Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules controlling vertebrate organogenesis [ATAC-seq]

While vertebrate species are superficially diverse, they share key commonalities in terms of overall morphology, and organ configuration and function. Maintenance of these traits during evolution is partially explained by conservation of critical genes governing embryonic development. However, for conserved genes to deliver consistent developmental outcomes between species, similar gene regulatory programmes and gene expression patterns must also be maintained. The endoderm germ layer makes major contributions to the respiratory and gastrointestinal tracts, and associated organs including liver and pancreas. We used functional genomics approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many CRMs governing pancreas developmental also likely acting within the nervous system. Furthermore, these highly conserved CRMs are strongly enriched for binding sites of “neuro-pancreatic” transcription factors governing both pancreas and nervous system development, potentially suggesting function across these distinct organ systems. Additionally, we identify highly conserved CRMs likely participating endodermal patterning of adjacent craniofacial structures and sensory tissues. The highly conserved CRMs we identify are characterised by conserved patterns of transcription factor binding site co-occurrence. However, they are not characterised by rigid arrangement of binding sites, suggesting more complex or individual grammatical rules. Overall, our analyses provide key insights into critical gene regulatory control during vertebrate endoderm organogenesis, and define a compendium of highly conserved CRMs that should be prioritised for analysis of neuro-pancreatic gene transcriptional control, and anterior embryonic patterning. Overall design: ATAC-seq analysis of cell populations isolated from zebrafish at 28 and 48 hours post-fertilisation using fluorescence activated cell sorting. Samples are enriched based on sox17:GFP reporter expression relative to endothelial and erythrocyte markers (kdrl:cherry and gata1a:dsRed respectively). Sox17E is endoderm-enriched; sox17M is sox17+ hematovascular cells; sox17N is sox17-negative lineages.