Skip to main content
SpringerLink
Log in

MicroRNA Profiling in CNS Tissue Using Microarrays

  • Chapter
Current Perspectives in microRNAs (miRNA)

MicroRNAs (miRNAs) are important regulators of gene expression in virtually all eukaryotic cell types including the diverse cell types found in the CNS. They are involved in repressing gene expression by complementary hybridization to cognate protein-coding mRNAs. The likely involvement of miRNAs in disease processes requires both accurate detection and expression analysis strategies. In comparison to conventional methodologies to study miRNA expression, microar-rays offer an advantage in terms of throughput, sensitivity and specificity. Although microarrays are almost routinely used in laboratories for the analysis of mRNA, the small size of miRNAs presents challenges for their analysis in terms of probe design, target labeling and hybridization conditions. We discuss these issues in this chapter as well as highlighting the emerging perspectives in this field.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abelson JF, Kwan KY, O’Roak BJ et al (2005) Sequence variants in SLITRK1 are associated with Tourette’s syndrome. Science 310:317-320

    Article  CAS  PubMed  Google Scholar 

  2. Allawi HT, Dahlberg JE, Olson S et al (2004) Quantitation of microRNAs using a modified Invader assay. RNA 10:1153-1161

    Article  CAS  PubMed  Google Scholar 

  3. Allison DB, Cui X, Page GP et al (2006) Microarray data analysis: from disarray to consolida-tion and consensus. Nat Rev Genet 7:55-65

    Article  CAS  PubMed  Google Scholar 

  4. Babak T, Zhang W, Morris Q et al (2004) Probing microRNAs with microarrays: tissue spe-cificity and functional inference. RNA 10:1813-1819

    Article  CAS  PubMed  Google Scholar 

  5. Barad O, Meiri E, Avniel A et al (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 14:2486-2494

    Article  CAS  PubMed  Google Scholar 

  6. Baroukh N, Ravier MA, Loder MK et al (2007) MicroRNA-124a regulates Foxa2 expression and intracellular signaling in pancreatic beta-cell lines. J Biol Chem 282:19575-19588

    Article  CAS  PubMed  Google Scholar 

  7. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297

    Article  CAS  PubMed  Google Scholar 

  8. Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent coex-pression with neighboring miRNAs and host genes. RNA 11:241-247

    Article  CAS  PubMed  Google Scholar 

  9. Beuvink I, Kolb FA, Budach W et al (2007) A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucleic Acids Res 35: e52

    Article  PubMed  Google Scholar 

  10. Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 8:1-7

    Article  CAS  PubMed  Google Scholar 

  11. Budach W, Neuschafer D, Wanke C et al (2003) Generation of transducers for fluorescence-based microarrays with enhanced sensitivity and their application for gene expression profil-ing. Anal Chem 75:2571-2577

    Article  CAS  PubMed  Google Scholar 

  12. Calin GA, Ferracin M, Cimmino A et al (2005) A MicroRNA signature associated with prog-nosis and progression in chronic lymphocytic leukemia. N Engl J Med 353:1793-1801

    Article  CAS  PubMed  Google Scholar 

  13. Castoldi M, Benes V, Hentze MW et al (2007) miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes. Methods 43:146-152

    Article  CAS  PubMed  Google Scholar 

  14. Castoldi M, Schmidt S, Benes V et al (2006) A sensitive array for microRNA expression pro-filing (miChip) based on locked nucleic acids (LNA). RNA 12:913-920

    Article  CAS  PubMed  Google Scholar 

  15. Chen C, Ridzon DA, Broomer AJ et al (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  Google Scholar 

  16. Conaco C, Otto S, Han JJ et al (2006) Reciprocal actions of REST and a microRNA promote neuronal identity. Proc Natl Acad Sci U S A 103:2422-2427

    Article  CAS  PubMed  Google Scholar 

  17. Cummins JM, He Y, Leary RJ et al (2006) The colorectal microRNAome. Proc Natl Acad Sci U S A 103:3687-3692

    Article  CAS  PubMed  Google Scholar 

  18. Davison TS, Johnson CD, Andruss BF (2006) Analyzing micro-RNA expression using micro-arrays. Methods Enzymol 411:14-34

    Article  CAS  PubMed  Google Scholar 

  19. Emmert-Buck MR, Bonner RF, Smith PD et al (1996) Laser capture microdissection. Science 274:998-1001

    Article  CAS  PubMed  Google Scholar 

  20. Enos JM, Duzeski JL, Roesch PL et al (2007) MicroRNA labeling methods directly influence the accuracy of expression profiling detection. Biotechniques 42:378-382

    Article  CAS  Google Scholar 

  21. Esquela-Kerscher A, Slack FJ (2006) Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6:259-269

    Article  CAS  PubMed  Google Scholar 

  22. Fu HJ, Zhu J, Yang M et al (2006) A novel method to monitor the expression of microRNAs. Mol Biotechnol 32:197-204

    Article  CAS  PubMed  Google Scholar 

  23. Giraldez AJ, Cinalli RM, Glasner ME et al (2005) MicroRNAs regulate brain morphogenesis in zebrafish. Science 308:833-838

