Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

Abstract
Data availability
Article and author information
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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

The following data sets were generated

1. Bell JC
2. Jukam D
3. Teran NA
4. Risca VI
5. Smith OK
6. Johnson WL
7. Skotheim J
8. Greenleaf WJ
9. Straight AF
(2017) Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE97131).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=urwviaqydzojjux&acc=GSE97131

The following previously published data sets were used

1. Quinn JJ
2. Qu K
3. Chang HY
(2014) Domain ChIRP reveals the modularity of long noncoding RNA architecture, function, and target genes
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE53020).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53020
1. Ramírez F
2. Lingg T
3. Toscano S
4. Lam KC
5. Plamen G
6. Ho-Ryung C
7. Lajoie B
8. de Wit E
9. Zhang Y
10. de Laat W
11. Dekker J
12. Manke T
13. Akhtar A
(2015) High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE58821).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58821
1. Li X
2. Zhou B
3. Chen L
4. Gou L
5. Li H
6. Fu X
(2017) GRID-seq reveals the global RNA-chromatin interactome
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE82312).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82312

Article and author information

Author details

Jason C Bell

Department of Biochemistry, Stanford University, Stanford, United States

For correspondence
jcbell@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5480-7975
David Jukam

Department of Biology, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4167-2754
Nicole A Teran

Department of Biochemistry, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9625-5010
Viviana I Risca

Department of Genetics, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Owen K Smith

Department of Biochemistry, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0880-2801
Whitney L Johnson

Department of Biochemistry, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Jan M Skotheim

Department of Biology, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
William James Greenleaf

Department of Genetics, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Aaron F Straight

Department of Biochemistry, Stanford University, Stanford, United States

For correspondence
astraigh@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5885-7881

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

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.