Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

  1. Lucas T Gray
  2. Zizhen Yao
  3. Thuc Nghi Nguyen
  4. Tae Kyung Kim
  5. Hongkui Zeng
  6. Bosiljka Tasic  Is a corresponding author
  1. Allen Institute for Brain Science, United States

Abstract

Mammalian cortex is a laminar structure, with each layer composed of a characteristic set of cell types with different morphological, electrophysiological, and connectional properties. Here, we define chromatin accessibility landscapes of major, layer-specific excitatory classes of neurons, and compare them to each other and to inhibitory cortical neurons using the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We identify a large number of layer-specific accessible sites, and significant association with genes that are expressed in specific cortical layers. Integration of these data with layer-specific transcriptomic profiles and transcription factor binding motifs enabled us to construct a regulatory network revealing potential key layer-specific regulators, including Cux1/2, Foxp2, Nfia, Pou3f2, and Rorb. This dataset is a valuable resource for identifying candidate layer-specific cis-regulatory elements in adult mouse cortex.

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The following previously published data sets were used

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Author details

  1. Lucas T Gray

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8814-6818
  2. Zizhen Yao

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Thuc Nghi Nguyen

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Tae Kyung Kim

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Hongkui Zeng

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0326-5878
  6. Bosiljka Tasic

    Allen Institute for Brain Science, Seattle, United States
    For correspondence
    bosiljkat@alleninstitute.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6861-4506

Funding

National Institute on Drug Abuse (1R01DA036909-01)

  • Lucas T Gray
  • Hongkui Zeng
  • Bosiljka Tasic

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mice were housed at the Allen Institute for Brain Science under Institutional Care and Use Committee protocols 0703, 1208, and 1508. No more than 5 animals per cage were maintained on a regular 12-h day/night cycle, with water and food provided ad libitum. All animal sacrifices were performed after careful isofluorane treatment to minimize suffering.

Copyright

© 2017, Gray 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. Lucas T Gray
  2. Zizhen Yao
  3. Thuc Nghi Nguyen
  4. Tae Kyung Kim
  5. Hongkui Zeng
  6. Bosiljka Tasic
(2017)
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
eLife 6:e21883.
https://doi.org/10.7554/eLife.21883

Share this article

https://doi.org/10.7554/eLife.21883

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