Limits...
PDX1 binds and represses hepatic genes to ensure robust pancreatic commitment in differentiating human embryonic stem cells.

Teo AK, Tsuneyoshi N, Hoon S, Tan EK, Stanton LW, Wright CV, Dunn NR - Stem Cell Reports (2015)

Bottom Line: ChIP-seq also revealed PDX1 occupancy at hepatic genes.In HepG2 cells and differentiating hESCs, we found that PDX1 binds and suppresses expression of endogenous liver genes.These findings rebrand PDX1 as a context-dependent transcriptional repressor and activator within the same cell type.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medical Biology, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore.

Show MeSH

Related in: MedlinePlus

PDX1 Binds and Potentially Regulates Numerous Developmentally Important Pancreatic Genes(A) Microarray gene expression heatmap of hESCs on days 0, 10, and 17 of pancreatic differentiation. Each time point is represented by four biological replicates.(B) Microarray gene expression heatmap of selected pluripotency, gastrulation/primitive streak-related, DE, and pancreatic lineage-related genes from days 0 to 17.(C) Schematic showing the number of PDX1-bound genes (±20 kb from the TSS) that are upregulated and downregulated on day 17 as compared with day 0 (>2-fold; FDR <0.05).(D) Of the 56 genes enriched in pancreatic progenitor cells isolated from the E10.5 mouse embryo (Gu et al., 2004), 15 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ± 20 kb from the TSS). Microarray gene expression heatmap showing the increase in gene expression of 6 of 15 common targets from days 0 to 17. The expression of IGFBP5, which encodes an endodermal marker, peaks at day 5, plummets on day 7, and continually increases beginning on day 12 by qPCR (data not shown).(E) In E10.5 microdissected Pdx1−/− E10.5 dorsal pancreatic buds, 73 genes were reported to be significantly downregulated (Svensson et al., 2007). Of these, 20 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ±20 kb from the TSS). Microarray gene expression heatmap depicting the increase in gene expression of 12 of 20 common targets from days 0 to 17 of pancreatic differentiation.See also Tables S1 and S2.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4400640&req=5

fig3: PDX1 Binds and Potentially Regulates Numerous Developmentally Important Pancreatic Genes(A) Microarray gene expression heatmap of hESCs on days 0, 10, and 17 of pancreatic differentiation. Each time point is represented by four biological replicates.(B) Microarray gene expression heatmap of selected pluripotency, gastrulation/primitive streak-related, DE, and pancreatic lineage-related genes from days 0 to 17.(C) Schematic showing the number of PDX1-bound genes (±20 kb from the TSS) that are upregulated and downregulated on day 17 as compared with day 0 (>2-fold; FDR <0.05).(D) Of the 56 genes enriched in pancreatic progenitor cells isolated from the E10.5 mouse embryo (Gu et al., 2004), 15 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ± 20 kb from the TSS). Microarray gene expression heatmap showing the increase in gene expression of 6 of 15 common targets from days 0 to 17. The expression of IGFBP5, which encodes an endodermal marker, peaks at day 5, plummets on day 7, and continually increases beginning on day 12 by qPCR (data not shown).(E) In E10.5 microdissected Pdx1−/− E10.5 dorsal pancreatic buds, 73 genes were reported to be significantly downregulated (Svensson et al., 2007). Of these, 20 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ±20 kb from the TSS). Microarray gene expression heatmap depicting the increase in gene expression of 12 of 20 common targets from days 0 to 17 of pancreatic differentiation.See also Tables S1 and S2.

Mentions: Microarray analyses performed in quadruplicate on days 0, 10, and 17 of differentiation revealed that these selected time points corresponded to unique gene expression signatures (Figure 3A; Table S2, parts A–C). Consistent with our qPCR studies, numerous pancreas-related genes were upregulated by day 17, including TM4SF4, MAFB, CDH1 (E-CAD), SPINK1, PDX1, PROX1, GHRL, RBP4, RFX6, PCSK2, HOXA2, and HNF1A, whereas several others such as PITX2, MEIS2, DACH1, ONECUT2, JAG1, FOXA2, MEIS1, ISL1, SOX9, HNF1B, KRT19, GATA4, GATA6, and MNX1 were expressed from day 10 onward (Figure 3B). Pluripotency genes NANOG, OCT4, and SOX2 were predictably downregulated by day 10, while mesendoderm (EOMES) and DE (SOX17) genes were downregulated on day 17 (Figure 3B). The slight increase in SOX2 on day 17 was consistent with the expression of Sox2 in the mouse anterior foregut (Que et al., 2007) (Figure 3B).


