Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
- Stanford University, United States
Abstract
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.
Data availability
All sequence data has been deposited in GEO under accession number GSE97131The software analysis pipeline is available at https://gitlab.com/charseq/flypipe
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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contactsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE97131).
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Domain ChIRP reveals the modularity of long noncoding RNA architecture, function, and target genesPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE53020).
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High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in DrosophilaPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE58821).
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GRID-seq reveals the global RNA-chromatin interactomePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE82312).
Article and author information
Author details
Funding
National Institutes of Health (Stanford Center for Systems Biology (NIH P50 GM107615) Seed Grant)
- Jason C Bell
- David Jukam
- Viviana I Risca
- Whitney L Johnson
Howard Hughes Medical Institute (HHMI-Simons Faculty Scholar Award)
- Jan M Skotheim
National Institutes of Health (P50HG00773501)
- William James Greenleaf
National Institutes of Health (R01GM106005)
- Aaron F Straight
Stanford University School of Medicine (Dean's Fellowship)
- Jason C Bell
National Institutes of Health (R01HG009909)
- William James Greenleaf
- Aaron F Straight
National Institutes of Health (R21HG007726)
- William James Greenleaf
National Institutes of Health (NIH Ruth Kirchstein National Research Service Award (F32GM116338))
- Jason C Bell
National Institutes of Health (NIH Ruth Kirchstein National Research Service Award (F32GM108295 ))
- David Jukam
Stanford University (Walter V. and Idun Berry Fellowship)
- Viviana I Risca
National Institutes of Health (Stanford Genetics Training Program (5T32HG000044-19))
- Nicole A Teran
National Institutes of Health (Molecular Pharmacology Training Grant (NIH T32-GM113854-02))
- Owen K Smith
National Institutes of Health (NIH T32 Training Fellowship (GM007276))
- Whitney L Johnson
National Science Foundation (DGE-114747)
- Whitney L Johnson
National Institutes of Health (RO1 HD085135)
- Jan M Skotheim
- Aaron F Straight
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Job Dekker, University of Massachusetts Medical School, United States
Version history
- Received: March 21, 2017
- Accepted: April 11, 2018
- Accepted Manuscript published: April 12, 2018 (version 1)
- Version of Record published: May 21, 2018 (version 2)
Copyright
© 2018, Bell et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
eLife 7:e27024.
https://doi.org/10.7554/eLife.27024
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