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Chromatin Immunoprecipitation- ChIP

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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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Related Experiment Video

Updated: Jul 4, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

Inputs and outputs for chromatin-targeted RNAi.

Simon W-L Chan¹

¹Department of Plant Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA. srchan@ucdavis.edu

Trends in Plant Science

|June 14, 2008

Summary

Plant gene silencing uses small RNAs to target repetitive DNA via RNA interference (RNAi). Research explores how double-stranded RNA (dsRNA) production is controlled and how RNAi affects chromatin, revealing new biological functions.

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Last Updated: Jul 4, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method

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Published on: April 30, 2026

Chromatin Isolation by RNA Purification (ChIRP)

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In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

Area of Science:

Molecular Biology
Genetics
Epigenetics

Background:

RNA interference (RNAi) pathways utilize small RNAs to target transposons and repetitive sequences in plants.
RNA-directed chromatin silencing, similar to classical RNAi, involves Dicer endonucleases cleaving double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that bind Argonaute proteins.

Purpose of the Study:

Investigate the mechanisms controlling double-stranded RNA (dsRNA) production to prevent inappropriate gene silencing.
Explore the poorly understood mechanisms of chromatin modification downstream of siRNA biogenesis.
Utilize genomic studies of siRNA target loci to uncover novel biological functions of chromatin-targeted RNAi.

Main Methods:

Analysis of RNA interference (RNAi) pathways in plants.
Investigating the role of Dicer endonucleases and Argonaute proteins in siRNA biogenesis.
Genomic studies focusing on small interfering RNA (siRNA) target loci and associated chromatin modifications.

Main Results:

Plant gene silencing is mediated by small RNAs through the RNA interference (RNAi) pathway, targeting transposons and repetitive sequences.
RNA-directed chromatin silencing involves Dicer-mediated cleavage of dsRNA into siRNAs, which associate with Argonaute proteins.
Plant RNA polymerase IV (Pol IV) initiates siRNA production at heterochromatin, with evidence for Pol IV-independent dsRNA synthesis.

Conclusions:

Control of double-stranded RNA (dsRNA) production is crucial for regulating gene silencing.
Argonaute-siRNA complexes are implicated in targeting various chromatin marks, though mechanisms require further elucidation.
Genomic investigation of siRNA target loci holds promise for discovering new roles of chromatin-targeted RNAi in plants.