Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest.

Timothy E. Baroni, Michele T. Lastro, Aparna R Sertil, Scott A. Tenenbaum, Douglas S. Conklin, Julio A. Aguirre-Ghiso

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)227-244
Number of pages18
JournalMethods in molecular biology (Clifton, N.J.)
Volume383
StatePublished - 2007
Externally publishedYes

Fingerprint

Gene Silencing
RNA Interference
Small Interfering RNA
Messenger RNA
Growth
Genes
Neoplasms
Gene Knockdown Techniques
Technology
RNA-Binding Proteins
Subcellular Fractions
Gene Library
Libraries
Maintenance
Gene Expression
Proteins
hnRNP A1

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest. / Baroni, Timothy E.; Lastro, Michele T.; Sertil, Aparna R; Tenenbaum, Scott A.; Conklin, Douglas S.; Aguirre-Ghiso, Julio A.

In: Methods in molecular biology (Clifton, N.J.), Vol. 383, 2007, p. 227-244.

Research output: Contribution to journalArticle

Baroni, Timothy E. ; Lastro, Michele T. ; Sertil, Aparna R ; Tenenbaum, Scott A. ; Conklin, Douglas S. ; Aguirre-Ghiso, Julio A. / Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest. In: Methods in molecular biology (Clifton, N.J.). 2007 ; Vol. 383. pp. 227-244.
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