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Methods to Identify and Validate WT1-RNA Interaction.

Ruthrothaselvi Bharathavikru1, Tatiana Dudnakova2

  • 1Medical 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.

Methods in Molecular Biology (Clifton, N.J.)
|July 16, 2016
PubMed
Summary

The Wilms Tumor 1 (Wt1) protein binds to both DNA and RNA. New techniques allow researchers to study Wt1

Keywords:
CLIPIPNGSRNA

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • The Wilms Tumor 1 (Wt1) protein is a transcription factor with DNA-binding capabilities, similar to Early Growth Response gene 1 (EGR1).
  • Biophysical and biochemical studies indicate Wt1's zinc fingers can bind to both DNA and RNA, with affinity potentially varying by isoform and nucleic acid type.

Purpose of the Study:

  • To explore the in vivo RNA binding interactome of the Wt1 protein.
  • To address limitations of previous SELEX-based RNA motif identification for Wt1.
  • To introduce recent technological advancements for studying Wt1's RNA interactions.

Main Methods:

  • Utilizing recent cross-linking techniques to capture RNA-protein interactions in vivo.
  • Employing high-throughput sequencing for comprehensive analysis of the Wt1 RNA interactome.
  • Reviewing established biophysical and biochemical validation methods.

Main Results:

  • Previous SELEX methods identified RNA motifs for Wt1 that were not fully reproducible in vivo.
  • Emerging technologies enable the study of Wt1's in vivo RNA binding partners.

Conclusions:

  • Investigating the Wt1 RNA interactome is crucial for understanding its biological functions.
  • Advanced cross-linking and sequencing technologies are essential for accurate in vivo interactome analysis.
  • This work provides a foundation for further research into Wt1's role in gene regulation via RNA binding.