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Updated: May 26, 2026
11:34
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
Published on: August 9, 2019
The genomic binding sites of a noncoding RNA
Matthew D Simon1, Charlotte I Wang, Peter V Kharchenko
1Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
Summary
Researchers developed Capture Hybridization Analysis of RNA Targets (CHART) to map where long noncoding RNAs (lncRNAs) bind to chromatin. This method revealed specific genomic targets for the roX2 lncRNA in Drosophila, aiding dosage compensation studies.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Long noncoding RNAs (lncRNAs) play crucial regulatory roles in biological processes.
- lncRNAs can interact with chromatin, influencing gene expression.
- Understanding lncRNA-chromatin interactions is essential for deciphering gene regulation.
Purpose of the Study:
- To develop a novel technique for identifying the genomic targets of endogenous long noncoding RNAs.
- To investigate the chromatin-binding sites of lncRNAs in both flies and humans.
- To map the genome-wide binding locations of the roX2 lncRNA in Drosophila melanogaster.
Main Methods:
- Development of Capture Hybridization Analysis of RNA Targets (CHART), a hybridization-based method.
- Enrichment of endogenous lncRNAs and their DNA and protein targets from cross-linked chromatin.
- Application of CHART for genome-wide mapping of the roX2 lncRNA in Drosophila.
Main Results:
- CHART successfully enriched lncRNA targets from chromatin extracts.
- Genome-wide mapping of roX2 in Drosophila revealed specific binding sites.
- roX2 binding sites coincided with the locations of dosage compensation complex proteins.
Conclusions:
- CHART is an effective method for studying lncRNA-chromatin interactions.
- The study identified genomic targets of roX2, providing insights into Drosophila dosage compensation.
- CHART offers a powerful tool for investigating RNA targets analogous to ChIP for proteins.
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