Fig. 3: Expression of neuron-specific imprinted genes after hypothalamic differentiation.
From: Rescue of imprinted genes by epigenome editing in human cellular models of Prader-Willi syndrome
a Schematic illustrating the methylation and expression status of PWS-associated imprinted genes during neural differentiation from epigenome-edited iPSCs. At the iPSC stage, epigenome editing activated the expression of SNORD116, IPW, and MAGEL2. Upon neural differentiation, the downstream genes, SNORD115 and UBE3A-ATS were activated. MKRN3 expression was partially activated. RT-qPCR analysis of the expression of SNORD115 (b), UBE3A-ATS and UBE3A (c), and MKRN3 (d) in iPSCs and organoids at day 60 (Mean ± SEM; iPSCs, n = 3 experiments, 1–3 iPSC line/clones; Organoids, n = 3 differentiations, 1–3 iPSC line/clones; One-way ANOVA with Tukey correction; SNORD115, F9, 20 = 43.62, ***P = 0.0002, ****P < 0.0001; UBE3A-ATS, F9, 20 = 27.85, *P = 0.0229 [TIG119 vs –/–], 0.0235 [WD39 vs –/–], ***P = 0.0001; UBE3A, F9, 20 = 23.67, **P = 0.0012 [TIG119 vs +/+], 0.0032 [WD39 vs +/+], 0.0033 [–/+ vs +/+]; Brown-Forsythe and Welch ANOVA with Dunnett’s T3 correction; MKRN3, *P = 0.0144, **P = 0.0011). e Methylation status of MKRN3 region in iPSCs (upper) and organoids at day 100 (bottom) by long-read sequencing analysis. The yellow highlighted region indicates differentially methylated regions in MKRN3 promoter. f Methylation status of MKRN3 region in organoids at d60, measured by genomic qPCR analysis following methylation-sensitive enzyme digestion (Mean ± SEM; n = 3 differentiations, 1–3 iPSC line/clones; One-way ANOVA with Tukey correction, F3, 8 = 22.79, ***P = 0.0009, **P = 0.0091, *P = 0.0495). ns not significant.
