EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [HiC-seq re-analysis]

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. 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'.