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
SOX9 targets in hESC-derived pancreatic progenitors
Homo sapiens
4 data files
| File | Type | Size |
|---|---|---|
| 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 |
hESC-derived liver transcriptome analysis
Homo sapiens
5 data files
| File | Type | Size |
|---|---|---|
| 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 |
Identification of Sox9/Pdx1-coregulated Genes During Pancreas Organogenesis
Mus musculus
Human fetal pancreas transcriptome analysis
Homo sapiens
4 data files
| File | Type | Size |
|---|---|---|
| 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 |
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) |