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| Status |
Public on Apr 17, 2024 |
| Title |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq] |
| Platform organism |
Mus musculus |
| Sample organisms |
Danio rerio; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. In tetrapods, posterior Hoxd genes transcription in digits is controlled by a well-characterized series of enhancers forming a large regulatory landscape, which has its syntenic counterpart in zebrafish. We show here that the deletion of the orthologous landscape in fishes does not affect the transcription of these genes in fin buds. Instead, it abrogates hoxd expression in the cloaca, an essential structure related to the mammalian uro-genital sinus. We also report that Hoxd gene function in the mammalian uro-genital sinus depends on enhancers located in the same regulatory landscape and thus conclude that an ancestral Hox ‘cloacal’ regulation was co-opted, in tetrapod, as a playground to subsequently accompany the evolution of both external genitals and digits regulatory landscapes, along with the emergence of these developmentally and phylogenetically related structures.
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| Overall design |
Histone mark ChIP-seq experiments in wild type mouse urogenital sinuses.
Please note that the CTCF ChIP-seq experiments in one mouse sample from GSE194418 and four zebrafish samples from GSE156096 have been re-analyzed:
BioProject accession: PRJNA800459
GEO Sample SRA Runs BioSample Title
========== ======== ========= =====
GSM5835468 SRR17750150 SAMN25248179 ChIP_CTCF_E105_PT_rep1
BioProject accession: PRJNA656773
GEO Sample SRA Runs BioSample Title
========== ======== ========= =====
GSM4724551 SRR12435909 SAMN15802273 ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 1
GSM5344491 SRR14670351 SAMN19371946 ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 2
GSM5344494 SRR14670354 SAMN19371948 ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 1
GSM5344495 SRR14670355 SAMN19371947 ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 2
Please see more details in the 're-analysis_readme.txt'.
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| Contributor(s) |
Hintermann A, Bolt C, Lopez-Delisle L, Gitto S, Mascrez B, Duboule D |
| Citation(s) |
38585989 |
| |
| Submission date |
Dec 15, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Aurelie Hintermann |
| E-mail(s) |
aur.hin@gmail.com
|
| Organization name |
University of Geneva
|
| Department |
Genetics and Evolution
|
| Street address |
30 quai Ernest-Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (3) |
| GSM7977989 |
ChIP against H3K27me3 in E18.5 mouse male urogenital sinus replicate 1 |
| GSM7977990 |
ChIP against H3K27ac in E18.5 mouse male urogenital sinus replicate 1 |
| GSM7977991 |
ChIP against H3K27ac in E18.5 mouse female urogenital sinus replicate 1 |
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| This SubSeries is part of SuperSeries: |
| GSE250267 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS |
|
| Relations |
| Reanalysis of |
GSM5835468 |
| Reanalysis of |
GSM4724551 |
| Reanalysis of |
GSM5344491 |
| Reanalysis of |
GSM5344492 |
| Reanalysis of |
GSM5344493 |
| BioProject |
PRJNA1053418 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE250367_CTCF_ChIP_mm_E105_PT_rep1.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE250367_CTCF_ChIP_mm_E105_PT_rep1.narrowPeak.gz |
2.9 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE250367_Franke_CTCF_ChIP_24hpf_rep1.bw |
63.3 Mb |
(ftp)(http) |
BW |
| GSE250367_Franke_CTCF_ChIP_24hpf_rep1.narrowPeak.gz |
2.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE250367_Franke_CTCF_ChIP_24hpf_rep2.bw |
15.5 Mb |
(ftp)(http) |
BW |
| GSE250367_Franke_CTCF_ChIP_24hpf_rep2.narrowPeak.gz |
904.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE250367_Franke_CTCF_ChIP_48hpf_rep1.bw |
24.2 Mb |
(ftp)(http) |
BW |
| GSE250367_Franke_CTCF_ChIP_48hpf_rep1.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE250367_Franke_CTCF_ChIP_48hpf_rep2.bw |
22.5 Mb |
(ftp)(http) |
BW |
| GSE250367_Franke_CTCF_ChIP_48hpf_rep2.narrowPeak.gz |
1018.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE250367_RAW.tar |
809.2 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
| GSE250367_re-analysis_readme.txt |
2.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
