, 2004; Griffiths-Jones et al., 2006), and many miRNAs that correspond to putative genes have also been identified. The miRNAs identified to date represent most likely the tip of the iceberg, and the number of miRNAs might turn out to be very large. Recent bioinformatic predictions combined with array analyses, small RNA cloning and Northern blot validation indicate that the total number of miRNAs in vertebrate genomes is significantly higher than previously estimated and maybe as many as 1000 (Bentwich et al., 2005; Berezikov et al., 2005; Xie et al., 2005). An increasing body of research shows that animal miRNAs play fundamental biological roles in cell growth and apoptosis (Brennecke et al., 2003), hematopoietic lineage differentiation (Chen et al., 2004), life-span regulation (Boehm and Slack, 2005), photoreceptor differentiation (Li and Carthew, 2005), homeobox gene regulation (Yekta et al., 2004; Hornstein et al., 2005), neuronal asymmetry (Johnston and Hobert, 2003), insulin secretion (Poy et al., 2004), brain morphogenesis (Giraldez et al., 2005), muscle proliferation and differentiation (Chan et al., 2005; Kwon et al., 2005; Sokol and Ambros, 2005), cardiogenesis (Zhao et al., 2005) and late embryonic development in vertebrates (Wienholds et al., 2005).

Type
Chapter
Information
MicroRNAs
From Basic Science to Disease Biology
 , pp. 229 - 241
Publisher: Cambridge University Press
Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Book purchase

Temporarily unavailable

References

Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M. and Lai, E. C. (2005). Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proceedings of the National Academy of Sciences USA, 102, 18 017–18 022.CrossRefGoogle Scholar
Barad, O., Meiri, E., Avniel, A.et al. (2004). MicroRNA expression detected microarrays: system establishment profiling in human tissues. Genome Research, 14, 2486–2494.CrossRefGoogle Scholar
Bentwich, I., Avniel, A., Karov, Y.et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genetics, 37, 766–770.CrossRefGoogle Scholar
Berezikov, E., Guryev, V., Belt, J.et al. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21–24.CrossRefGoogle Scholar
Boehm, M. and Slack, F. (2005). A developmental timing microRNA and its target regulate life span in C. elegans. Science, 310, 1954–1957.CrossRefGoogle Scholar
Braasch, D. A. and Corey, D. R. (2001). Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chemistry and Biology, 8, 1–7.CrossRefGoogle Scholar
Braasch, D. A., Liu, Y. and Corey, D. R. (2002). Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design. Nucleic Acids Research, 30, e 5160–5167.CrossRefGoogle Scholar
Brennecke, J., Hipfner, D. R., Stark, A., Russel, R. B. and Cohen, S. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25–36.CrossRefGoogle Scholar
Castoldi, M., Schmidt, S., Benes, V.et al. (2006). A sensitive array for microRNA expression profiling (mi-Chip) based on locked nucleic acids (LNA). RNA. (In press.)CrossRefGoogle Scholar
Chan, J. A., Krichevsky, A. M. and Kosik, K. S. (2005). MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Research, 65, 6029–6033.CrossRefGoogle Scholar
Chen, C. Z., Li, L., Lodish, H. F. and Bartel, D. P. (2004). MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83–86.CrossRefGoogle Scholar
Farh, K. K., Grimson, A., Jan, C.et al. (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science, 310, 1817–1821.CrossRefGoogle Scholar
Fluiter, K., ten Asbroek, A. L. M., Wissel, M. B.et al. (2003). In vivo tumor growth inhibition and biodistribution studies of locked nucleic acid (LNA) antisense oligonucleotides. Nucleic Acids Research, 31, 953–962.CrossRefGoogle Scholar
Fodor, S. P., Read, J. L., Pirrung, M. C.et al. (1991). Light-directed, spatially addressable parallel chemical synthesis. Science, 251, 767–773.CrossRefGoogle Scholar
