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GEO Series: GSE87653

Title: Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [RNA-seq]

Summary

Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how they are integrated in the genome is poorly understood. Here we identified the Xenopus foregut and hindgut progenitor transcriptomes, which are largely conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/b-catenin acts as a genome-wide toggle between foregut and hindgut programs. In addition to b-catenin-Tcf promoting hindgut gene transcription, we unexpectedly observed Wnt-repressed foregut genes associated with b-catenin-binding to DNA lacking Tcf motifs, suggesting a novel direct repression. We define how BMP and Wnt signaling are integrated in the genome with Smad1 and β-catenin co-occupying DNA elements associated with hundreds of key regulatory genes. These results extend our understanding of GI organogenesis and how Wnt and BMP may coordinate genomic responses in other contexts.


Contributors: Aaron Zorn, Mariana Stevens, Praneet Chaturvedi, Scott Rankin, Melissa Macdonald, Sajjeev Jagannathan, Masashi Yukawa, Artem Barski

Experiment Type: mRNA profile of foregut and hindgut explants from BMP and Wnt manipulated embryos.

Experiment Reagents: 6BIO, DMH-1.

Phenotypes:
Xla Wt + BIO + foregut NF20 - RNA-Seq (RNA)

Article: XB-ART-53106, PubMed

Source: NCBI GEO, Xenbase Download

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
hindgut - NF20 GSM2337700  GSM2337701  GSM2337702  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
   hindgut + BIO - NF20 DEG GSM2337706  GSM2337707  GSM2337708  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical 6BIO NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
   hindgut + DMH1 - NF20 DEG GSM2337703  GSM2337704  GSM2337705  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical DMH-1 NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
foregut - NF20 GSM2337691  GSM2337692  GSM2337693  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
   foregut + BIO - NF20 DEG GSM2337697  GSM2337698  GSM2337699  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical 6BIO NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
   foregut + DMH1 - NF20 DEG GSM2337694  GSM2337695  GSM2337696  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical DMH-1 NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
hindgut - NF20 GSM2337716  GSM2337717  RNA-Seq
Background: Xla.Tg(hsp70:Xtr.dkk1;cryga:GFP)Jmws
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
   hindgut + dkk1 - NF20 DEG GSM2337718  GSM2337719  RNA-Seq
Background: Xla.Tg(hsp70:Xtr.dkk1;cryga:GFP)Jmws
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
heat shock   NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
foregut - NF20 GSM2337712  GSM2337713  RNA-Seq
Background: Xla.Tg(hsp70:Xtr.dkk1;cryga:GFP)Jmws
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
   foregut + dkk1 - NF20 DEG GSM2337714  GSM2337715  RNA-Seq
Background: Xla.Tg(hsp70:Xtr.dkk1;cryga:GFP)Jmws
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
heat shock   NF stage 12 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
dorsal embryo - NF20 GSM2337709  GSM2337710  GSM2337711  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
dorsal NF stage 20  
foregut endoderm - NF20 GSM2337720  GSM2337721  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
foregut endoderm NF stage 20  
foregut mesoderm - NF20 GSM2337722  GSM2337723  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
foregut NF stage 20  
hindgut endoderm - NF20 GSM2337724  GSM2337725  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut endoderm NF stage 20  
hindgut mesoderm - NF20 GSM2337726  GSM2337727  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
hindgut NF stage 20  
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Xtr   
Xla 

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