|
| Status |
Public on Dec 22, 2023 |
| Title |
Human gene regulatory evolution is driven by divergence in cis and trans |
| Organisms |
Macaca mulatta; Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Gene regulation can evolve either by cis-acting local changes to regulatory element DNA sequences or by global changes to the trans-acting regulatory environment; however, the modes favored during recent human evolution are unknown. To date, studies investigating gene regulatory divergence between closely-related species have produced limited estimates on the relative contributions of cis and trans effects on DNA regulatory element activities at a global-scale. By leveraging a comparative ATAC-STARR-seq framework, we identified 10,779 regulatory regions with divergent activity in cis and 10,608 regulatory regions with divergent activity in trans between human and rhesus macaque lymphoblastoid cell lines (LCLs). This revealed substantially more trans effects than predicted and indicates trans-regulatory mechanisms play a larger role in human evolution than previously expected. We also discover that most species-specific regulatory elements (67%) diverge in both cis and trans, suggesting these two mechanisms jointly drive divergent regulatory activity in a single sequence.
|
| |
|
| Overall design |
Comparative ATAC-STARR-seq and RNA-seq of human (GM12878) and macaque (LCL8664) lymphoblastoid cell lines
|
| |
|
| Contributor(s) |
Hansen TJ, Fong S, Capra JA, Hodges E |
| Citation(s) |
38604126 |
| |
| Submission date |
Oct 31, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Tyler J Hansen |
| E-mail(s) |
tyler.j.hansen@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Biochemistry
|
| Street address |
2215 Garland Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL27943 |
Illumina NovaSeq 6000 (Macaca mulatta) |
| GPL32794 |
Illumina NovaSeq 6000 (Homo sapiens; Macaca mulatta) |
|
| Samples (22)
|
|
| Relations |
| BioProject |
PRJNA896179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE216917_GM12878+LCL8664_DESeq2-normalized_counts.tsv.gz |
633.2 Kb |
(ftp)(http) |
TSV |
| GSE216917_GM12878+LCL8664_TPM-normalized_counts.tsv.gz |
791.6 Kb |
(ftp)(http) |
TSV |
| GSE216917_HH_active.regions.bed.gz |
78.2 Kb |
(ftp)(http) |
BED |
| GSE216917_HH_merged-reps_RNA-to-DNA_log2.bw |
224.1 Mb |
(ftp)(http) |
BW |
| GSE216917_HM_active.regions.bed.gz |
77.6 Kb |
(ftp)(http) |
BED |
| GSE216917_HM_merged-reps_RNA-to-DNA_log2.bw |
251.1 Mb |
(ftp)(http) |
BW |
| GSE216917_MH_active.regions.bed.gz |
78.8 Kb |
(ftp)(http) |
BED |
| GSE216917_MH_merged-reps_RNA-to-DNA_log2.crossmap.bw |
183.5 Mb |
(ftp)(http) |
BW |
| GSE216917_MM_active.regions.bed.gz |
76.8 Kb |
(ftp)(http) |
BED |
| GSE216917_MM_merged-reps_RNA-to-DNA_log2.crossmap.bw |
201.5 Mb |
(ftp)(http) |
BW |
| GSE216917_conserved_active.regions.bed.gz |
25.5 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific.regions.bed.gz |
55.4 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific_cis+trans.bed.gz |
37.9 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific_cis-only.bed.gz |
9.7 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific_cis.bed.gz |
46.5 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific_trans-only.bed.gz |
7.1 Kb |
(ftp)(http) |
BED |
| GSE216917_human-specific_trans.bed.gz |
44.2 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific.regions.bed.gz |
54.8 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific_cis+trans.bed.gz |
32.8 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific_cis-only.bed.gz |
9.0 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific_cis.bed.gz |
40.6 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific_trans-only.bed.gz |
10.2 Kb |
(ftp)(http) |
BED |
| GSE216917_macaque-specific_trans.bed.gz |
41.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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