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| Status |
Public on Feb 26, 2022 |
| Title |
Gain of gene regulatory network interconnectivity at the origin of vertebrates [ATAC-seq] |
| Organisms |
Branchiostoma lanceolatum; Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. Here we show that gain of interconnectivity between signaling pathways, and the GRNs they control, may have played a critical contribution to the origin of vertebrates. We perturbed the retinoic acid, Wnt, FGF and Nodal signaling pathways during gastrulation in amphioxus and zebrafish and comparatively examined its effects in gene expression and cis-regulatory elements (CREs). We found that multiple developmental genes gain response to these pathways through novel CREs in the vertebrate lineage. Moreover, in contrast to amphioxus, many of these CREs are highly interconnected and respond to multiple pathways in zebrafish. Furthermore, we found that vertebrate-specific cell types are more enriched in highly interconnected genes than those tissues with more ancestral origin. Thus, the increase of CREs in vertebrates integrating inputs from different signaling pathways probably contributed to gene expression complexity and the formation of new cell types and morphological novelties in this lineage.
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| Overall design |
ATAC-seq experiments in zebrafish and amphioxus embryos after modifying different signaling pathways
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| Contributor(s) |
Gil-Gálvez A, Jiménez-Gancedo S, Acemel RD, Bertrand S, Schubert M, Escrivá H, Tena JJ, Gómez-Skarmeta JL |
| Citation(s) |
35263228 |
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| Submission date |
Apr 16, 2020 |
| Last update date |
May 29, 2022 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
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| Organization name |
CABD/CSIC
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| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
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| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platforms (2) |
| GPL21741 |
Illumina HiSeq 4000 (Danio rerio) |
| GPL24210 |
Illumina HiSeq 4000 (Branchiostoma lanceolatum) |
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| Samples (24)
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| GSM4478806 |
ATAC-seq in amphioxus, control sample, replicate 1 |
| GSM4478807 |
ATAC-seq in amphioxus, control sample, replicate 2 |
| GSM4478808 |
ATAC-seq in amphioxus, control sample, replicate 3 |
| GSM4478809 |
ATAC-seq in amphioxus, control sample, replicate 4 |
| GSM4478810 |
ATAC-seq in amphioxus, FGF treatment, replicate 1 |
| GSM4478811 |
ATAC-seq in amphioxus, FGF treatment, replicate 2 |
| GSM4478812 |
ATAC-seq in amphioxus, FGF treatment, replicate 3 |
| GSM4478813 |
ATAC-seq in amphioxus, FGF treatment, replicate 4 |
| GSM4478814 |
ATAC-seq in amphioxus, Nodal treatment, replicate 1 |
| GSM4478815 |
ATAC-seq in amphioxus, Nodal treatment, replicate 2 |
| GSM4478816 |
ATAC-seq in amphioxus, RA treatment, replicate 1 |
| GSM4478817 |
ATAC-seq in amphioxus, RA treatment, replicate 2 |
| GSM4478818 |
ATAC-seq in amphioxus, Wnt treatment, replicate 1 |
| GSM4478819 |
ATAC-seq in amphioxus, Wnt treatment, replicate 2 |
| GSM4478820 |
ATAC-seq in zebrafish, control sample, replicate 1 |
| GSM4478821 |
ATAC-seq in zebrafish, control sample, replicate 2 |
| GSM4478822 |
ATAC-seq in zebrafish, FGF treatment, replicate 1 |
| GSM4478823 |
ATAC-seq in zebrafish, FGF treatment, replicate 2 |
| GSM4478824 |
ATAC-seq in zebrafish, Nodal treatment, replicate 1 |
| GSM4478825 |
ATAC-seq in zebrafish, Nodal treatment, replicate 2 |
| GSM4478826 |
ATAC-seq in zebrafish, RA treatment, replicate 1 |
| GSM4478827 |
ATAC-seq in zebrafish, RA treatment, replicate 2 |
| GSM4478828 |
ATAC-seq in zebrafish, Wnt treatment, replicate 1 |
| GSM4478829 |
ATAC-seq in zebrafish, Wnt treatment, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE148783 |
Gain of gene regulatory network interconnectivity at the origin of vertebrates |
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| Relations |
| BioProject |
PRJNA625714 |
| SRA |
SRP256586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148781_Amphi_ATAC_Control_IDR_peaks.bed.gz |
775.4 Kb |
(ftp)(http) |
BED |
| GSE148781_Amphi_ATAC_FGF_IDR_peaks.bed.gz |
986.6 Kb |
(ftp)(http) |
BED |
| GSE148781_Amphi_ATAC_Nodal_IDR_peaks.bed.gz |
833.6 Kb |
(ftp)(http) |
BED |
| GSE148781_Amphi_ATAC_RA_IDR_peaks.bed.gz |
731.5 Kb |
(ftp)(http) |
BED |
| GSE148781_Amphi_ATAC_Wnt_IDR_peaks.bed.gz |
559.7 Kb |
(ftp)(http) |
BED |
| GSE148781_Danrer_ATAC_Control_IDR_peaks.bed.gz |
4.1 Mb |
(ftp)(http) |
BED |
| GSE148781_Danrer_ATAC_FGF_IDR_peaks.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
| GSE148781_Danrer_ATAC_Nodal_IDR_peaks.bed.gz |
3.4 Mb |
(ftp)(http) |
BED |
| GSE148781_Danrer_ATAC_RA_IDR_peaks.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
| GSE148781_Danrer_ATAC_Wnt_IDR_peaks.bed.gz |
3.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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