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Immunoprecipitation

Immunoprecipitation

Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...

Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

Protein-Protein Interfaces

Protein-Protein Interfaces

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Related Experiment Video

Updated: Aug 11, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Temporal-iCLIP captures co-transcriptional RNA-protein interactions.

Ross A Cordiner^1,2, Yuhui Dou^1,3, Rune Thomsen¹

¹Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000, Aarhus, Denmark.

Nature Communications

|February 8, 2023

Summary

This study reveals dynamic RNA-protein interactions during transcription using temporal iCLIP (tiCLIP). Key factors bind nascent RNA as it exits RNA polymerase II (RNAPII), with splicing and processing influencing binding times.

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Last Updated: Aug 11, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

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Published on: May 9, 2020

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification

Published on: May 18, 2020

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

RNA-protein interactions are crucial for co-transcriptional RNA processing and packaging.
Current understanding relies heavily on static, steady-state analyses, limiting insights into dynamic in vivo processes.

Purpose of the Study:

To investigate the temporal dynamics of RNA-protein interactions during nascent RNA processing in vivo.
To characterize the binding kinetics of specific RNA-binding proteins (ALYREF, RBM7, CBC) to transcripts exiting RNA polymerase II.

Main Methods:

Developed and applied temporal iCLIP (tiCLIP) by synchronizing RNA polymerase II transcription and collecting complexes at serial timepoints.
Utilized tiCLIP to profile interactions of ALYREF, RBM7, and CBC with nascent RNA.

Main Results:

All tested factors (ALYREF, RBM7, CBC) interact with nascent RNA as it emerges from RNA polymerase II.
Pre-mRNA splicing steps temporally segregate ALYREF and RBM7 binding to intermediates.
Exon-exon junction density influences ALYREF's 5' end binding.
Identified novel roles for RBM7 in snoRNA 3' end processing.

Conclusions:

The study provides a dynamic, temporal map of RNA-protein interactions during early transcription.
Splicing and RNA structure significantly regulate the timing and location of RNA-binding protein recruitment.