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Updated: May 7, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

RIPiT-Seq: a high-throughput approach for footprinting RNA:protein complexes.

Guramrit Singh¹, Emiliano P Ricci¹, Melissa J Moore¹

¹Howard Hughes Medical Institute, RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.

Methods (San Diego, Calif.)

|October 8, 2013

Summary

This summary is machine-generated.

We developed RIPiT-Seq, a new method to map RNA binding sites for RNA binding proteins (RBPs) and ribonucleoprotein (RNP) complexes. This technique enhances understanding of gene regulation by identifying RBP occupancy across the transcriptome.

Keywords:

Formaldehyde crosslinking High-throughput sequencing Immunoprecipitation RIP-Seq RIPiT RNA binding proteins

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Related Experiment Videos

Last Updated: May 7, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

High-throughput methods are crucial for mapping RNA-protein interactions.
Understanding post-transcriptional gene regulation by RNA binding proteins (RBPs) is essential.
Existing methods have limitations in identifying all RBPs and differentiating complex RNP compositions.

Purpose of the Study:

To develop a novel high-throughput approach for mapping RNA interaction sites of individual RBPs and RNP complexes.
To provide a method applicable to all RBPs, including those with low UV crosslinkability.
To enable differentiation of binding sites for RNPs with overlapping protein components.

Main Methods:

Development of a ribonucleoprotein (RNP) footprinting approach.
Utilizing RNA:protein immunoprecipitation in tandem (RIPiT) for specific RNP isolation.
High-throughput sequencing (Seq) to identify RNA footprints generated by RIPiT.

Main Results:

RIPiT-Seq provides highly specific RNA footprints of cellular RNPs.
The method is broadly applicable to diverse RBPs and RNP complexes.
RIPiT-Seq can distinguish binding sites of RNPs with shared protein constituents.

Conclusions:

RIPiT-Seq is a versatile tool for mapping RBP and RNP binding sites transcriptome-wide.
The approach overcomes limitations of previous methods, particularly for RBPs with poor UV crosslinkability.
This technique is ideal for studying dynamic RNP complexes during gene expression.