Fig 2: Epistatic relationship between H2A.Z and CDX2. a Caco-2/15 cells were transfected using siRNA targeting CDX2 mRNA or control, upon or not siRNA-mediated H2A.Z depletion. 72 h later, total RNA was extracted and subjected to RT-qPCR analysis for the expression of the indicated genes (calculated relative to ß2m mRNA level). The mean and standard error are shown (n = 3 independent experiments). Statistical analysis was done using Student’s t-Test (*p < 0.05; **p < 0.02 vs control siRNA). b Caco-2/15 cells were transfected using siRNA targeting H2A.Z or control, as indicated. 72 h later, ChIPs were performed using an H2A.Z antibody or no antibody as a control (No Ab). The amount of LPH or MUCDHL promoters, or an intergenic sequence were analyzed by qPCR, and the percentage of input was calculated. The mean and standard error are shown (n = 3 independent experiments). Statistical analysis was done using unilateral Student’s t-Test. c Same in b for CDX2 ChIP samples

Fig 3: Depletion of architectural proteins alters histone modifications and transcription factor occupancy. (A)–(C) ChIP for H3K9me3 (A), H3K9ac (B) and H3K27ac (C) in Caco2 cells transfected with NC siRNA (gray) or a siRNA targeting CTCF (black). Data are shown as percent recovery over input and each histone modification is normalized to recovery over input of unmodified histone H3 at each site, n = 3. ? indicate sites that are statistically different after knockdown as determined by an unpaired, two-tailed Student's t-test, P-values are listed in Supplementary Table S2. Other sites of interest are marked with arrows. (D)–(F) ChIP for FOXA1 (D), FOXA2 (E) and CDX2 (F) in Caco2 cells transfected with NC siRNA (gray) or siRNAs targeting CTCF and RAD21 (black). Data are shown as percent recovery over input, n = 3. *P < 0.05; **P < 0.01 as determined by an unpaired, two-tailed Student's t-test.

Fig 4: Neoglandular epithelium in the esophagus expressed markers of intestinal differentiation and Pdx1 similar to that of native jejunal epithelium. (A) Immunostaining for markers of intestinal and gastric differentiation in native jejunal epithelium (left side of each pair) and neoglandular epithelium (right side of each pair). Both the jejunal epithelium and neoglandular epithelium stained positively for intestinal markers such as caudal-related homeobox transcription factor (Cdx)2, Muc2, Villin, and cluster of differentiation (CD)10, and negative for gastric markers Muc5AC and Muc6 (not shown). Scale bar: 100 µm. (B) Both the neoglandular epithelium and native jejunal epithelium stained positively for Pdx1. Scale bar: 50 µm.