FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation

Abstract

SUMMARY Transcriptional regulatory mechanisms of lineage priming in embryonic development are largely uncharacterized because of the difficulty of isolating transient progenitor populations. Directed differentiation of human pluripotent stem cells (hPSCs) combined with gene editing provides a powerful system to define precise temporal gene requirements for progressive chromatin changes during cell fate transitions. Here, we map the dynamic chromatin landscape associated with sequential stages of pancreatic differentiation from hPSCs. Our analysis of chromatin accessibility dynamics led us to uncover a requirement for FOXA2 , known as a pioneer factor, in human pancreas specification not previously shown from mouse knockout studies. FOXA2 knockout hPSCs formed reduced numbers of pancreatic progenitors accompanied by impaired recruitment of GATA6 to pancreatic enhancers. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming. This work highlights the power of combining hPSC differentiation, genome editing, and computational genomics for discovering transcriptional mechanisms during development.

Circadian Entrainment Triggers Maturation of Human In Vitro Islets

“…The promise of in-vitro-derived tissues for regenerative medicine benefits from a better understanding of mechanisms governing their development and function. Prior SC-islet studies described epigenetic processes influencing pancreatic specification (Cebola et al, 2015;Lee et al, 2019;Wang et al, 2015;Xie et al, 2013;Xu et al, 2014). Extending these to specification of endocrine cell types has been hampered by their inefficient/incomplete derivation, which yields highly heterogenous preparations Rezania et al, 2014;Russ et al, 2015).…”

A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates

“…Thus, current evidence supports a model wherein FOXA1/2 render foregut endoderm competent to activate organ-specific genes by broadly priming pancreas-, liver-, and lung-specific enhancers before organinductive signals trigger enhancer activation and target gene expression. 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 (Genga et al, 2019;Lee et al, 2005;Lee et al, 2019;Wan et al, 2005). However, the extent to which the full repertoire of organ lineage-specific enhancers undergoes chromatin priming is unknown.…”

“…The competence of organ lineage precursors to activate lineage-specific genes in response to inductive signals is acquired during endoderm development (Wang et al, 2015;Zorn and Wells, 2009). Coincident with the acquisition of competence, the transcription factors (TFs) FOXA1 and FOXA2 (henceforth abbreviated FOXA1/2) are recruited to enhancers of foregut-derived organ lineages, leading to a gain in chromatin accessibility and H3K4me1 deposition (Genga et al, 2019;Lee et al, 2019;Wang et al, 2015), a phenomenon referred to as enhancer priming. Thus, current evidence supports a model wherein FOXA1/2 render foregut endoderm competent to activate organ-specific genes by broadly priming pancreas-, liver-, and lung-specific enhancers before organinductive signals trigger enhancer activation and target gene expression.…”

Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of leukemia

“…We used FIMO to search for motif hits in the ATAC-seq atlas with default parameters using CIS-BP Single Species DNA Homo_sapiens motif database (http://meme-suite.org/db/motifs), restricted to expressed TFs only, based on our RNA-seq filtering thresholds. For each motif, we compared accessibility log2FC distribution of peaks containing the motif with the accessibility log2FC of the atlas by KS test, as described previously 37 . The KS statistic was then plotted against the percentage of motif hits in the atlas.…”

“…Tornado plots were generated using the bigWig file format for each stage, averaged across replicates. The 99 th percentile of the bigWig file readout of the ATAC-seq data was used to set the maximum color in the tornado plots to reduce the outlier effect of highly accessible peaks, as described 37 . The peaks were centered on their summit and sorted by their mean signal.…”