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.
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Braxton S, Bedilion T (1998) Integration of microarray information in the drug development process. Curr Opin Biotechnol 9:643-649
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):9608-9613
Lord PG, Nie A, McMillian M (2006) Applications of Genomics in preclinical drug safety evaluation. Basic Clin Pharmacol Toxicol 98(6):537-546
http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm
Moore MJ (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309:1514-1518
Keene JD (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98(13):7018-7024
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):101-109
Keene JD (2002) Tenenbaum SA: eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9(6):1161-1167
Hieronymus H, Silver P (2004) A systems view of mRNP biology. Genes Dev 18:2845-2860
López de Silanes I, Lal A, Gorospe M (2005) HuR: post-transcriptional paths to malignancy. RNA Biol 2(1):11-13
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 27:6151-6163
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 68:7730-7735
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 13:434-442
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 97:14085-14090
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):191-198
Penalva LO, Tenenbaum SA, Keene JD (2004) Gene expression analysis of messenger RNP complexes. Methods Mol Biol 257:125-134
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):182-190
Affymetrix. GeneChip WT sense strand target labeling assay manual, 701880. http://www.affymetrix,com/support/downloads/manuals/wt_sensetarget_label_manual
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Jain, R. et al. (2010). RIP-CHIP in Drug Development. In: Chittur, S.V. (eds) Microarray Methods for Drug Discovery. Methods in Molecular Biology, vol 632. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-663-4_10
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DOI: https://doi.org/10.1007/978-1-60761-663-4_10
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