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
The following previously published data sets were used
    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).

Article and author information

Author details

  1. 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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5480-7975
  2. David Jukam

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4167-2754
  3. Nicole A Teran

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9625-5010
  4. Viviana I Risca

    Department of Genetics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Owen K Smith

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0880-2801
  6. Whitney L Johnson

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Jan M Skotheim

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. William James Greenleaf

    Department of Genetics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. 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.
    ORCID icon "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

  1. Job Dekker, University of Massachusetts Medical School, United States

Version history

  1. Received: March 21, 2017
  2. Accepted: April 11, 2018
  3. Accepted Manuscript published: April 12, 2018 (version 1)
  4. 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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  1. Jason C Bell
  2. David Jukam
  3. Nicole A Teran
  4. Viviana I Risca
  5. Owen K Smith
  6. Whitney L Johnson
  7. Jan M Skotheim
  8. William James Greenleaf
  9. Aaron F Straight
(2018)
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
eLife 7:e27024.
https://doi.org/10.7554/eLife.27024

Share this article

https://doi.org/10.7554/eLife.27024

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