Giraldez, A. J., Cinalli, R. M., Glasner, M. E.et al. (2005). MicroRNAs regulate brain morphogenesis in zebrafish. Science, 308, 833–838.CrossRefGoogle Scholar
Griffiths-Jones, S. (2004). The microRNA Registry. Nucleic Acids Research, 32, D109–D111.CrossRefGoogle Scholar
Griffiths-Jones, S., Grocock, R. J., Dongen, S., Bateman, A. and Enright, A. J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Research 34, D140–D144.CrossRefGoogle Scholar
Hornstein, E., Mansfield, J. H., Yekta, S.et al. (2005). The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature, 438, 671–674.CrossRefGoogle Scholar
Hutvágner, G., Simard, M. J., Mello, C. C. and Zamore, P. D. (2004). Sequence-specific inhibition of small RNA function. Public Library of Science Biology, 2, 1–11.CrossRefGoogle Scholar
Jacobsen, N., Fenger, M., Bentzen, J.et al. (2002a). Genotyping of the apolipoprotein B R3500Q mutation using immobilized locked nucleic acid capture probes. Clinical Chemistry, 48(4), 657–660.Google Scholar
Jacobsen, N., Bentzen, J.Meldgaard, M.et al. (2002b). LNA-enhanced detection of single nucleotide polymorphisms in the apoli-poprotein E. Nucleic Acids Research, 30, e100.Google Scholar
Jacobsen, N., Nielsen, P. S., Jeffares, D. C.et al. (2004). Direct isolation of poly(A) + RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture. Nucleic Acids Research, 32, e64.CrossRefGoogle Scholar
Johnston, R. J. and Hobert, O. (2003). A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature, 426, 845–849.CrossRefGoogle Scholar
Juarez, M. T., Kui, J. S., Thomas, J., Heller, B. A. and Timmermans, M. C. (2004). MicroRNA-mediated repression of rolled leaf 1 specifies maize leaf polarity. Nature, 428, 84–88.CrossRefGoogle Scholar
Kloosterman, W. P., Wienholds, E., Bruijn, E., Kauppinen, S. and Plasterk, R. H. (2006). In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nature Methods, 3, 27–29.CrossRefGoogle Scholar
Koshkin, A. A., Singh, S. K., Nielsen, P.et al. (1998). LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron, 54, 3607–3630.CrossRefGoogle Scholar
Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K. and Kosik, K. S. (2003). A microRNA array reveals extensive regulation of microRNAs during brain development. RNA, 9, 1274–1281.CrossRefGoogle Scholar
Krützfeldt, J., Rajewsky, N., Braich, R.et al. (2005). Silencing of microRNAs in vivo with ‘antagomirs’. Nature, 438, 685–689.CrossRefGoogle Scholar
Kurreck, J., Wyszko, E., Gillen, C. and Erdmann, V. A. (2002). Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Research, 30, 1911–1918.CrossRefGoogle Scholar
Kwon, C., Han, Z., Olson, E. N. and Srivastava, D. (2005). MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proceedings of the National Academy of Sciences USA, 102, 18 986–18 991.CrossRefGoogle Scholar
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858.CrossRefGoogle Scholar
Leaman, D., Chen, P,Y., Fak, J.et al. (2005). Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell, 121, 1097–1108.CrossRefGoogle Scholar
Lecellier, C. H., Dunoyer, P., Arar, K.et al. (2005). A cellular microRNA mediates antiviral defense in human cells. Science, 308, 557–560.CrossRefGoogle Scholar
Lee, R. C. and Ambros, V. (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862–864.CrossRefGoogle Scholar
Li, X. and Carthew, R. W. (2005). A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye. Cell, 123, 1267–1277.CrossRefGoogle Scholar
Lim, L. P., Lau, N. C., Garrett-Engele, P.et al. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773.CrossRefGoogle Scholar
Liu, C.-G., Calin, G. A., Meloon, B.et al. (2004). An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences USA, 101, 9740–9744.CrossRefGoogle Scholar
