ArticlePLoS computational biology2014
Reconstruction of the gene regulatory network involved in the sonic hedgehog pathway with a potential role in early development of the mouse brain.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- Advances in large-scale DNA engineering with the CRISPR system.Experimental & molecular medicine · 2025Review
- Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.Molecular biology and evolution · 2025Article
- Interpretable AI for inference of causal molecular relationships from omics data.Science advances · 2025Article
- Sex differences in the genetic architecture of cognitive resilience to Alzheimer's disease.Brain : a journal of neurology · 2022Article
- Mutations in the sonic hedgehog pathway cause macrocephaly-associated conditions due to crosstalk to the PI3K/AKT/mTOR pathway.American journal of medical genetics. Part A · 2019Article
- Common and distinct transcriptional signatures of mammalian embryonic lethality.Nature communications · 2019Article
- Super-enhancers: novel target for pancreatic ductal adenocarcinoma.Oncotarget · 2019Article
- Embryology of the Parathyroid Glands.Endocrinology and metabolism clinics of North America · 2018Review
- Brain transcriptome atlases: a computational perspective.Brain structure & function · 2017Review
- Crocetinic acid inhibits hedgehog signaling to inhibit pancreatic cancer stem cells.Oncotarget · 2015Article
- Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Sonic hedgehog (Shh) signaling pathway is crucial for pattern formation in early central nervous system development. By systematically analyzing high-throughput in situ hybridization data of E11.5 mouse brain, we found that Shh and its receptor Ptch1 define two adjacent mutually exclusive gene expression domains: Shh+Ptch1- and Shh-Ptch1+. These two domains are associated respectively with Foxa2 and Gata3, two transcription factors that play key roles in specifying them. Gata3 ChIP-seq experiments and RNA-seq assays on Gata3-knockdown cells revealed that Gata3 up-regulates the genes that are enriched in the Shh-Ptch1+ domain. Important Gata3 targets include Slit2 and Slit3, which are involved in the process of axon guidance, as well as Slc18a1, Th and Qdpr, which are associated with neurotransmitter synthesis and release. By contrast, Foxa2 both up-regulates the genes expressed in the Shh+Ptch1- domain and down-regulates the genes characteristic of the Shh-Ptch1+ domain. From these and other data, we were able to reconstruct a gene regulatory network governing both domains. Our work provides the first genome-wide characterization of the gene regulatory network involved in the Shh pathway that underlies pattern formation in the early mouse brain.
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