The molecular basis of specific functions of Brachyury and Eomes for mesoderm and endoderm lineage specification

The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs. Wildtype (WT) embryonic stem cells (ESCs) and ESCs deficient for Eomes or Brachyury were differentiated for 5 days as embryoid bodies (EBs) treated with Activin A. EOMES-GFP and BRACHYURY-GFP expression was induced by the addition of doxycycline (Eomes-GFP and Brachyury-GFP was introduced into the doxycycline-inducible locus (TRE) of EoKO, BraKO ESCs; hereafter EoKO+EoGFP, BraKO+BraGFP). Differentiated EBs were characterized by RNA-seq, ChIP-seq and ATAC-seq. 3 and 4 biological replicates were used for RNA-seq of ESCs or embryos, respectively, and biological duplicates were used for ChIP- and ATAC-seq. In addition, the inability of Brachury to rescue the EomesΔEpi (epiblast-specific deletion of Eomes) phenotype was shown by RNA-seq of EomesBraΔEpi E7.5 embryos (knock-in allele of Brachyury coding sequence into the first exon of the Eomes genomic locus (EomesBraΔEpi); EomesBra/+, Sox2:Cre males were crossed with EomesCA/CA females to generate EomesBraΔEpi).