The Wilms' Tumor (WT1) Gene pp 197-209 | Cite as
Methods to Identify and Validate WT1–RNA Interaction
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Abstract
Tumor suppressor protein, Wt1 is a transcription factor that binds to DNA sequence similar to the Early Growth Response gene, EGR1 consensus binding sequence. Biophysical and biochemical validations have shown that the zinc fingers of Wt1 are capable of binding to both DNA and RNA albeit with different binding affinities which potentially is also isoform specific. SELEX based identification of the RNA binding motifs led to the identification of motifs which could not be translated into the in vivo context. With the advent of recent technologies that allow cross-linking of RNA and protein and high throughput sequencing techniques, it is now possible to analyze the in vivo RNA binding interactome of Wt1. This chapter outlines the initial studies that were aimed at addressing the Wt1 RNA interactome and also provides a detailed overview of some of the recent techniques used.
Key words
RNA NGS IP CLIPReferences
- 1.Hohenstein P, Hastie ND (2006) The many facets of the Wilms’ tumour gene, WT1. Hum Mol Genet 15(Spec No 2):R196–R201CrossRefPubMedGoogle Scholar
- 2.Ladomery M, Sommerville J, Woolner S et al (2003) Expression in Xenopus oocytes shows that WT1 binds transcripts in vivo, with a central role for zinc finger one. J Cell Sci 116(Pt 8):1539–1549CrossRefPubMedGoogle Scholar
- 3.Niksic M, Slight J, Sanford JR et al (2004) The Wilms’ tumour protein (WT1) shuttles between nucleus and cytoplasm and is present in functional polysomes. Hum Mol Genet 13(4):463–471CrossRefPubMedGoogle Scholar
- 4.Zhai G, Iskandar M, Barilla K et al (2001) Characterization of RNA aptamer binding by the Wilms’ tumor suppressor protein WT1. Biochemistry 40(7):2032–2040CrossRefPubMedGoogle Scholar
- 5.Morrison AA, Venables JP, Dellaire G et al (2006) The Wilms’ tumour suppressor protein WT1 (+KTS isoform) binds alpha-actinin 1 mRNA via its zinc-finger domain. Biochem Cell Biol 84(5):789–798Google Scholar
- 6.König J, Zarnack K, Luscombe NM et al (2012) Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13(2):77–83CrossRefPubMedGoogle Scholar
- 7.Helwak A, Tollervey D (2014) Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nat Protoc 9(3):711–728CrossRefPubMedPubMedCentralGoogle Scholar