Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity sequence domains (LCDs), but how these LCDs drive transactivation remains unclear. We used live-cell single-molecule imaging to reveal that TF LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF LCD hubs stabilize DNA binding, recruit RNA polymerase II (RNA Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the RNA Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for drugs targeting gene regulatory interactions implicated in disease.
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http://dx.doi.org/10.1126/science.aar2555 | DOI Listing |
J Cell Biol
April 2025
Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France.
Retroviruses carry a genomic intron-containing RNA with a long structured 5'-untranslated region, which acts either as a genome encapsidated in the viral progeny or as an mRNA encoding the key structural protein, Gag. We developed a single-molecule microscopy approach to simultaneously visualize the viral mRNA and the nascent Gag protein during translation directly in the cell. We found that a minority of the RNA molecules serve as mRNA and that they are translated in a fast and efficient process.
View Article and Find Full Text PDFCharacterizing the movement of biomolecules in single cells quantitatively is essential to understanding fundamental biological mechanisms. RNA fluorescent in situ hybridization (RNA-FISH) is a technique for visualizing RNA in fixed cells using fluorescent probes. Automated processing of the resulting images is essential for large datasets.
View Article and Find Full Text PDFProtein Sci
February 2025
IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
Super-resolution microscopy has revolutionized biological imaging, enabling the visualization of structures at the nanometer length scale. Its application in live cells, however, has remained challenging. To address this, we adapted LIVE-PAINT, an approach we established in yeast, for application in live mammalian cells.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
Nanjing University, School of Chemistry and Chemical Engineering, 163 Xianlin Avenu, 210023, Nanjing, CHINA.
Glycans, unlike uniformly charged DNA and compositionally diverse peptides, are typically uncharged and exhibit rich stereoisomeric diversity in the glycosidic bonds between two monosaccharide units. This heterogeneity of charge and the structural complexity present significant challenges for accurate analysis. Herein, we developed a novel single-molecule oligosaccharide sensor, OmpF nanopore.
View Article and Find Full Text PDFSheng Wu Gong Cheng Xue Bao
January 2025
School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing 210023, Jiangsu, China.
Proteins are fundamental carriers as the structural elements and biochemically active entities responsible for catalysis, transport, and regulation. These functions are depending on the protein folding into precise three-dimensional structures, interacting with ligands, and conformational changes. This article reviews the recent progress of nanopores in single-molecule protein sensing, involving the identification of polypeptides and proteins, the conformation changes of protein folding, the molecular structure responsible to the pH of solutions, the molecular interactions, and protein sequencing.
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