New technique offers bigger and better window into RNA activity in complex tissue

Amazing stuff!

"For the first time, scientists can view RNA molecules directly inside cells and tissue in minute detail and across the entire human genome concurrently, thanks to new technology created by a Yale research team.

The technique, known as Reverse-padlock Amplicon Encoding Fluorescence In Situ Hybridization (RAEFISH), solves a trade-off that researchers have long been forced to make: detail versus scope. Earlier tools required researchers to choose between seeing either a limited number of genes in high detail or seeing many genes but with a limited level of detail regarding their transcripts’ (RNAs’) location and how they interacted. ..."

From the highlights and abstract:

"Highlights

• RAEFISH enables genome-scale spatial transcriptome imaging with high resolution

• An efficient and robust probing and readout scheme that covers long and short transcripts

• RAEFISH maps spatially dependent transcriptomes in diverse cell and tissue contexts

• RAEFISH enables direct readout of gRNAs in image-based, high-content CRISPR screens

Summary

Recent breakthroughs in spatial transcriptomics technologies have enhanced our understanding of diverse cellular identities, spatial organizations, and functions. Yet existing spatial transcriptomics tools are still limited in either transcriptomic coverage or spatial resolution, hindering unbiased, hypothesis-free transcriptomic analyses at high spatial resolution.

Here, we develop reverse-padlock amplicon-encoding fluorescence in situ hybridization (RAEFISH), an image-based spatial transcriptomics method with whole-genome coverage and single-molecule resolution in intact tissues.

We demonstrate the spatial profiling of transcripts from 23,000 human or 22,000 mouse genes in single cells and tissue sections. 

Our analyses reveal transcript-specific subcellular localization, cell-type-specific and cell-type-invariant zonation-dependent transcriptomes, and gene programs underlying preferential cell-cell interactions.

Finally, we further develop our technology for the direct spatial readout of guide RNAs (gRNAs) in an image-based, high-content CRISPR screen.

Overall, these developments offer a broadly applicable technology that enables high-coverage, high-resolution spatial profiling of both long and short, native and engineered RNAs in many biomedical contexts."

New technique offers bigger and better window into RNA activity in complex tissue | Yale News "Yale researchers have created a new tool that will enable researchers to better view how RNA molecules function in tissue space."

Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution (open access)

Figure 1 RAEFISH enables genome-wide spatial transcriptomic profiling at single-molecule resolution

Figure 5 RAEFISH uncovers characteristics of spatial transcriptomic architectures and cell-cell interactions in mouse placenta