    Article  CAS  PubMed  Google Scholar 

  24. Goff LA, Yang M, Bowers J et al (2005) Rational Probe Optimization and Enhanced Detection Strategy for MicroRNAs Using Microarrays. RNA Biol 2:93-100

    CAS  PubMed  Google Scholar 

  25. Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342:129-138

    CAS  PubMed  Google Scholar 

  26. Hansen T, Olsen L, Lindow M et al (2007) Brain Expressed microRNAs Implicated in Schizophrenia Etiology. PLoS ONE 2:e873

    Article  PubMed  Google Scholar 

  27. Heetebrij RJ, Talman EG, v Velzen MA et al (2003) Platinum(II)-based coordination com-pounds as nucleic acid labeling reagents: synthesis, reactivity, and applications in hybridiza-tion assays. Chembiochem 4:573-583

    Article  CAS  PubMed  Google Scholar 

  28. Hohjoh H, Fukushima T (2007) Expression profile analysis of microRNA (miRNA) in mouse central nervous system using a new miRNA detection system that examines hybridization signals at every step of washing. Gene 391:39-44

    Article  CAS  PubMed  Google Scholar 

  29. Igloi GL (1996) Nonradioactive labeling of RNA. Anal Biochem 233:124-129

    Article  CAS  PubMed  Google Scholar 

  30. Jin P, Zarnescu DC, Ceman S et al (2004) Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nat Neurosci 7:113-117

    Article  CAS  PubMed  Google Scholar 

  31. Jonstrup SP, Koch J, Kjems J (2006) A microRNA detection system based on padlock probes and rolling circle amplification. RNA 12:1747-1752

    Article  CAS  PubMed  Google Scholar 

  32. Kim J, Inoue K, Ishii J et al (2007) A MicroRNA feedback circuit in midbrain dopamine neu-rons. Science 317:1220-1224

    Article  CAS  PubMed  Google Scholar 

  33. Kloosterman WP, Wienholds E, de Bruijn E et al (2006) In situ detection of miRNAs in ani-mal embryos using LNA-modified oligonucleotide probes. Nat Methods 3:27-29

    Article  CAS  PubMed  Google Scholar 

  34. Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495-500

    Article  CAS  PubMed  Google Scholar 

  35. Krichevsky AM, King KS, Donahue CP et al (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9:1274-1281

    Article  CAS  PubMed  Google Scholar 

  36. Kye MJ, Liu T, Levy SF et al (2007) Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR. RNA 13:1224-1234

    Article  CAS  PubMed  Google Scholar 

  37. Lagos-Quintana M, Rauhut R, Yalcin A et al (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12:735-739

    Article  CAS  PubMed  Google Scholar 

  38. Landthaler M, Yalcin A, Tuschl T (2004) The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14:2162-2167

    Article  CAS  PubMed  Google Scholar 

  39. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862-864

    Article  CAS  PubMed  Google Scholar 

  40. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20

    Article  CAS  PubMed  Google Scholar 

  41. Lewis BP, Shih IH, Jones-Rhoades MW et al (2003) Prediction of mammalian microRNA targets. Cell 115:787-798

    Article  CAS  PubMed  Google Scholar 

  42. Liang RQ, Li W, Li Y et al (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res 33:e17

    Article  PubMed  Google Scholar 

  43. Lim LP, Lau NC, Garrett-Engele P et al (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-773

    Article  CAS  PubMed  Google Scholar 

  44. Lind KE, Mohan V, Manoharan M et al (1998) Structural characteristics of2’-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations. Nucleic Acids Res 26:3694-3799

    Article  CAS  PubMed  Google Scholar 

  45. Liu CG, Calin GA, Meloon B et al (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 101: 9740-9744

    Article  CAS  PubMed  Google Scholar 

  46. Lu J, Getz G, Miska EA et al (2005) MicroRNA expression profiles classify human cancers. Nature 435:834-838

    Article  CAS  PubMed  Google Scholar 

  47. Lukiw WJ (2007) Micro-RNA speciation in fetal, adult and Alzheimer’s disease hippocam-pus. Neuroreport 18:297-300

    Article  CAS  PubMed  Google Scholar 

  48. Miska EA, Alvarez-Saavedra E, Townsend M et al (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5:R68

    Article  PubMed  Google Scholar 

  49. Mocellin S, Rossi CR (2007) Principles of gene microarray data analysis. Adv Exp Med Biol 593:19-30

    Article  PubMed  Google Scholar 

  50. Nelson PT, Baldwin DA, Kloosterman WP et al (2006) RAKE and LNA-ISH reveal micro-RNA expression and localization in archival human brain. RNA 12:187-191

    Article  CAS  PubMed  Google Scholar 

  51. Obernosterer G, Martinez J, Alenius M (2007) Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2:1508-1514

    Article  CAS  PubMed  Google Scholar 

  52. Pall GS, Codony-Servat C, Byrne J et al (2007) Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res 35:e60

    Article  PubMed  Google Scholar 

  53. Perkins DO, Jeffries CD, Jarskog LF et al (2007) microRNA expression in the prefrontal cor-tex of individuals with schizophrenia and schizoaffective disorder. Genome Biol 8:R27

