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Related Experiment Video

Updated: Mar 24, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Resources for the Comprehensive Discovery of Functional RNA Elements.

Balaji Sundararaman1, Lijun Zhan2, Steven M Blue1

  • 1Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.

Molecular Cell
|March 19, 2016
PubMed
Summary

Researchers created a validated antibody repository for 365 RNA binding proteins (RBPs) to map RBP-RNA interactions. This resource aids studies in cancer, neurobiology, and development, overcoming a key bottleneck in RBP research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA binding proteins (RBPs) are crucial for gene regulation.
  • Mapping RBP-RNA interactions requires high-quality antibodies, which are often lacking.
  • Existing methods like RNA IP (RIP) and CLIP are limited by antibody availability.

Purpose of the Study:

  • To develop a comprehensive repository of validated antibodies for human RBPs.
  • To facilitate transcriptome-wide mapping of RBP-RNA interactions.
  • To support research in RBP functions across various biological contexts.

Main Methods:

  • Immunoprecipitation (IP) followed by immunoblot assays were used to validate antibodies.
  • A repository of 438 antibodies targeting 365 unique RBPs was created.
  • Specificity of antibodies was confirmed using 362 short-hairpin RNA (shRNA) constructs.

Main Results:

  • A validated collection of 438 antibodies for 365 RBPs was established.
  • Antibodies were confirmed for IP-quality and can determine subcellular RBP localization.
  • The resource includes 362 shRNA constructs for RBP specificity confirmation.

Conclusions:

  • The validated antibody repository addresses a critical need in RBP research.
  • This resource enables robust studies of RBP-RNA interactions and functions.
  • Public availability via the ENCODE portal maximizes scientific community access and utility.