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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.

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PDX1 Binds the Regulatory Regions of Genes Expressed in Foregut/Midgut Derivatives in hESC-Derived Human Pancreatic Progenitors(A) De novo motif analyses identify PDX1, PBX1, FOXA2, and FOXA1 binding motifs as the top ranking motifs in PDX1-bound regions identified via ChIP-seq.(B) Relative frequency of PDX1 binding events within ±20 kb of the TSS of candidate target genes (FDR <10%).(C) Representative view of PDX1-binding sites within the PDX1, ONECUT1 (HNF6) and RFX6 genomic loci.(D) ChIP-qPCR independently confirms the presence of PDX1 on regulatory regions of selected pancreas-related genes. Error bars indicate the SD of three technical replicates from a single ChIP-qPCR experiment. These data were independently confirmed in repeat pull-down qPCR experiments (data not shown). Normal goat IgG is the negative control.See also Table S1.
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fig2: PDX1 Binds the Regulatory Regions of Genes Expressed in Foregut/Midgut Derivatives in hESC-Derived Human Pancreatic Progenitors(A) De novo motif analyses identify PDX1, PBX1, FOXA2, and FOXA1 binding motifs as the top ranking motifs in PDX1-bound regions identified via ChIP-seq.(B) Relative frequency of PDX1 binding events within ±20 kb of the TSS of candidate target genes (FDR <10%).(C) Representative view of PDX1-binding sites within the PDX1, ONECUT1 (HNF6) and RFX6 genomic loci.(D) ChIP-qPCR independently confirms the presence of PDX1 on regulatory regions of selected pancreas-related genes. Error bars indicate the SD of three technical replicates from a single ChIP-qPCR experiment. These data were independently confirmed in repeat pull-down qPCR experiments (data not shown). Normal goat IgG is the negative control.See also Table S1.

Mentions: PDX1 plays a preeminent, evolutionarily conserved role in orchestrating pancreatic morphogenesis, but surprisingly little is known about the identity of its transcriptional targets during embryonic development. We therefore combined high-affinity polyclonal PDX1 antibodies with chromatin immunoprecipitation and deep sequencing (ChIP-seq) in an effort to uncover those immediate downstream genes that govern the early growth and development of the human pancreatic anlagen. For these studies, we selected day 17 of differentiation—a time point that consistently yielded large numbers (≥65%) of PDX1+ ePP cells (Figure 1D). These analyses revealed 15,436 PDX1-bound regions that map to 6,212 genes (false discovery rate [FDR] < 0.1 with no distance cutoff; Table S1, part A). The PDX1/PBX1-complex homeodomain-binding motif was the most highly enriched among the sequence reads, followed by the FOXA1/FOXA2 forkhead/winged helix DNA-binding motif (Figure 2A). PBX1 binds 5′ to its half-site ATGATT, whereas PDX1/HOX binds 3′ to the half-site TTAATGG, with an overlap at the middle TT (underlined), and these proteins heterodimerize to modulate gene transcription (Dutta et al., 2001; Knoepfler et al., 1996; Liu et al., 2001; Swift et al., 1998). These findings provide strong evidence that our ChIP-seq data are highly enriched for specific PDX1 binding events and further suggest that some PDX1-bound targets in ePP cells are co-regulated by PBX1 and FOXA proteins.


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 the Regulatory Regions of Genes Expressed in Foregut/Midgut Derivatives in hESC-Derived Human Pancreatic Progenitors(A) De novo motif analyses identify PDX1, PBX1, FOXA2, and FOXA1 binding motifs as the top ranking motifs in PDX1-bound regions identified via ChIP-seq.(B) Relative frequency of PDX1 binding events within ±20 kb of the TSS of candidate target genes (FDR <10%).(C) Representative view of PDX1-binding sites within the PDX1, ONECUT1 (HNF6) and RFX6 genomic loci.(D) ChIP-qPCR independently confirms the presence of PDX1 on regulatory regions of selected pancreas-related genes. Error bars indicate the SD of three technical replicates from a single ChIP-qPCR experiment. These data were independently confirmed in repeat pull-down qPCR experiments (data not shown). Normal goat IgG is the negative control.See also Table S1.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4400640&req=5

fig2: PDX1 Binds the Regulatory Regions of Genes Expressed in Foregut/Midgut Derivatives in hESC-Derived Human Pancreatic Progenitors(A) De novo motif analyses identify PDX1, PBX1, FOXA2, and FOXA1 binding motifs as the top ranking motifs in PDX1-bound regions identified via ChIP-seq.(B) Relative frequency of PDX1 binding events within ±20 kb of the TSS of candidate target genes (FDR <10%).(C) Representative view of PDX1-binding sites within the PDX1, ONECUT1 (HNF6) and RFX6 genomic loci.(D) ChIP-qPCR independently confirms the presence of PDX1 on regulatory regions of selected pancreas-related genes. Error bars indicate the SD of three technical replicates from a single ChIP-qPCR experiment. These data were independently confirmed in repeat pull-down qPCR experiments (data not shown). Normal goat IgG is the negative control.See also Table S1.
Mentions: PDX1 plays a preeminent, evolutionarily conserved role in orchestrating pancreatic morphogenesis, but surprisingly little is known about the identity of its transcriptional targets during embryonic development. We therefore combined high-affinity polyclonal PDX1 antibodies with chromatin immunoprecipitation and deep sequencing (ChIP-seq) in an effort to uncover those immediate downstream genes that govern the early growth and development of the human pancreatic anlagen. For these studies, we selected day 17 of differentiation—a time point that consistently yielded large numbers (≥65%) of PDX1+ ePP cells (Figure 1D). These analyses revealed 15,436 PDX1-bound regions that map to 6,212 genes (false discovery rate [FDR] < 0.1 with no distance cutoff; Table S1, part A). The PDX1/PBX1-complex homeodomain-binding motif was the most highly enriched among the sequence reads, followed by the FOXA1/FOXA2 forkhead/winged helix DNA-binding motif (Figure 2A). PBX1 binds 5′ to its half-site ATGATT, whereas PDX1/HOX binds 3′ to the half-site TTAATGG, with an overlap at the middle TT (underlined), and these proteins heterodimerize to modulate gene transcription (Dutta et al., 2001; Knoepfler et al., 1996; Liu et al., 2001; Swift et al., 1998). These findings provide strong evidence that our ChIP-seq data are highly enriched for specific PDX1 binding events and further suggest that some PDX1-bound targets in ePP cells are co-regulated by PBX1 and FOXA proteins.

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