title: Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest.
abstract: In this chapter, we present an approach using genomic and ribonomic profiling to investigate functional gene programs in a tumor growth model. To reach this goal, ribonomic profiling was combined with RNA interference in a tumor dormancy model. Strategies merging functional genomic technologies are outlined for the identification of novel posttranscriptionally regulated targets of p38 to show that they are functionally linked to the induction or interruption of cellular growth in cancer. In the first section of this chapter, we describe a method for the detection of mRNA subsets associated with RNA-binding proteins such as hnRNP A1 using (1) immunopurification of mRNA-protein complexes, from either whole cell lysates or subcellular fractions and (2) gene expression arrays to find those mRNAs bound to hnRNP A1. In the second section, short hairpin RNA technology was used to create a library of shRNAs that target p38 induced mRNAs expression libraries are utilized to "knockdown" the genes identified in the first section. Finally, this library of gene candidates is evaluated in vivo to address their functional role in the induction or maintenance of dormancy.
authors.affiliation: Gen*NY*Sis Center for Excellence in Cancer Genomics, Department of Biomedical Sciences, School of Public Health, University of Albany, SUNY, Rensselaer, NY, USA.
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Baroni
authors.forename: Michele T
authors.initials: MT
authors.lastname: Lastro
authors.forename: Aparna C
authors.initials: AC
authors.lastname: Ranganathan
authors.forename: Scott A
authors.initials: SA
authors.lastname: Tenenbaum
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Conklin
authors.forename: Julio A
authors.initials: JA
authors.lastname: Aguirre-Ghiso
mesh_terms: D002455:Cell Division / Q000235:genetics*; D015536:Down-Regulation; D020869:Gene Expression Profiling; D015723:Gene Library; D020868:Gene Silencing; D006801:Humans; D035683:MicroRNAs / Q000502:physiology; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D016601:RNA-Binding Proteins / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000502:physiology*; D048051:p38 Mitogen-Activated Protein Kinases / Q000235:genetics
chemical_list: D035683:MicroRNAs; D016601:RNA-Binding Proteins; D034743:RNA-Induced Silencing Complex; D048051:p38 Mitogen-Activated Protein Kinases