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| Status |
Public on Oct 03, 2020 |
| Title |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution [ChIP-Seq] |
| Organisms |
Macaca mulatta; Pan troglodytes |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex re- main largely unexplored. Here we report epigenomic and tran- scriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome- wide profiling of the H3K27ac histone modification, we identify neuron-subtype–specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regula- tory changes are uncovered in multiple genes, including those as- sociated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a sub- stantial fraction of pan-neuronal regulatory elements undergos subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell- type–dependent gene-expression programs, and provides a re- source for further exploration of human brain evolution and function.
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| Overall design |
ChIP-seq Histone 3 Lysine 27 acetylation (H3K27ac) profiling was performed on sorted nuclei of glutamatergic and MGE-derived GABAergic neurons, obtained from prefrontal cortex of chimpanzees, rhesus macaques and humans.
Raw data (fastq) for human samples were taken from: Kozlenkov et al, 2018, Science Advances, 4(9):eaau6190
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| |
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| Contributor(s) |
Dracheva S, Kozlenkov A |
| Citation(s) |
33109720 |
| |
| Submission date |
Oct 02, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Stella Dracheva |
| E-mail(s) |
[email protected]
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Dept. of Psychiatry
|
| Street address |
James J. Peters VA Medical Center,130 W Kingsbridge Rd
|
| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10468 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL19129 |
Illumina HiSeq 2500 (Macaca mulatta) |
| GPL19148 |
Illumina HiSeq 2500 (Pan troglodytes) |
|
| Samples (32)
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| This SubSeries is part of SuperSeries: |
| GSE158934 |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution |
|
| Relations |
| BioProject |
PRJNA667055 |
| SRA |
SRP286185 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE158931_Glu_vs_MGE-GABA_differentially_acetylated_peaks_in_3_species.xlsx |
49.7 Mb |
(ftp)(http) |
XLSX |
| GSE158931_Hu276_GLU_S2.bw |
334.6 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu276_SOX_S2.bw |
298.8 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu344_GLU_S4.bw |
242.7 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu344_SOX_S4.bw |
273.3 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu372_GLU_S2.bw |
306.0 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu372_SOX_S2.bw |
268.6 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu444_GLU_S3.bw |
276.7 Mb |
(ftp)(http) |
BW |
| GSE158931_Hu444_SOX_S3.bw |
307.5 Mb |
(ftp)(http) |
BW |
| GSE158931_Interspecies_differentially_acetylated_peaks_in_Glu_or_MGE-GABA.xlsx |
25.9 Mb |
(ftp)(http) |
XLSX |
| GSE158931_Lists_of_peaks_detected_in_each_species_and_celltype.xlsx |
15.0 Mb |
(ftp)(http) |
XLSX |
| GSE158931_RAW.tar |
5.1 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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