|
| Status |
Public on Mar 06, 2015 |
| Title |
Evolutionary changes in promoter and enhancer activity during human corticogenesis (human) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex in humans. However, the lack of a regulatory map of the human embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in human, rhesus, and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in human based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing human cortex. We identified multiple modules enriched in human lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into human cortical evolution.
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| Overall design |
For Human and Mouse samples, two biological replicates from four cortical tissue stages, each stage with separate H3K27ac and H3K4me2 ChIPs as well as an input control. Identical ChIPs for two replicates at two stages in Rhesus cortex, and one rhesus stage without replication.
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| |
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| Contributor(s) |
Reilly SK, Noonan JP |
| Citation(s) |
25745175 |
| Submission date |
Nov 25, 2014 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Steven K Reilly |
| E-mail(s) |
steven.reilly@yale.edu
|
| Organization name |
Yale University
|
| Department |
Genetics
|
| Lab |
Noonan
|
| Street address |
333 Cedar St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (24)
|
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| This SubSeries is part of SuperSeries: |
| GSE63649 |
Evolutionary changes in promoter and enhancer activity during human corticogenesis |
|
| Relations |
| BioProject |
PRJNA268529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE63648_12Fpcw_ac_Hu_gain.bed.gz |
9.5 Kb |
(ftp)(http) |
BED |
| GSE63648_12Fpcw_me2_Hu_gain.bed.gz |
21.2 Kb |
(ftp)(http) |
BED |
| GSE63648_12Opcw_ac_Hu_gain.bed.gz |
13.2 Kb |
(ftp)(http) |
BED |
| GSE63648_12Opcw_me2_Hu_gain.bed.gz |
34.0 Kb |
(ftp)(http) |
BED |
| GSE63648_7pcw_ac_Hu_gain.bed.gz |
24.3 Kb |
(ftp)(http) |
BED |
| GSE63648_7pcw_me2_Hu_gain.bed.gz |
50.0 Kb |
(ftp)(http) |
BED |
| GSE63648_8_5pcw_ac_Hu_gain.bed.gz |
18.3 Kb |
(ftp)(http) |
BED |
| GSE63648_8_5pcw_me2_Hu_gain.bed.gz |
32.8 Kb |
(ftp)(http) |
BED |
| GSE63648_RAW.tar |
43.9 Gb |
(http)(custom) |
TAR (of BED, BW) |
| GSE63648_ReadMe_Bed_files_contents.txt |
260 b |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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