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Updated: May 15, 2026
09:36
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
Capture hybridization analysis of RNA targets (CHART)
1Department of Molecular Biophysics and Biochemistry and Chemical Biology Institute, Yale University, West Haven, Connecticut, USA.
Current Protocols in Molecular Biology
|January 5, 2013
Summary
Large non-coding RNAs regulate chromatin at distant sites. This study presents a method to identify these RNA targets using enriched chromatin and deep sequencing for genome-wide analysis.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- The genome's regulation involves trans-acting factors binding to specific chromatin loci.
- Large non-coding RNAs (ncRNAs) are increasingly recognized for their role in chromatin regulation, acting at sites distant from their transcription.
- Understanding the genomic targets of these ncRNAs is crucial for deciphering their regulatory mechanisms.
Purpose of the Study:
- To describe a method for identifying the genomic targets of large non-coding RNAs.
- To provide a practical approach for investigating the interactions between ncRNAs and chromatin.
Main Methods:
- Enrichment of endogenous large non-coding RNA from cross-linked chromatin extracts using biotinylated complementary oligodeoxyribonucleotides.
- Identification of RNA targets by analyzing co-enriched proteins and DNA.
- Genome-wide target determination through deep sequencing of the enriched DNA.
Main Results:
- The described method successfully enriches specific large non-coding RNAs from chromatin extracts.
- Analysis of enriched fractions reveals associated proteins and DNA, indicating direct or indirect interactions.
- Deep sequencing enables comprehensive, genome-wide mapping of ncRNA targets.
Conclusions:
- This unit provides a robust methodology for identifying genomic targets of large non-coding RNAs.
- The approach facilitates the study of ncRNA-mediated epigenetic regulation.
- The method is adaptable for various ncRNAs and can be extended for genome-wide analyses.
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