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Series GSE216917 Query DataSets for GSE216917
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 missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 31, 2022
Last update date Dec 22, 2023
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)
GSM6697722 GM12878-DNA_in_LCL8664-cells_DNA_Rep1
GSM6697723 GM12878-DNA_in_LCL8664-cells_DNA_Rep2
GSM6697724 GM12878-DNA_in_LCL8664-cells_DNA_Rep3
Relations
BioProject PRJNA896179

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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