ArticleCell systems2019
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Human iPSC-derived neural stem cells displaying radial glia signature exhibit long-term safety in mice.Nature communications · 2024Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula.BMC biology · 2022Article
- Dynamic regulatory module networks for inference of cell type-specific transcriptional networks.Genome research · 2022Article
- Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder.PLoS genetics · 2021Article
- Post-transcriptional control of cellular differentiation by the RNA exosome complex.Nucleic acids research · 2020Review
- Data integration for inferring context-specific gene regulatory networks.Current opinion in systems biology · 2020Article
- Identification of FMR1-regulated molecular networks in human neurodevelopment.Genome research · 2020Article
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Authors and funding
12 authors.
Funding
Abstract
Neuroepithelial stem cells (NSC) from different anatomical regions of the embryonic neural tube's rostrocaudal axis can differentiate into diverse central nervous system tissues, but the transcriptional regulatory networks governing these processes are incompletely understood. Here, we measure region-specific NSC gene expression along the rostrocaudal axis in a human pluripotent stem cell model of early central nervous system development over a 72-h time course, spanning the hindbrain to cervical spinal cord. We introduce Escarole, a probabilistic clustering algorithm for non-stationary time series, and combine it with prior-based regulatory network inference to identify genes that are regulated dynamically and predict their upstream regulators. We identify known regulators of patterning and neural development, including the HOX genes, and predict a direct regulatory connection between the transcription factor POU3F2 and target gene STMN2. We demonstrate that POU3F2 is required for expression of STMN2, suggesting that this regulatory connection is important for region specificity of NSCs.
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Registered trials
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