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A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.

Hung Ping Shih, Philip A Seymour, Nisha A Patel, Ruiyu Xie, Allen Wang, Patrick P Liu, Gene W Yeo, Mark A Magnuson, Maike Sander

Cell reports · 2015 · Vol. 13 (2) · pp. 326-36

Abstract

The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox9 as cooperative inducers of a gene regulatory network that distinguishes the pancreatic from the intestinal lineage. Genetic studies demonstrate dual and cooperative functions for Pdx1 and Sox9 in pancreatic lineage induction and repression of the intestinal lineage choice. Pdx1 and Sox9 bind to regulatory sequences near pancreatic and intestinal differentiation genes and jointly regulate their expression, revealing direct cooperative roles for Pdx1 and Sox9 in gene activation and repression. Our study identifies Pdx1 and Sox9 as important regulators of a transcription factor network that initiates pancreatic fate and sheds light on the gene regulatory circuitry that governs the development of distinct organs from multi-lineage-competent foregut progenitors.

Linked datasets 5

GSE61947 GSE · via ncbi_elink
GEO ↗

SOX9 targets in hESC-derived pancreatic progenitors

Homo sapiens

4 data files
FileTypeSize
FGC0350_s_6.fastq.gz ChIP-Seq 8.0 GB
FGC0779_s_5_GCCAAT.fastq.fastq ChIP-Seq 2.7 GB
SRR1593951_GSM1517602 ChIP-Seq 8.0 GB
SRR1593952_GSM1517603 ChIP-Seq 2.7 GB
GSE61946 GSE · via ncbi_elink
GEO ↗

hESC-derived liver transcriptome analysis

Homo sapiens

5 data files
FileTypeSize
FGC0186_s_7_sequence.fastq.gz RNA-Seq 1.5 GB
FGC0186_s_8_sequence.fastq.gz RNA-Seq 1.6 GB
SRR1593955 RNA-Seq 1.5 GB
SRR1593955_GSM1517600 RNA-Seq 1.5 GB
SRR1593956_GSM1517601 RNA-Seq 1.6 GB
GSE62023 GSE · via ncbi_elink
GEO ↗

Identification of Sox9/Pdx1-coregulated Genes During Pancreas Organogenesis

Mus musculus

GSE61945 GSE · via ncbi_elink
GEO ↗

Human fetal pancreas transcriptome analysis

Homo sapiens

4 data files
FileTypeSize
FGC0170_s_7_sequence.fastq.gz RNA-Seq 1.9 GB
FGC0175_s_7_sequence.fastq RNA-Seq 4.3 GB
SRR1593953_GSM1517598 RNA-Seq 1.9 GB
SRR1593954_GSM1517599 RNA-Seq 4.3 GB
GSE61948 GSE · via ncbi_elink
GEO ↗

Transcriptome and cistrome analysis reveals synergistic roles for Sox9 and Pdx1 in lineage allocation of foregut progenitor cells

Mus musculus

Potentially related datasets 4

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
GSE61945 GSE · GEO GEO ↗ Human fetal pancreas transcriptome analysis
GSE61947 GSE · GEO GEO ↗ SOX9 targets in hESC-derived pancreatic progenitors
GSE62023 GSE · GEO GEO ↗ Identification of Sox9/Pdx1-coregulated Genes During Pancreas Organogenesis
GSE61946 GSE · GEO GEO ↗ hESC-derived liver transcriptome analysis

Analysis pipelines 5

Pipeline Assay Steps Dataset
GSE61945 RNA-seq Data Processing geo_data_processing RNA-seq 9 GSE61945
GSE61946 RNA-seq Data Processing geo_data_processing RNA-seq 9 GSE61946
GSE61947 ChIP-seq Data Processing geo_data_processing ChIP-seq 3 GSE61947
GSE61948 Data Processing geo_data_processing — 9 GSE61948
GSE62023 Data Processing geo_data_processing — 5 GSE62023
Funding 10 grants
Grant Funder
R01 HG004659 NHGRI NIH HHS (United States)
R01 NS075449 NINDS NIH HHS (United States)
R01 DK068471 NIDDK NIH HHS (United States)
R01 DK078803 NIDDK NIH HHS (United States)
DK089567 NIDDK NIH HHS (United States)
U01 DK089523 NIDDK NIH HHS (United States)
U01 DK089567 NIDDK NIH HHS (United States)
DK078803 NIDDK NIH HHS (United States)
DK89523 NIDDK NIH HHS (United States)
DK68471 NIDDK NIH HHS (United States)