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

Ryan J Geusz,Darrell N Kotton,Kyle J Gaulton,Jinzhao Wang,Allen Wang,Yunjiang Qiu,Joshua Chiou,Maike Sander,Samy Kefalopoulou,Bing Ren,Araceli Ramirez,Nicholas K Vinckier,David A Roberts,Konstantinos-Dionysios Alysandratos,Dieter K Lam

doi:10.1038/s41467-021-26950-0

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.

Highlights

FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors
FOXA1 and FOXA2 were expressed from the definitive endoderm (DE) stage onwards (Supplementary Fig. 1a, b), and levels of FOXA1 and FOXA2 were similar in gut tube (GT), PP1, and PP2 (Supplementary Fig. 1a)
Pancreas induction was blocked in FOXA1/2−/− cells, as evidenced by an almost complete absence of PDX1+ and NKX6.1+ cells, reduced expression of early pancreatic TFs, and down-regulation (≥2-fold change, FDR ≤ 0.05) of genes associated with pancreas-specific biological processes (Fig. 1d–f and Supplementary Data 1, 2)

Summary

Introduction

FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Current evidence suggests that FOXA1/2’s role in endodermal organ development is to render foregut endoderm competent to activate organ-specific genes by broadly priming pancreas-, liver-, and lung-specific enhancers before organ-inductive signals trigger enhancer activation Consistent with this model, studies in model organisms and human pluripotent stem cell (hPSC)-based differentiation systems have shown a requirement for FOXA1/2 in pancreas, liver, and lung development, with the two FOXA TFs functioning in a partially or fully redundant manner[3,4,5,6]. In vitro experiments have shown that FOXA TFs possess pioneering activity, which refers to the specific ability of a TF to engage target sites on nucleosomal DNA and to remodel such regions to increase chromatin accessibility[7,8,9] Through their chromatin remodeling activity, FOXA TFs facilitate subsequent binding of other TFs and co-factors that further modify chromatin state and initiate gene expression[9,10,11,12,13,14]. We propose that priming of a small enhancer subset permits precise spatial and temporal regulation of organ induction by lineageinductive signals, whereas cooperative FOXA binding with lineage-specific TFs ensures cell type specificity of gene expression, providing a safeguard against broad activation of alternative lineage programs during developmental transitions

Methods

Results

Conclusion