Methods are provided for generating pancreatic endocrine cells from pluripotent stem cells (PSCs) using epigenetic modifiers. A
fusion protein comprising catalytically inactivated Cas9 (dCas9) and an embryonic
ectoderm development (EED)-
binding domain (EBdCas9) is used with guide RNAs (gRNAs) to target regulatory regions of transcriptional regulators including EOMES, PDX1, and NGN3. Sequential targeting of PDX1 and NGN3 promoters with EBdCas9 removes repressive H3K27me3 marks, increases activating H3K27ac modifications, and accelerates differentiation into
insulin-producing β-cells. The methods significantly increase β-
cell yields (~4-6 fold), reduce non-pancreatic lineage contaminants (CDX2+, SOX2+, enteroendocrine cells), enhance mitochondrial function, and produce glucose-responsive cells with superior functional maturation
in vivo. The epigenetic interventions enforce pancreatic developmental fates while activating NGN3-dependent transcriptional programs necessary for endocrine
cell differentiation,
insulin secretion, and metabolic maturation. Cells and compositions produced by these methods are also provided.