A team from Tsukuba, Japan, has developed "tomoseqr," a software suite designed to visualize and analyze 3D gene expression patterns*.
This innovation addresses the challenges of understanding the spatial distribution of gene expression, crucial for developmental biology, disease research, and regenerative medicine. The method, known as RNA tomography, creates detailed 3D maps of gene expression within tissues.
RNA tomography involves preparing frozen tissue sections aligned along three orthogonal axes, followed by RNA sequencing. The resulting data is then superimposed to reconstruct a 3D model showing gene activity. Tomoseqr simplifies this process with a user-friendly interface, aiding in tissue morphology data creation and 3D gene expression model visualization.
The software's effectiveness was demonstrated using zebrafish, where it reproduced known gene expression patterns. Researchers also analyzed approximately 18,000 genes in planarians, organisms known for their regenerative abilities, identifying genes with spatial fluctuations potentially linked to wound healing and regeneration.
Tomoseqr has been adopted by Bioconductor, enhancing collaboration and resource sharing. