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RIP-CHIP in Drug Development

  • Ritu Jain
  • Francis Doyle
  • Ajish D. George
  • Marcy Kuentzel
  • David Frank
  • Sridar V. Chittur
  • Scott A. Tenenbaum
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 632)

Abstract

Microarrays are extensively used to evaluate the effects of compounds on gene expression in the cells. Most of the studies so far have analyzed the transcriptome of the cell. The basic assumption of this approach is that the changes in gene expression occur at the level of transcription of a gene. However, changes often occur at the posttranscriptional level and are not reflected in the analysis of whole transcriptome. We have pioneered the development of “ribonomic profiling” as a high-throughput method to study posttranscriptional regulation of gene expression in the cell. This method is also often referred to as RIP-CHIP. In this chapter, we describe how to use the RIP-CHIP technology to assess the posttranscriptional changes occurring in the cell in response to treatment with a drug.

Key words

RIP-CHIP Ribonomics Posttranscriptional gene regulation RNA-binding Protein (RBP) Immunoprecipitation (IP) Microarray expression profiling Drug development 

References

  1. 1.
    Braxton S, Bedilion T (1998) Integration of microarray information in the drug development process. Curr Opin Biotechnol 9:643-649PubMedCrossRefGoogle Scholar
  2. 2.
    Gunther EC, Stone DJ, Gerwien RW, Bento P, Heyes MP (2003) Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro. Proc Natl Acad Sci USA 100(16):9608-9613PubMedCrossRefGoogle Scholar
  3. 3.
    Lord PG, Nie A, McMillian M (2006) Applications of Genomics in preclinical drug safety evaluation. Basic Clin Pharmacol Toxicol 98(6):537-546PubMedCrossRefGoogle Scholar
  4. 4.
  5. 5.
    Moore MJ (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309:1514-1518PubMedCrossRefGoogle Scholar
  6. 6.
    Keene JD (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98(13):7018-7024PubMedCrossRefGoogle Scholar
  7. 7.
    Sanchez-Diaz P, Penalva LO (2006) Post-transcription meets post-genomic: the saga of RNA binding proteins in a new era. RNA Biol 3(3):101-109PubMedCrossRefGoogle Scholar
  8. 8.
    Keene JD (2002) Tenenbaum SA: eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9(6):1161-1167PubMedCrossRefGoogle Scholar
  9. 9.
    Hieronymus H, Silver P (2004) A systems view of mRNP biology. Genes Dev 18:2845-2860PubMedCrossRefGoogle Scholar
  10. 10.
    López de Silanes I, Lal A, Gorospe M (2005) HuR: post-transcriptional paths to malignancy. RNA Biol 2(1):11-13PubMedCrossRefGoogle Scholar
  11. 11.
    Mazan-Mamczarz K, Hagner PR, Corl S, Srikantan S, Wood WH, Becker KG, Gorospe M, Keene JD, Levenson AS, Gartenhaus RB (2008) Post-transcriptional gene regulation by HuR promotes a more tumorigenic phenotype. Oncogene 27:6151-6163PubMedCrossRefGoogle Scholar
  12. 12.
    Mazan-Mamczarz K, Patrick RH, Dai B, Wood WH, Zhang Y, Becker KG, Liu Z, Gartenhaus RB (2008) Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach. Cancer Res 68:7730-7735PubMedCrossRefGoogle Scholar
  13. 13.
    Kato T, Hayama S, Yamabuki T, Ishikawa N, Miyamoto M, Ito T, Tsuchiya E, Kondo S, Nakamura Y, Daigo Y (2007) Increased expression of insulin-like growth factor-II messenger RNA binding protein-1 is associated with tumor progression in patients with lung cancer. Clin Cancer Res 13:434-442PubMedCrossRefGoogle Scholar
  14. 14.
    Tenenbaum SA, Carson CC, Lager PJ, Keene JD (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci USA 97:14085-14090PubMedCrossRefGoogle Scholar
  15. 15.
    Tenenbaum SA, Lager PJ, Carson CC, Keene JD (2002) Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26(2):191-198PubMedCrossRefGoogle Scholar
  16. 16.
    Penalva LO, Tenenbaum SA, Keene JD (2004) Gene expression analysis of messenger RNP complexes. Methods Mol Biol 257:125-134PubMedGoogle Scholar
  17. 17.
    Niranjanakumari S, Lasda E, Brazas R, Garcia-Blanco MA (2002) Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. Methods 26(2):182-190PubMedCrossRefGoogle Scholar
  18. 18.
    Affymetrix. GeneChip WT sense strand target labeling assay manual, 701880. http://www.affymetrix,com/support/downloads/manuals/wt_sensetarget_label_manualGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Ritu Jain
    • 1
  • Francis Doyle
    • 1
  • Ajish D. George
    • 2
  • Marcy Kuentzel
    • 3
  • David Frank
    • 3
  • Sridar V. Chittur
    • 3
  • Scott A. Tenenbaum
    • 1
  1. 1.NanoBio ConstellationCollege of Nanoscale Science and Engineering, University at Albany-SUNYAlbanyUSA
  2. 2.Department of Biomedical SciencesGen*NY*Sis Center for Excellence in Cancer Genomics, School of Public Health, University at Albany-SUNYRensselaerUSA
  3. 3.Department of Biomedical SciencesCenter for Functional Genomics, School of Public Health, University at Albany-SUNYRensselaerUSA

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