title: Methods to Identify and Validate WT1-RNA Interaction.
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.
authors.affiliation: Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. uthrothaselvi.bharathavikru@igmm.ed.ac.uk.
authors.forename: Ruthrothaselvi
authors.initials: R
authors.lastname: Bharathavikru
authors.affiliation: Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, EH9 3JR, UK.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Dudnakova
mesh_terms: D000818:Animals; D002460:Cell Line; D003432:Cross-Linking Reagents; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism*; D052156:SELEX Aptamer Technique / Q000379:methods*; D017423:Sequence Analysis, RNA; D025721:WT1 Proteins; D016335:Zinc Fingers
chemical_list: D003432:Cross-Linking Reagents; D012097:Repressor Proteins; D025721:WT1 Proteins; C000602896:WT1 protein, mouse; D012313:RNA
keywords: CLIP; IP; NGS; RNA