Advertisement

Application of RNA-Seq Technology in Cancer Chemoprevention

  • Frauke GoemanEmail author
  • Maurizio Fanciulli
Part of the Methods in Molecular Biology book series (MIMB, volume 1379)

Abstract

RNA-sequencing is a revolutionary tool to follow differential expression after treatment with cancer chemopreventive agents. It allows a real genome-wide screening independent of prior assumptions and is well suited for analyzing coding but also long noncoding RNAs. It still consents the discovery of new genes and isoforms and increased our knowledge of antisense and other noncoding RNAs in a tremendous manner. Moreover, it permits to detect low-abundance and biologically critical isoforms and reveals genetic variants and gene fusions in one single assay. Here, we provide a detailed protocol for stranded RNA-sequencing.

Key words

RNA-Seq Deep-sequencing Chemoprevention Transcriptome profiling Long noncoding RNA Stranded RNA-Seq Transcriptional signature Novel transcript and isoform discovery 

Notes

Acknowledgements

We greatly appreciate the support given by the Progetto Finalizzato Ministero della Salute “Tumori Femminili.”

References

  1. 1.
    Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87–98PubMedCentralCrossRefPubMedGoogle Scholar
  2. 2.
    Zhao S, Fung-Leung WP, Bittner A et al (2014) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One 9:e78644PubMedCentralCrossRefPubMedGoogle Scholar
  3. 3.
    Zhao J, Ohsumi TK, Kung JT et al (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939–953PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Chi SW, Zang JB, Mele A et al (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479–486PubMedCentralPubMedGoogle Scholar
  5. 5.
    Ingolia NT, Brar GA, Rouskin S et al (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7:1534–1550PubMedCentralCrossRefPubMedGoogle Scholar
  6. 6.
    Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845–1848PubMedCentralCrossRefPubMedGoogle Scholar
  7. 7.
    Goeman F, De Nicola F, D’Onorio De Meo P et al (2014) VDR primary targets by genome-wide transcriptional profiling. J Steroid Biochem Mol Biol 143C:348–356CrossRefGoogle Scholar
  8. 8.
    Roberts A, Pimentel H, Trapnell C et al (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27:2325–2329CrossRefPubMedGoogle Scholar
  9. 9.
    Trapnell C, Roberts A, Goff L et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    Perocchi F, Xu Z, Clauder-Munster S et al (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35:e128PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Translational Oncogenomics UnitItalian National Cancer Institute “Regina Elena”RomeItaly
  2. 2.Laboratory of Epigenetic, Molecular Medicine AreaItalian National Cancer Institute “Regina Elena”RomeItaly

Personalised recommendations