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Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART)
1Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK. k.w.vance@bath.ac.uk.
Methods in Molecular Biology (Clifton, N.J.)
|September 25, 2016
Summary
Capture Hybridization Analysis of RNA Targets (CHART) maps where chromatin-associated RNAs bind across the genome. This method identifies long noncoding RNA (long ncRNA) interactions with chromatin and their direct transcriptional targets.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Chromatin-associated RNAs play crucial roles in gene regulation.
- Understanding the genome-wide binding profiles of these RNAs is essential for deciphering their functions.
- Existing methods have limitations in comprehensively mapping RNA-chromatin interactions.
Purpose of the Study:
- To introduce and validate the Capture Hybridization Analysis of RNA Targets (CHART) protocol.
- To enable genome-wide mapping of chromatin-associated RNAs.
- To identify direct transcriptional targets of long noncoding RNAs (long ncRNAs).
Main Methods:
- Utilizes biotinylated antisense oligonucleotides complementary to accessible RNA regions.
- Purifies RNA from cross-linked chromatin extracts.
- Immobilizes RNA-chromatin complexes on beads, followed by RNase H-mediated elution.
- Sequences associated genomic DNA using high-throughput sequencing.
Main Results:
- CHART successfully maps the genome-wide binding profile of chromatin-associated RNAs.
- The protocol allows for the identification of long ncRNA association with chromatin.
- Direct long ncRNA transcriptional targets can be identified using CHART.
Conclusions:
- CHART is a powerful new tool for studying RNA-chromatin interactions genome-wide.
- This method facilitates the investigation of long ncRNA functions in gene regulation.
- CHART provides insights into the direct transcriptional regulation by long ncRNAs.
