ArticleGenome biology2025
Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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Authors and funding
28 authors.
Funding
Abstract
backgroundCell type-specific transcriptional heterogeneity in embryonic mouse skin is well-documented, but few studies have investigated the regulatory mechanisms. Here, we present high-throughput single-cell chromatin accessibility and transcriptome sequencing (HT-scCAT-seq), a method that simultaneously profiles transcriptome and chromatin accessibility. We utilized HT-scCAT-seq to dissect the gene regulatory mechanism governing epidermal stratification, periderm terminal differentiation, and fibroblast specification.
resultsBy linking chromatin accessibility to gene expression, we identify candidate cis-regulatory elements (cCREs) and their target genes which are crucial for dermal and epidermal development. We describe cells with similar gene expression profiles that exhibit distinct chromatin accessibility statuses during periderm terminal differentiation. Finally, we characterize the underlying lineage-determining transcription factors and demonstrate that ALX4 and RUNX2 are candidate transcription factors regulators of the dermal papilla lineage development through in silico perturbation analysis and CUT&Tag experiment.
conclusionsOverall, HT-scCAT-seq represents a powerful tool for unraveling the spatiotemporal dynamics of gene regulation in single cells. Our results advance the understanding of embryonic skin development while providing a scalable framework for investigating regulatory mechanisms across diverse biological systems and disease contexts.
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