title: Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.
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, includingCux1/2,Foxp2,Nfia,Pou3f2, andRorb. This dataset is a valuable resource for identifying candidate layer-specific cis-regulatory elements in adult mouse cortex.
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Lucas T
authors.identifier: 0000-0002-8814-6818
authors.initials: LT
authors.lastname: Gray
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Zizhen
authors.identifier: 0000-0002-1210-4195
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Thuc Nghi
authors.identifier: 0000-0002-6466-5883
authors.initials: TN
authors.lastname: Nguyen
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Tae Kyung
authors.identifier: 0000-0001-9646-5969
authors.initials: TK
authors.lastname: Kim
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Hongkui
authors.identifier: 0000-0002-0326-5878
authors.initials: H
authors.lastname: Zeng
authors.affiliation: Allen Institute for Brain Science, Seattle, United States.
authors.forename: Bosiljka
authors.identifier: 0000-0002-6861-4506
authors.initials: B
authors.lastname: Tasic
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D009474:Neurons / Q000502:physiology*; D011485:Protein Binding; D019895:Transposases / Q000378:metabolism; D014793:Visual Cortex / Q000502:physiology*
chemical_list: D002843:Chromatin; D019895:Transposases
keywords: ATAC-seq; chromatin accessibility; evolutionary biology; genomics; mouse; neuroscience; transcription; visual cortex