Real-time single-molecule imaging of transcriptional regulatory networks in living cells

A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin

In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion. Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts. Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.

Lanthanide-Doped Upconversion Nanoparticles for Single-Particle Imaging

Lanthanide-doped upconversion nanoparticles (UCNPs) have recently demonstrated great promise in single-particle imaging (SPI) due to their exceptional photostability and minimal background fluorescence. However, their limited brightness has posed a significant barrier to wider adoption in SPI applications. This review highlights recent advances in applying UCNPs for SPI, focusing on strategies to enhance their brightness and reduce quenching effects in aqueous environments. Additionally, it summarizes the latest progress in using UCNPs for single-particle tracking and super-resolution imaging, underscoring their potential in biomedical research. Finally, the review outlines current challenges and future directions in this field.

Single-molecule live-cell RNA imaging with CRISPR-Csm

Understanding the diverse dynamic behaviors of individual RNA molecules in single cells requires visualizing them at high resolution in real time. However, single-molecule live-cell imaging of unmodified endogenous RNA has not yet been achieved in a generalizable manner. Here, we present single-molecule live-cell fluorescence in situ hybridization (smLiveFISH), a robust approach that combines the programmable RNA-guided, RNA-targeting CRISPR-Csm complex with multiplexed guide RNAs for direct and efficient visualization of single RNA molecules in a range of cell types, including primary cells. Using smLiveFISH, we track individual native NOTCH2 and MAP1B transcripts in living cells and identify two distinct localization mechanisms including the cotranslational translocation of NOTCH2 mRNA at the endoplasmic reticulum and directional transport of MAP1B mRNA toward the cell periphery. This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.

Aberrant pre-mRNA processing in cancer

Dysregulation of the flow of information from genomic DNA to RNA to protein occurs within all cancer types. In this review, we described the current state of understanding of how RNA processing is dysregulated in cancer with a focus on mutations in the RNA splicing factor machinery that are highly prevalent in hematologic malignancies. We discuss the downstream effects of these mutations highlighting both individual genes as well as common pathways that they perturb. We highlight examples of how alterations in RNA processing have been harnessed for therapeutic intent as well as to promote the selective toxicity of cancer cells.

Visualizing DNA/RNA, Proteins, and Small Molecule Metabolites within Live Cells

Live cell imaging is essential for obtaining spatial and temporal insights into dynamic molecular events within heterogeneous individual cells, in situ intracellular networks, and in vivo organisms. Molecular tracking in live cells is also a critical and general requirement for studying dynamic physiological processes in cell biology, cancer, developmental biology, and neuroscience. Alongside this context, this review provides a comprehensive overview of recent research progress in live-cell imaging of RNAs, DNAs, proteins, and small-molecule metabolites, as well as their applications in molecular diagnosis, immunodiagnosis, and biochemical diagnosis. A series of advanced live-cell imaging techniques have been introduced and summarized, including high-precision live-cell imaging, high-resolution imaging, low-abundance imaging, multidimensional imaging, multipath imaging, rapid imaging, and computationally driven live-cell imaging methods, all of which offer valuable insights for disease prevention, diagnosis, and treatment. This review article also addresses the current challenges, potential solutions, and future development prospects in this field.

Fast and Selective Cysteine Conjugation Using para-Quinone Methides

An efficient and selective method for cysteine conjugation utilizing para-quinone methides (p-QMs) was developed. p-QM labeling exhibits high specificity toward the cysteine residue, as evidenced by its reactivity with various amino acid derivatives, peptides, and proteins. Notably, the p-QM-cysteine reactions display robust kinetics with rate constants up to 1.67 × 104 M-1·s-1. Furthermore, p-QM conjugation enables us to attach a fluorescent probe to a HER2 nanobody, resulting in selective labeling of HER2-positive SK-BR-3 cells.

Near-Infrared Emissive π-Conjugated Oligomer Nanoparticles for Three- and Four-Photon Deep-Brain Microscopic Imaging Beyond 1700 nm Excitation

High-resolution visualization of the deep brain is still a challenging and very significant issue. Multiphoton microscopy (MPM) holds great promise for high-spatiotemporal deep-tissue imaging under NIR-III and NIR-IV excitation. However, thus far, their applications have been seriously restricted by the scarcity of efficient organic probes. Herein, we designed and synthesized two donor-acceptor-donor-type conjugated small molecules (TNT and TNS) for in vivo mouse deep-brain imaging with three- and four-photon microscopy under 1700 and 2200 nm excitation. With a selenium (Se) substitution, we synthesized two conjugated small molecules to promote their emission into the deep near-infrared region with high quantum yields of 55% and 20% in THF solvent, respectively, and their water-dispersive nanoparticles have relatively large absorption cross-sections in the 1700 and 2200 nm windows, respectively, with good biosafety. With these superiorities, these organic NPs achieve high-resolution deep-brain imaging via three-photon and four-photon microscopy with excitation at 1700 and 2200 nm windows, and 1620 μm deep in the brain vasculature can be visualized in vivo. This study demonstrates the efficiency of NIR-emissive conjugated small molecules for high-performance MPM imaging in the NIR-III and NIR-IV window and provides a route for the future design of organic MPM probes.

Single-molecule live-cell RNA imaging with CRISPR-Csm

High-resolution, real-time imaging of RNA is essential for understanding the diverse, dynamic behaviors of individual RNA molecules in single cells. However, single-molecule live-cell imaging of unmodified endogenous RNA has not yet been achieved. Here, we present single-molecule live-cell fluorescence in situ hybridization (smLiveFISH), a robust approach that combines the programmable RNA-guided, RNA-targeting CRISPR-Csm complex with multiplexed guide RNAs for efficient, direct visualization of single RNA molecules in a range of cell types, including primary cells. Using smLiveFISH, we tracked individual endogenous NOTCH2 and MAP1B mRNA transcripts in living cells and identified two distinct localization mechanisms: co-translational translocation of NOTCH2 mRNA at the endoplasmic reticulum, and directional transport of MAP1B mRNA toward the cell periphery. This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.

Chromatin structure and dynamics: one nucleosome at a time

Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.

Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle

Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.