ArticleGenome research2016
Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
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- ATOH8 is crucial for the differentiation of human trophoblast stem cells into extravillous trophoblasts.Scientific reports · 2025Article
- A Sox2 enhancer cluster regulates region-specific neural fates from mouse embryonic stem cells.G3 (Bethesda, Md.) · 2025Article
- Synchrotron radiation FTIR microspectroscopy enables measuring dynamic cell identity patterning during human 3D differentiation.Frontiers in cell and developmental biology · 2025Article
- NaV1.1 contributes to the cell cycle of human mesenchymal stem cells by regulating AKT and CDK2.Journal of cell science · 2024Article
- Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids.Nature cell biology · 2023Article
- Sfrp4 is required to maintain Ctsk-lineage periosteal stem cell niche function.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The cellular response to extracellular vesicles is dependent on their cell source and dose.Science advances · 2023Article
- Diseased, differentiated and difficult: Strategies for improved engineering ofFrontiers in cellular neuroscience · 2022Review
- Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding.Neuron · 2021Article
- Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance.Cell stem cell · 2019Article
- Sequentially acting SOX proteins orchestrate astrocyte- and oligodendrocyte-specific gene expression.EMBO reports · 2018Article
- Article
- Pioneer transcription factors shape the epigenetic landscape.The Journal of biological chemistry · 2018Review
- SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs.PLoS genetics · 2018Article
- Sox2 is required for olfactory pit formation and olfactory neurogenesis through BMP restriction andDevelopment (Cambridge, England) · 2018Article
- Cyclin-Dependent Kinase-Dependent Phosphorylation of Sox2 at Serine 39 Regulates Neurogenesis.Molecular and cellular biology · 2017Article
- Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.Cell reports · 2017Article
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatially distinct gene expression profiles in neural stem cells (NSCs) are a prerequisite to the formation of neuronal diversity, but how these arise from the regulatory interactions between chromatin accessibility and transcription factor activity has remained unclear. Here, we demonstrate that, despite their distinct gene expression profiles, NSCs of the mouse cortex and spinal cord share the majority of their DNase I hypersensitive sites (DHSs). Regardless of this similarity, domain-specific gene expression is highly correlated with the relative accessibility of associated DHSs, as determined by sequence read density. Notably, the binding pattern of the general NSC transcription factor SOX2 is also largely cell type specific and coincides with an enrichment of LHX2 motifs in the cortex and HOXA9 motifs in the spinal cord. Interestingly, in a zebrafish reporter gene system, these motifs were critical determinants of patterned gene expression along the rostral-caudal axis. Our findings establish a predictive model for patterned NSC gene expression, whereby domain-specific expression of LHX2 and HOX proteins act on their target motifs within commonly accessible cis-regulatory regions to specify SOX2 binding. In turn, this binding correlates strongly with these DHSs relative accessibility-a robust predictor of neighboring gene expression.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.