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Fluorescence in situ hybridization (FISH) is a method to localize nucleic acid targets in fixed cells for cytogenetic or gene expression studies. It relies on fluorophore-labelled DNA or RNA probes to count and localize specific genes or regions along chromosomes, detect mutations, or analyze temporal and spatial gene expression.
Wei et al. perform spatial transcriptomic profiling on synovial tissue biopsy samples from individuals with recent-onset rheumatoid arthritis, finding TGFβ signaling and fibrogenic fibroblast activation drive a treatment-refractory tissue phenotype.
Many spatial RNA monitoring assays can be hindered by barriers that limit short-transcript detection and mask cellular diversity. Here, the authors show TDDN-FISH – Tetrahedral DNA Dendritic Nanostructure–enhanced Fluorescence In Situ Hybridization. This is a rapid, enzyme-free method that uses self-assembling DNA nanostructures, thus accelerating RNA detection.
Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in both iST and live imaging experiments.
Methods for analysing spatial gene expression in plants have been limited in their throughput. Now the imaging method PHYTOMap allows the spatial expression of dozens of genes to be analysed in three-dimensional whole-mount tissue at single-cell resolution, in a transgene-free manner.
An approach combining in situ tagmentation and transcription with MERFISH enables spatial profiling of the epigenome in tissues with single-cell resolution.
Researchers use electric fields to transfer RNA from a tissue sample onto a surface for subsequent fluorescence in situ hybridization-based profiling of transcriptomes at the single-cell level.
Composite in situ imaging leverages gene expression patterns to improve the efficiency of highly multiplexed single-molecule FISH measurements by orders of magnitude.
A study in Cell presents a new approach that increases resolution and throughput compared with existing imaging methods and provides insights into the relationship between transcription and the 3D genome.
