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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 [ATAC-seq] |
| Organisms |
Danio rerio; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| 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 |
To assay chromatin accessibility, we conducted ATAC-seq experiments. We collected different mouse and zebrafish tissues. Samples were processed as described in 10.1038/nmeth.2688.
UPDATE: [08-12-2024] For Samples GSM7976428, GSM7976429, and GSM7976430, the stage was corrected from 16hpf to 30hpf in the titles, stage characteristics, and processed data files. The raw data and processed data associated with these Sample accession numbers did not change.
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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 |
Aug 12, 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 |
| |
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| Platforms (3) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
| GPL21741 |
Illumina HiSeq 4000 (Danio rerio) |
|
| Samples (14)
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| GSM7976421 |
ATAC-seq in fish 16 hpf head replicate 1 |
| GSM7976422 |
ATAC-seq in fish 16 hpf posterior trunk replicate 1 |
| GSM7976423 |
ATAC-seq in fish 30 hpf head replicate 1 |
| GSM7976424 |
ATAC-seq in fish 16 hpf posterior trunk replicate 2 |
| GSM7976425 |
ATAC-seq in fish 16 hpf posterior trunk replicate 3 |
| GSM7976426 |
ATAC-seq in fish 16 hpf anterior trunk replicate 1 |
| GSM7976427 |
ATAC-seq in fish 16 hpf rhombomeres replicate 1 |
| GSM7976428 |
ATAC-seq in fish 30 hpf cloaca replicate 1 |
| GSM7976429 |
ATAC-seq in fish 30 hpf tail bud replicate 1 |
| GSM7976430 |
ATAC-seq in fish 30 hpf trunk replicate 1 |
| GSM7976431 |
ATAC-seq in mouse E18.5 male urogenital sinus replicate 1 |
| GSM7976432 |
ATAC-seq in mouse E18.5 female urogenital sinus replicate 1 |
| GSM7976433 |
ATAC-seq in mouse E18.5 male urogenital sinus replicate 2 |
| GSM7976434 |
ATAC-seq in mouse E18.5 female urogenital sinus replicate 2 |
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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 |
| BioProject |
PRJNA1053267 |
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