Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
| Autor: | Tae Kyung Kim, Zizhen Yao, Lucas T. Gray, Thuc Nghi Nguyen, Hongkui Zeng, Bosiljka Tasic |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Cell type Mouse QH301-705.5 Science Transposases Computational biology Biology General Biochemistry Genetics and Molecular Biology Mice 03 medical and health sciences 0302 clinical medicine medicine Animals Gene Regulatory Networks visual cortex Biology (General) Gene Transcription factor ChIA-PET Neurons Genetics General Immunology and Microbiology Gene Expression Profiling General Neuroscience High-Throughput Nucleotide Sequencing FOXP2 General Medicine ATAC-seq Chromatin Tools and Resources 030104 developmental biology Visual cortex medicine.anatomical_structure Genomics and Evolutionary Biology NFIA chromatin accessibility Medicine transcription 030217 neurology & neurosurgery Protein Binding Neuroscience |
| Zdroj: | eLife, Vol 6 (2017) eLife |
| Popis: | 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. DOI: http://dx.doi.org/10.7554/eLife.21883.001 |
| Databáze: | OpenAIRE |
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