Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Abstract

During embryogenesis, chromatin accessibility profiles control lineage-specific gene expression by modulating transcription, thus impacting 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. We found that multiple cis-regulatory elements, with distinct chromatin accessibility profiles and motif compositions, are required to activate Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that these ‘combined enhancers’ foster spatially and temporally accurate fate choices, by increasing the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity.

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

“…In the developing mouse heart, GATA4 also promotes the deposition of H3K27ac at heart enhancers ( 58 ). In Ciona , putative GATA binding sites are enriched in noncoding elements that open specifically in multipotent cardiopharyngeal progenitors in response to fibroblast growth factor (FGF)–mitogen-activated protein kinase signaling ( 59 ). Consistent with these previous studies, we observed GATA binding sites within the majority of regions losing accessibilities upon Gata5/6 KD (74.7 to 91.4%; data S4).…”

“…5993-100). The atrial siphon muscle/pharyngeal muscle progenitors were identified with an Ebf>H2B::mCherry reporter ( 23 , 59 ) or by FISH as previously described ( 59 ). Note that only one side of the embryo is imaged.…”

Affinity-optimizing variants within cardiac enhancers disrupt heart development and contribute to cardiac traits

“…Having seen the importance of low-affinity ETS sites within the FoxF enhancer, we wanted to see if low-affinity binding sites were found within other Ciona developmental heart enhancers. Using published ATAC-seq data for Ciona heart cells at 6.5hr post fertilization, a time at which FGF signaling is received by the heart precursor cells, we identified 15,174 putative Ciona heart enhancers (Racioppi et al, 2019). The mean affinity of putative ETS sites within these putative enhancers was 0.12, suggesting that low-affinity sites are prevalent within Ciona putative heart enhancers.…”

“…Alignment of ATAC-seq reads. ATAC-seq alignment was performed following the methods in (Racioppi et al, 2019). Raw reads from 6 hours post fertilization (hpf) (GEO accession GSE126691, LacZ_6hpf_1-3, LacZ_10hpf_1-4) were first preprocessed by FastQC (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc).…”

Brain Sensory Organs of the Ascidian Ciona robusta: Structure, Function and Developmental Mechanisms

“…Applying this technique in embryos, at different developmental stages and on different cell types, permits to investigate the regulatory pathways in the regions of interest ( Magri et al, 2019 ). ATAC-seq has been recently developed for Ciona to profile chromatin accessibility through transitions from mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors ( Racioppi et al, 2019a ).…”