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Series GSE250368 Query DataSets for GSE250368
Status Public on Apr 17, 2024
Title EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [HiC-seq re-analysis]
Sample organism Danio rerio
Experiment type Other
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.
 
Overall design To assay chromatin conformation at the hoxDa locus, we reanalysed published HiC-seq sequencing data conducted on wild type zebrafish collected at either 24 hpf (2 samples from GSE156099 and 1 sample from GSE152741) or 48 hpf (2 samples from GSE156099). All individual samples were aggregated into a single interaction matrix.

BioProject accession: PRJNA656767
GEO Sample SRA Runs BioSample Title
========== ======== ========= =====
GSM4724554 SRR12435867 SAMN15802270 HiC in zebrafish wild-type embryos at 48hpf, replicate 1
GSM4724555 SRR12435868 SAMN15802269 HiC in zebrafish wild-type embryos at 48hpf, replicate 2
GSM5344533 SRR14670388 SAMN19372006 HiC in zebrafish wild-type embryos at 24hpf, replicate 1
GSM5344534 SRR14670389 SAMN19372005 HiC in zebrafish wild-type embryos at 24hpf, replicate 2

BioProject accession: PRJNA640313
GEO Sample SRA Runs BioSample Title
========== ======== ========= =====
GSM4625562 SRR12044304,SRR12044305,SRR12044306,SRR12044307,SRR12044308,SRR12044309 SAMN15314075 WT_ZF_Embryos_24hpf

Please see more details in the 're-analysis_readme.txt'.
 
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 17, 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
 
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 GSM4724554
Reanalysis of GSM4724555
Reanalysis of GSM5344533
Reanalysis of GSM5344534
Reanalysis of GSM4625562

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
GSE250368_Franke_24hpf_wt_rep1.10kb.cool.gz 46.5 Mb (ftp)(http) COOL
GSE250368_Franke_24hpf_wt_rep1.validPairs.csort.txt.gz 518.1 Mb (ftp)(http) TXT
GSE250368_Franke_24hpf_wt_rep2.10kb.cool.gz 121.5 Mb (ftp)(http) COOL
GSE250368_Franke_24hpf_wt_rep2.validPairs.csort.txt.gz 1.3 Gb (ftp)(http) TXT
GSE250368_Franke_48hpf_wt_rep1.10kb.cool.gz 108.6 Mb (ftp)(http) COOL
GSE250368_Franke_48hpf_wt_rep1.validPairs.csort.txt.gz 1.1 Gb (ftp)(http) TXT
GSE250368_Franke_48hpf_wt_rep2.10kb.cool.gz 33.5 Mb (ftp)(http) COOL
GSE250368_Franke_48hpf_wt_rep2.validPairs.csort.txt.gz 294.1 Mb (ftp)(http) TXT
GSE250368_HiC_hpf2448merge_WE_10kb.cool.gz 347.2 Mb (ftp)(http) COOL
GSE250368_Wike_24hpf.10kb.cool.gz 134.4 Mb (ftp)(http) COOL
GSE250368_Wike_24hpf.validPairs.csort.txt.gz 1.4 Gb (ftp)(http) TXT
GSE250368_re-analysis_readme.txt 3.9 Kb (ftp)(http) TXT

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