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Multicellular organisms consist of multiple cell types. The identity of these cells is primarily maintained by cell-type-specific gene expression programs; however, mechanisms that suppress these programs are poorly defined. Here we show that serum response factor (Srf), a transcription factor that is activated by various extracellular stimuli, can repress cell-type-specific genes and promote cellular reprogramming to pluripotency. Manipulations that decrease β-actin monomer quantity result in the nuclear accumulation of Mkl1 and the activation of Srf, which downregulate cell-type-specific genes and alter the epigenetics of regulatory regions and chromatin organization. Mice overexpressing Srf exhibit various pathologies including an ulcerative colitis-like symptom and a metaplasia-like phenotype in the pancreas. Our results demonstrate an unexpected function of Srf via a mechanism by which extracellular stimuli actively destabilize cell identity and suggest Srf involvement in a wide range of diseases.
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http://dx.doi.org/10.1038/s41467-018-03748-1 | DOI Listing |
Cell Rep
September 2025
Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA. Electronic address:
Progranulin-deficient frontotemporal dementia (GRN-FTD) is a major cause of familial FTD with TAR DNA-binding protein 43 (TDP-43) pathology, which is linked to exon dysregulation. However, little is known about this dysregulation in glial and neuronal cells. Here, using splice-junction-covering enrichment probes, we introduce single-nuclei long-read RNA sequencing 2 (SnISOr-Seq2), targeting 3,630 high-interest genes without loss of precision, and complete the first single-cell, long-read-resolved case-control study for neurodegeneration.
View Article and Find Full Text PDFJ Biol Chem
September 2025
School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chines
Long non-coding RNAs (lncRNAs) play crucial roles in plant growth, development, and stress responses. With the advancement of single-cell RNA sequencing (scRNA-seq) technology, it is now possible to investigate lncRNA expression and function at single-cell resolution. Although several plant single-cell transcriptome databases have been established, they predominantly focus on protein-coding genes while largely overlooking lncRNAs.
View Article and Find Full Text PDFZebrafish
September 2025
Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA.
DaniocellDesktop is a cross-platform interactive desktop application designed to facilitate reanalysis of a previously published 462,243-cell single-cell RNAseq dataset that profiled cell-type-specific gene expression across the first 5 days of wild-type zebrafish development. DaniocellDesktop enables custom redefinition of cell populations, identification of differentially expressed genes, and generation of several types of publication-ready plots to show gene expression patterns, gene co-expression patterns, and gene expression over time within these previously published data without requiring any specific programming knowledge. This software is available from https://daniocell.
View Article and Find Full Text PDFUnlabelled: Abnormal development of the intricate trabecular meshwork (TM) or Schlemm's canal (SC) structures in the eye can result in reduced aqueous humor fluid drainage and elevated intraocular pressure. If left untreated, these processes can lead to retinal ganglion cell loss, damage to the optic nerve, and infant-onset vision loss, termed congenital glaucoma. To identify gene expression important for development of these specialized aqueous humor outflow pathway (AHOP) structures, single-cell RNA sequencing was performed on rat AHOP tissues during three major periods of growth.
View Article and Find Full Text PDFFront Immunol
September 2025
Wound Healing Center, Peking University Third Hospital, Beijing, China.
Background And Objective: Melanoma exhibits profound biological complexity, driven by immune evasion, phenotypic plasticity, and resistance to therapy. While programmed cell death (PCD) shapes tumor-immune interactions, its mechanistic landscape in melanoma remains incompletely defined. This study aims to comprehensively characterize PCD-related signatures and their associations with tumor heterogeneity, prognosis, and immunotherapeutic outcomes.
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