Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

Abstract

FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.

Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation

“…Moreover, these CREs were accessible in pluripotent conditions as well as in CLE. Co-factor-mediated recruitment to low-affinity sites has been implicated in cell-type-specific CRE activity and gene expression 33 , 34 , 46 , 47 . For SOX2, we found evidence of the involvement of CDX2 and T/BRA in directing binding to low-affinity sites.…”

Chromatin remodeling is restricted by transient GATA6 binding during iPSC differentiation to definitive endoderm

“…The EOMES binding motif was enriched with high statistical confidence at the regions of interest and the EOMES protein robustly occupied these sites independent of GATA6. Growing evidence points toward chromatin remodeling by transcription factors being highly influenced by motif-encoded binding stability and stabilizing transcription factors ( Donaghey et al., 2018 ; Geusz et al., 2021 ; Meers et al., 2019 ). As such, the presented evidence for aberrant chromatin opening in GATA6 −/− cells being EOMES-dependent is provocative.…”

Developmental cell fate choice employs two distinct cis regulatory strategies

“…FOXA TFs are required for the development of endoderm-derived lineages, pancreas, liver and lung, where they play partially redundant roles (Cernilogar et al, 2019; Geusz et al, 2021; Lee et al, 2005, 2019; Wan et al, 2005; Wang et al, 2015). Whereas many TFs play roles in multiple tissues, they are generally thought to act via different enhancers in a combinatorial fashion with other tissue-specific TFs (Meredith et al, 2013; Zinzen et al, 2009).…”

“…Many of these elements then bind the p3-specific TF, NKX2.2. Intriguingly, a subset of the elements bound and opened by FOXA2 in neural progenitors are also bound by FOXA2 during endoderm differentiation, where it plays a parallel role opening elements later required for specific endoderm lineages (Geusz et al, 2021).…”

“…FOXA2 has been proposed to act as a pioneer factor in the endoderm, where it remodels chromatin to allow the binding of other TFs (Geusz et al, 2021; Zaret and Carroll, 2011). Although TFs often have roles in multiple tissues, they are usually thought to act in a combinatorial fashion with other TFs via different elements in different tissues (Donaghey et al, 2018; Meredith et al, 2013; Zinzen et al, 2009).…”