ArticleNature communications2024
Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.
Article in Nature communications, 2024. 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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Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells.Nature biotechnology · 2026Article
- Restoring pluripotency to pluripotent stem cells.Nature biotechnology · 2026Article
- A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease.Nature communications · 2026Article
- Engineered LINC MIR503HG-loaded extracellular vesicles maintain stemness and pluripotency during long-term hiPSCs culture.Bioactive materials · 2026Article
- Distinguishing causal from tagging enhancers using single-cell multiome data.medRxiv : the preprint server for health sciences · 2026Article
- LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiation.Nucleic acids research · 2026Article
- Human pluripotent stem cell models of Friedreich's ataxia: innovations, considerations, and future perspectives.Stem cell research & therapy · 2026Review
- Review
- Quantifying human pluripotent stem cell attributes with population balance modeling.Stem cell research & therapy · 2025Article
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Pluripotent cell states and fates in human embryo models.Development (Cambridge, England) · 2025Review
- Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants.Cell genomics · 2025Article
- IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium.Journal of molecular and cellular cardiology plus · 2025Article
- Pluripotency genes of mammals: a network at work.Frontiers in bioengineering and biotechnology · 2025Review
- UBR-5 and UBE2D mediate timely exit from stem fate via destabilization of poly(A)-binding protein PABP-2 in cell state transition.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes.Stem cell reports · 2024Article
- Generation of human hepatobiliary organoids with a functional bile duct from chemically induced liver progenitor cells.Stem cell research & therapy · 2024Article
- Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.Nature communications · 2024Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
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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.