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Harvard scientists have unveiled a new technique called expansion in situ genome sequencing (ExIGS) that combines existing in situ genome sequencing (IGS) with expansion microscopy (ExM). The innovation allowed researchers to link nucleus abnormalities to alterations in gene regulation within a single cell with precise measurements of DNA-protein interactions at the nanometer scale.

Microscopy is an essential tool for characterizing cell function. Imaging methods are limited by the diffraction limit of optical microscopy, preventing reliable measurement at the scale of DNA-protein interactions.

Expansion microscopy is a clever technique that overcomes the problem of seeing things hidden by the diffraction limit by making them bigger. By embedding the sample in a swellable polymer gel and expanding it, researchers can get superresolution imaging of spatial organizations within cells using conventional microscopes.

In ExIGS, expansion microscopy is integrated with in situ genome sequencing to simultaneously sequence genomic DNA and image nuclear proteins at nanoscale resolution within single cells.

The process begins with embedding fixed cells in a polyacrylate-based gel, which serves as a scaffold for expansion. Genomic DNA and proteins are chemically linked to the gel using DNA oligo hooks that bind to DNA hairpins attached to genomic fragments and proteins. These hooks contain chemical groups that form covalent bonds with the gel during polymerization.

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