    Article  PubMed  Google Scholar 

  54. Ramdas L, Cogdell DE, Jia JY et al (2004) Improving signal intensities for genes with low-expression on oligonucleotide microarrays. BMC Genomics 5:35

    Article  PubMed  Google Scholar 

  55. Relogio A, Schwager C, Richter A et al (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 30:e51

    Article  PubMed  Google Scholar 

  56. Ro S, Park C, Jin J et al (2006) A PCR-based method for detection and quantification of small RNAs. Biochem Biophys Res Commun 351:756-763

    Article  CAS  PubMed  Google Scholar 

  57. Saba R, Booth SA (2006) Target labelling for the detection and profiling of microRNAs expressed in CNS tissue using microarrays. BMC Biotechnol 6:47

    Article  PubMed  Google Scholar 

  58. Schena M. (2003) Microarray Analysis. John Wiley & Sons, Inc., Hoboken, New Jersey

    Google Scholar 

  59. Schratt GM, Tuebing F, Nigh EA et al (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439:283-289

    Article  CAS  PubMed  Google Scholar 

  60. Sempere LF, Freemantle S, Pitha-Rowe I 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:R13

    Article  PubMed  Google Scholar 

  61. Shi R, Chiang VL (2005) Facile means for quantifying microRNA expression by real-time PCR. BioTechniques 39:519-525

    Article  CAS  PubMed  Google Scholar 

  62. Shingara J, Keiger K, Shelton J et al (2005) An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11:1461-1470

    Article  CAS  PubMed  Google Scholar 

  63. Sioud M, Rosok O (2004) Profiling microRNA expression using sensitive cDNA probes and filter arrays. BioTechniques 37:574-6, 578-80

    Google Scholar 

  64. Smirnova L, Grafe A, Seiler A et al (2005) Regulation of miRNA expression during neural cell specification. Eur J Neurosci 21:1469-1477

    Article  PubMed  Google Scholar 

  65. Stears RL, Getts RC, Gullans SR (2000) A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol Genomics 3:93-99

    CAS  PubMed  Google Scholar 

  66. Sun Y, Koo S, White N et al (2004) Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res 32:e188

    Article  PubMed  Google Scholar 

  67. Tang X, Gal J, Zhuang X et al (2007) A simple array platform for microRNA analysis and its application in mouse tissues. RNA 13:1803-1822

    Article  CAS  PubMed  Google Scholar 

  68. Thomson JM, Parker J, Perou CM et al (2004) A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1:47-53

    Article  CAS  PubMed  Google Scholar 

  69. Valoczi 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 Res 32: e175

    Article  PubMed  Google Scholar 

  70. Varallyay E, Burgyan J, Havelda Z (2007) Detection of microRNAs by Northern blot analyses using LNA probes. Methods 43:140-145

    Article  CAS  PubMed  Google Scholar 

  71. Visvanathan J, Lee S, Lee B et al (2007) The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 21:744-749

    Article  CAS  PubMed  Google Scholar 

  72. Vo N, Klein ME, Varlamova O et al (2005) A cAMP-response element binding protein- induced microRNA regulates neuronal morphogenesis. Proc Natl Acad Sci U S A 102:16426-16431

    Article  CAS  PubMed  Google Scholar 

  73. Wang H, Ach RA, Curry B (2007) Direct and sensitive miRNA profiling from low-input total RNA. RNA 13:151-159

    Article  CAS  PubMed  Google Scholar 

  74. Wiegant JC, van Gijlswijk RP, Heetebrij RJ et al (1999) ULS: a versatile method of labeling nucleic acids for FISH based on a monofunctional reaction of cisplatin derivatives with gua- nine moieties. Cytogenet Cell Genet 87:47-52

    Article  CAS  PubMed  Google Scholar 

  75. Williams KP, Bartel DP (1995) PCR product with strands of unequal length. Nucleic Acids Res 23:4220-4221

    Article  CAS  PubMed  Google Scholar 

  76. Xie X, Lu J, Kulbokas EJ et al (2005) Systematic discovery of regulatory motifs in human promoters and 3’ UTRs by comparison of several mammals. Nature 434:338-345

    Article  CAS  PubMed  Google Scholar 

  77. Zhao JJ, Hua YJ, Sun DG et al (2006) Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray. Childs Nerv Syst 22:1419-1425

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3E 0W3, Canada

    Reuben Saba & Stephanie A. Booth

  2. Prion Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada

    Reuben Saba & Stephanie A. Booth

Authors
  1. Reuben Saba
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephanie A. Booth
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Southern California, Los Angeles, CA, USA

    Shao-Yao Ying

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer Science + Business Media B.V

About this chapter

Cite this chapter

Saba, R., Booth, S.A. (2008). MicroRNA Profiling in CNS Tissue Using Microarrays. In: Ying, SY. (eds) Current Perspectives in microRNAs (miRNA). Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8533-8_5

Download citation

Publish with us

Policies and ethics

Search

Navigation