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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

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Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq.

Sabarinath Jayaseelan1, Francis Doyle1, Scott A Tenenbaum1

  • 1SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA.

Methods (San Diego, Calif.)
|November 22, 2013
PubMed
Summary
This summary is machine-generated.

This study details a method to map RNA-binding protein (RBP) and messenger RNA (mRNA) interactions. Understanding these RBP-mRNA networks is crucial for deciphering gene expression regulation.

Keywords:
Microarray expression profilingPost-TranscriptionRIP-ChipRIP-SeqRNA-binding proteins (RBPs)RibonomicsmRNA localization

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Area of Science:

  • Molecular Biology
  • Genomics
  • Gene Expression Regulation

Background:

  • Post-transcriptional regulation governs gene expression through messenger RNA (mRNA) modifications.
  • RNA-binding proteins (RBPs) are key regulators, influencing mRNA splicing, stability, localization, and translation.
  • Characterizing RBP-mRNA interactions is essential for mapping functional post-transcriptional regulatory networks.

Purpose of the Study:

  • To provide a detailed methodology for isolating mRNA associated with RBPs.
  • To enable the comprehensive mapping of RBP-mRNA interactions within the cell.
  • To facilitate a deeper understanding of post-transcriptional gene regulation.

Main Methods:

  • RNA-binding protein immunoprecipitation (RIP) is employed as a primary technique.
  • Immunoprecipitated RBP-mRNA complexes are analyzed using microarray (Chip) or next-generation sequencing (NGS).
  • Specific antibodies are utilized to capture target RBPs and their associated RNA molecules.

Main Results:

  • The study outlines a robust protocol for RBP-mRNA complex isolation and analysis.
  • The described methodology, RIP-Chip/Seq, is presented as a versatile genomic technique.
  • This approach allows for the study of endogenous RBP-RNA associations.

Conclusions:

  • The methodology enables the characterization of RBP-mRNA association networks.
  • This work contributes to a functional map of post-transcriptional regulatory systems.
  • RIP-Chip/Seq is a powerful tool for investigating RBP-mediated gene regulation.