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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.

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Allen Institute for Brain Science, Seattle, United States.


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.


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

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