Format

Send to

Choose Destination
Elife. 2017 Jan 23;6. pii: e21883. doi: 10.7554/eLife.21883.

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

Author information

1
Allen Institute for Brain Science, Seattle, 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.

KEYWORDS:

ATAC-seq; chromatin accessibility; evolutionary biology; genomics; mouse; neuroscience; transcription; visual cortex

PMID:
28112643
PMCID:
PMC5325622
DOI:
10.7554/eLife.21883
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for eLife Sciences Publications, Ltd Icon for PubMed Central
Loading ...
Support Center