Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

TLDR

Identifying transcript location in cells has been limited by technology and imaging capabilities, but expansion microscopy improves visualization by expanding tissues with a polymer‑ and hydrogel‑based system. ExSeq combines expansion microscopy with long‑read in situ RNA sequencing to precisely visualize transcripts, enabling detection of both novel and known RNAs, and provides spatial resolution, multiplexing, and an unbiased approach to uncover RNA localization and physiological roles. Unlike other in situ sequencing methods, ExSeq does not target sets of genes. Alon et al., Science, this issue p.

Abstract

Identifying transcript location in cells Identifying where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy has allowed for better visualization of small structures by expanding the tissues with a polymer- and hydrogel-based system. Alon et al. combined expansion microscopy with long-read in situ RNA sequencing, resulting in a more precise visualization of the location of specific transcripts. This method, termed “ExSeq” for expansion sequencing, was used to detect RNAs, both new transcripts and those previously demonstrated to localize to neuronal dendrites. Unlike other in situ sequencing methods, ExSeq does not target sets of genes. This technology thus unites spatial resolution, multiplexing, and an unbiased approach to reveal insights into RNA localization and its physiological roles in developing and active tissue. Science , this issue p. eaax2656