Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Abstract

In embryos, lineage-specific profiles of chromatin accessibility control gene expression by modulating transcription, and thus impact multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors’ competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. Combinations of cis-regulatory elements with distinct chromatin accessibility profiles are required to activate of Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that this higher order combinatorial logic increases the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity, thus fostering spatially and temporally accurate fate choices.

Functional genomic approaches to elucidate the role of enhancers during development

“…Atlases of animal development have not yet been directly applied to the study of enhancers, although additional insight into developmental gene regulation could be achieved by combining scRNA‐seq with single‐cell ATAC‐seq to assay chromatin accessibility, which may reveal putative developmental enhancers. This principle was recently demonstrated in Ciona embryos by bulk RNA‐seq and ATAC‐seq performed on FACS sorted cardiac progenitor cells, which led to the identification of novel enhancers (Racioppi, Wiechecki, & Christiaen, ). Pairing single‐cell approaches within the context of a whole developing embryo will likely expand our ability to identify and functionally validate enhancer sequences.…”

GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate

“…6e-g; 43 ). As Ebf acts as a master regulator of pharyngeal muscle identity and is sufficient to inhibit the cardiac fate 43,[69][70][71] , this result indicates that Gata4/5/6 is necessary to both promote cardiac and prevent ectopic pharyngeal muscle fate in the common cardiopharyngeal progenitors. This further suggests that function of GATA4/5/6 family members in the divergence of the cardiopharyngeal lineage is conserved between vertebrates and tunicates and is thus likely to be an ancestral feature of cardiac GATA factors.…”

“…and promote an open chromatin state in vitro 26 . In Ciona, putative GATA binding sites are enriched in non-coding elements that open specifically in multipotent cardiopharyngeal progenitors in response to FGF-MAPK signaling 70 . It is thus possible that GATA4/5/6 contributes to opening a substantial fraction of the cardiopharyngeal-lineage-specific cisregulatory elements that control cardiac gene expression.…”

Cardiopharyngeal Progenitor Specification: Multiple Roads to the Heart and Head Muscles

“…Finally, the dynamic gene expression changes involved in transitions from pluripotency to cardiogenic mesoderm are accompanied by modifications of the epigenetic landscape or chromatin accessibility, with regulatory regions of genes being first primed then activated, and other regions involved in alternative fates being de-commissioned (Paige et al 2012;Wamstad et al 2012;Racioppi et al 2019). Transcription factors cooperate to induce these changes, through interactions with each other and specific chromatin modifiers (Chang and Bruneau 2012;Luna-Zurita et al 2016).…”