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Chromatin Isolation by RNA Purification ChIRP
Published on: March 25, 2012
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Mapping Chromatin Occupancy of Ppp1r1b-lncRNA Genome-Wide Using Chromatin Isolation by RNA Purification (ChIRP)-seq.
John Hwang1,2,3, Xuedong Kang1,2, Charlotte Wolf1,4
1Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
Cells
|December 22, 2023
Summary
Long non-coding RNA (lncRNA) Ppp1r1b-lncRNA regulates muscle cell differentiation by interacting with chromatin. This study maps its genome-wide binding sites, revealing roles in transcription initiation and enhancer activity.
Area of Science:
- Epigenetics
- Molecular Biology
- Genomics
Background:
- Long non-coding RNAs (lncRNAs) are key gene regulators in development and disease.
- Ppp1r1b-lncRNA is an epigenetic regulator of myogenic differentiation, interacting with PRC2 to control TBX5 and MyoD1 promoters.
Purpose of the Study:
- To map the genome-wide chromatin occupancy of Ppp1r1b-lncRNA.
- To understand its role in myogenic differentiation and transcriptional regulation.
Main Methods:
- Chromatin isolation by RNA purification (ChIRP) followed by high-throughput sequencing.
- Bioinformatic analysis to identify Ppp1r1b-lncRNA binding sites and associated genomic features.
Main Results:
- Identified 99,732 high-confidence Ppp1r1b-lncRNA binding sites genome-wide.
- 46% of sites mapped to gene elements, including 1180 promoters involved in myogenic transcription factors and heart development.
- Significant occupancy at intronic regions and enhancer sequences, with cell-type specific enrichment in fetal heart and muscles.
Conclusions:
- Ppp1r1b-lncRNA interacts with a vast network of chromatin elements, including promoters and enhancers.
- These interactions support its role in regulating myogenic transcription initiation and potentially other cellular processes.
- Provides a comprehensive map of the Ppp1r1b-lncRNA interactome.