Mansfield, J. H., Harfe, B. D., Nissen, R.et al. (2004). MicroRNA-responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genetics, 36, 1079–1083.CrossRefGoogle Scholar
Miska, E. A., Alvarez-Saavedra, E., Townsend, M.et al. (2004). Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biology, 5, R68.CrossRefGoogle Scholar
Mouritzen, P., Nielsen, A. T., Pfundheller, H. M., et al. (2003). Single nucleotide polymorphism genotyping using locked nucleic acid (LNA). Expert Review of Molecular Diagnostics, 3, 27–38.CrossRefGoogle Scholar
Neely, L. A., Patel, S., Garver, J.et al. (2006). A single-molecule method for the quantitation of microRNA gene expression. Nature Methods, 3, 41–46.CrossRefGoogle Scholar
Nelson, P. T., Baldwin, D. A., Kloosterman, W. P.et al. (2006). RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA, 12, 187–191.CrossRefGoogle Scholar
Nielsen, K. E., Rasmussen, J., Kumar, R.et al. (2004). NMR studies of fully modified locked nucleic acid (LNA) hybrids: Solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid. Bioconjugate Chemistry, 15, 449–457.CrossRefGoogle Scholar
Ørom, U. A., Kauppinen, S. and Lund, A. (2006). LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene. (In press.)CrossRefGoogle Scholar
Petersen, M., Nielsen, C. B., Nielsen, K. E.et al. (2000). The conformations of locked nucleic acids (LNA). Journal of Molecular Recognition, 13, 44–53.3.0.CO;2-6>CrossRefGoogle Scholar
Petersen, M., Bondensgaard, K., Wengel, J. and Jacobsen, J. P. (2002). Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids. Journal of American Chemical Society, 124, 5974–5982.CrossRefGoogle Scholar
Poy, M. N., Eliasson, L., Krutzfeldt, J.et al. (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature, 432, 226–230.CrossRefGoogle Scholar
Reinhart, B. J., Slack, F. J., Basson, M.et al. (2000). The 21 nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901–906.CrossRefGoogle Scholar
Schena, M., Shalon, D., Davis, R. W. and Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467–470.CrossRefGoogle Scholar
Singh, S. K., Nielsen, P., Koshkin, A., Olsen, C. E. and Wengel, J. (1998). LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chemical Communications, 4, 455–456.CrossRefGoogle Scholar
Sokol, N. S. and Ambros, V. (2005). Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes and Development, 19, 2343–2354.CrossRefGoogle Scholar
Stark, A., Brennecke, J., Bushati, N., Russell, R. B. and Cohen, S. M. (2005). Animal microRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell, 123, 1133–1146.CrossRefGoogle Scholar
Thomson, J. M., Parker, J., Perou, C. M. and Hammond, S. M. (2004). A custom microarray platform for analysis of microRNA gene expression. Nature Methods, 1, 1–6.CrossRefGoogle Scholar
Tolstrup, N., Nielsen, P. S., Kolberg, J.et al. (2003). OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Research, 31, 3758–3762.CrossRefGoogle Scholar
Válóczi, A., Hornyik, C., Varga, N.et al. (2004). Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Research, 32, e175.CrossRefGoogle Scholar
Wahlestedt, C., Salmi, P., Good, L.et al. (2000). Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proceedings of the National Academy of Sciences USA, 97, 5633–5638.CrossRefGoogle Scholar
Wienholds, E., Kloosterman, W. P., Miska, E.et al. (2005). MicroRNA expression in zebrafish embryonic development. Science, 309, 310–311.CrossRefGoogle Scholar
Xie, X., Lu, J., Kulbokas, E. J.et al. (2005). Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature, 434, 338–345.CrossRefGoogle Scholar
Yekta, S., Shih, I.-S. and Bartel, D. (2004). MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594–596.CrossRefGoogle Scholar
Zhao, Y., Samal, E. and Srivastava, D. (2005). Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature, 436, 214–220.CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×