PDX1 binds and represses hepatic genes to ensure robust pancreatic commitment in differentiating human embryonic stem cells.

Teo AK, Tsuneyoshi N, Hoon S, Tan EK, Stanton LW, Wright CV, Dunn NR - Stem Cell Reports (2015)

PDX1 Binds and Potentially Regulates Numerous Developmentally Important Pancreatic Genes(A) Microarray gene expression heatmap of hESCs on days 0, 10, and 17 of pancreatic differentiation. Each time point is represented by four biological replicates.(B) Microarray gene expression heatmap of selected pluripotency, gastrulation/primitive streak-related, DE, and pancreatic lineage-related genes from days 0 to 17.(C) Schematic showing the number of PDX1-bound genes (±20 kb from the TSS) that are upregulated and downregulated on day 17 as compared with day 0 (>2-fold; FDR <0.05).(D) Of the 56 genes enriched in pancreatic progenitor cells isolated from the E10.5 mouse embryo (Gu et al., 2004), 15 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ± 20 kb from the TSS). Microarray gene expression heatmap showing the increase in gene expression of 6 of 15 common targets from days 0 to 17. The expression of IGFBP5, which encodes an endodermal marker, peaks at day 5, plummets on day 7, and continually increases beginning on day 12 by qPCR (data not shown).(E) In E10.5 microdissected Pdx1−/− E10.5 dorsal pancreatic buds, 73 genes were reported to be significantly downregulated (Svensson et al., 2007). Of these, 20 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ±20 kb from the TSS). Microarray gene expression heatmap depicting the increase in gene expression of 12 of 20 common targets from days 0 to 17 of pancreatic differentiation.See also Tables S1 and S2.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400640&req=5

fig3: PDX1 Binds and Potentially Regulates Numerous Developmentally Important Pancreatic Genes(A) Microarray gene expression heatmap of hESCs on days 0, 10, and 17 of pancreatic differentiation. Each time point is represented by four biological replicates.(B) Microarray gene expression heatmap of selected pluripotency, gastrulation/primitive streak-related, DE, and pancreatic lineage-related genes from days 0 to 17.(C) Schematic showing the number of PDX1-bound genes (±20 kb from the TSS) that are upregulated and downregulated on day 17 as compared with day 0 (>2-fold; FDR <0.05).(D) Of the 56 genes enriched in pancreatic progenitor cells isolated from the E10.5 mouse embryo (Gu et al., 2004), 15 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ± 20 kb from the TSS). Microarray gene expression heatmap showing the increase in gene expression of 6 of 15 common targets from days 0 to 17. The expression of IGFBP5, which encodes an endodermal marker, peaks at day 5, plummets on day 7, and continually increases beginning on day 12 by qPCR (data not shown).(E) In E10.5 microdissected Pdx1−/− E10.5 dorsal pancreatic buds, 73 genes were reported to be significantly downregulated (Svensson et al., 2007). Of these, 20 homologs are bound by PDX1 on day 17 of differentiation (2,817 within ±20 kb from the TSS). Microarray gene expression heatmap depicting the increase in gene expression of 12 of 20 common targets from days 0 to 17 of pancreatic differentiation.See also Tables S1 and S2.
Mentions: Microarray analyses performed in quadruplicate on days 0, 10, and 17 of differentiation revealed that these selected time points corresponded to unique gene expression signatures (Figure 3A; Table S2, parts A–C). Consistent with our qPCR studies, numerous pancreas-related genes were upregulated by day 17, including TM4SF4, MAFB, CDH1 (E-CAD), SPINK1, PDX1, PROX1, GHRL, RBP4, RFX6, PCSK2, HOXA2, and HNF1A, whereas several others such as PITX2, MEIS2, DACH1, ONECUT2, JAG1, FOXA2, MEIS1, ISL1, SOX9, HNF1B, KRT19, GATA4, GATA6, and MNX1 were expressed from day 10 onward (Figure 3B). Pluripotency genes NANOG, OCT4, and SOX2 were predictably downregulated by day 10, while mesendoderm (EOMES) and DE (SOX17) genes were downregulated on day 17 (Figure 3B). The slight increase in SOX2 on day 17 was consistent with the expression of Sox2 in the mouse anterior foregut (Que et al., 2007) (Figure 3B).

Bottom Line: ChIP-seq also revealed PDX1 occupancy at hepatic genes.In HepG2 cells and differentiating hESCs, we found that PDX1 binds and suppresses expression of endogenous liver genes.These findings rebrand PDX1 as a context-dependent transcriptional repressor and activator within the same cell type.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medical Biology, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore.

Show MeSH
Related in: MedlinePlus