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

Elife. 2017 Jan 23:6:e21883. doi: 10.7554/eLife.21883.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromatin / metabolism*
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Mice
  • Neurons / physiology*
  • Protein Binding
  • Transposases / metabolism
  • Visual Cortex / physiology*


  • Chromatin
  • Transposases