Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

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.
Types of ChIP
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...
Immunoprecipitation01:20

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Epigenetic landscape, key transcriptional regulators, and in vivo identification of human Tr1 cells.

Science advances·2026
Same author

XIST RNA-protein complex in female-biased autoimmunity: From molecular scaffolds to new clinical biomarkers.

The Journal of investigative dermatology·2026
Same author

Somatic mutations reveal the ontogeny of human microglia.

bioRxiv : the preprint server for biology·2026
Same author

Correction: Annotation of nuclear lncRNAs based on chromatin interactions.

PloS one·2026
Same author

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.

bioRxiv : the preprint server for biology·2026
Same author

A recipe for chaos: Extrachromosomal DNA and the hallmarks of cancer.

Cell·2026

Related Experiment Video

Updated: May 23, 2026

Chromatin Isolation by RNA Purification (ChIRP)
11:09

Chromatin Isolation by RNA Purification (ChIRP)

Published on: March 25, 2012

Chromatin isolation by RNA purification (ChIRP).

Ci Chu1, Jeffrey Quinn, Howard Y Chang

  • 1Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine.

Journal of Visualized Experiments : Jove
|April 5, 2012
PubMed
Summary

Long noncoding RNAs (lncRNAs) regulate gene expression by interacting with chromatin. A new method, Chromatin Isolation by RNA Purification (ChIRP), maps lncRNA binding sites genome-wide at high resolution.

More Related Videos

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
13:34

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP
09:26

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

Published on: January 20, 2016

Related Experiment Videos

Last Updated: May 23, 2026

Chromatin Isolation by RNA Purification (ChIRP)
11:09

Chromatin Isolation by RNA Purification (ChIRP)

Published on: March 25, 2012

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
13:34

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP
09:26

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

Published on: January 20, 2016

Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Long noncoding RNAs (lncRNAs) are crucial regulators of chromatin states, influencing gene expression, dosage compensation, and imprinting.
  • lncRNAs associate with chromatin modification complexes like PRC2, suggesting gene-specific roles in chromatin management.
  • Previous methods for mapping lncRNA occupancy were limited to single gene loci, hindering genome-wide understanding.

Purpose of the Study:

  • To introduce and validate a high-resolution, genome-wide method for mapping long noncoding RNA occupancy at chromatin.
  • To overcome limitations of previous techniques that only analyzed lncRNA interactions at individual gene sites.

Main Methods:

  • Chromatin Isolation by RNA Purification (ChIRP) utilizes tiling antisense oligos to affinity capture lncRNA:chromatin complexes.
  • This method enables the generation of genomic binding site maps for lncRNAs.
  • ChIRP provides high sensitivity and low background, with a resolution of several hundred bases.

Main Results:

  • ChIRP successfully maps lncRNA genomic binding sites genome-wide at high resolution.
  • The method demonstrates high sensitivity and low background noise.
  • ChIRP is broadly applicable to various lncRNAs, requiring only their sequence for probe design.

Conclusions:

  • Chromatin Isolation by RNA Purification (ChIRP) is an effective strategy for mapping lncRNA occupancy genome-wide.
  • This technique significantly advances the understanding of lncRNA roles in chromatin regulation.
  • ChIRP offers a sensitive and high-resolution approach applicable to numerous lncRNAs.