Enhancers are principal regulators that allow spatiotemporal tissue-specific control of gene expression. While mounting evidence suggests that enhancer-derived long noncoding RNAs (long ncRNAs), including enhancer RNAs (eRNAs), are an important component of enhancer function, their expression has not been broadly analyzed at a single cell level via imaging techniques. This protocol describes a method to image eRNA in single cells by in situ hybridization followed by tyramide signal amplification (TSA). The procedure can be multiplexed to simultaneously visualize both eRNA and protein-coding transcript at the site of transcriptional elongation, thereby permitting analysis of dynamics between the two transcript species in single cells. Our approach is not limited to eRNAs, but can be implemented on other transcripts.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-4035-6_3 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Profiling signaling mediators for cell-cell interactions and communications with microfluidics-based single-cell analysis tools.
iScience
January 2025
School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266113, China.
Cell-cell interactions and communication represent the fundamental cornerstone of cells' collaborative efforts in executing diverse biological processes. A profound understanding of how cells interface through various mediators is pivotal across a spectrum of biological systems. Recent strides in microfluidic technologies have significantly bolstered the precision and prowess in capturing and manipulating cells with exceptional spatial and temporal resolution.
View Article and Find Full Text PDFSingle-Cell RNA-Seq Uncovers Cellular Heterogeneity from Deep Fascia in Necrotizing Fasciitis Patients.
J Inflamm Res
January 2025
Department of Orthopaedic Surgery, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China.
Purpose: Necrotizing fasciitis (NF) is a scarce but potentially life-threatening infection. However, no research has reported the cellular heterogeneity in patients with NF. We aim to investigate the change of cells from deep fascia in response to NF by single-cell RNA-seq.
View Article and Find Full Text PDFGeneration and characterization of OX40-ligand fusion protein that agonizes OX40 on T-Lymphocytes.
Front Immunol
January 2025
Laboratory of Molecular Cell Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
OX40, a member of the tumor necrosis factor (TNF) receptor superfamily, is expressed on the surface of activated T cells. Upon interaction with its cognate ligand, OX40L, OX40 transmits costimulatory signals to antigen-primed T cells, promoting their activation, differentiation, and survivalprocesses essential for the establishment of adaptive immunity. Although the OX40-OX40L interaction has been extensively studied in the context of disease treatment, developing a substitute for the naturally expressed membrane-bound OX40L, particularly a multimerized OX40L trimers, that effectively regulates OX40-driven T cell responses remains a significant challenge.
View Article and Find Full Text PDFSingle-cell transcriptome analysis of medaka lymphocytes reveals absence of fully mature T cells in the thymus and the T-lineage commitment in the kidney.
Front Immunol
January 2025
Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan.
The cellular and molecular mechanisms underlying lymphocyte development are diverse among teleost species. Although recent scRNA-seq analyses of zebrafish hematopoietic cells have advanced our understanding of teleost hematopoiesis, comparative studies using another genetic model, medaka, which is evolutionarily distant among teleosts, is useful for understanding commonality and species-specificity in teleosts. In order to gain insight into how different molecular and cellular mechanisms of lymphocyte development in medaka and zebrafish, we established a () mutant medaka, which exhibited defects in V(D)J rearrangement of lymphocyte antigen receptor genes, accordingly lacking mature B and T cells.
View Article and Find Full Text PDFInfiltrating lipid-rich macrophage subpopulations identified as a regulator of increasing prostate size in human benign prostatic hyperplasia.
Front Immunol
January 2025
Division of Urology, Department of Surgery, Endeavor Health (formerly NorthShore University HealthSystem), Evanston, IL, United States.
Introduction: Macrophages exhibit marked phenotypic heterogeneity within and across disease states, with lipid metabolic reprogramming contributing to macrophage activation and heterogeneity. Chronic inflammation has been observed in human benign prostatic hyperplasia (BPH) tissues, however macrophage activation states and their contributions to this hyperplastic disease have not been defined. We postulated that a shift in macrophage phenotypes with increasing prostate size could involve metabolic alterations resulting in prostatic epithelial or stromal hyperplasia.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!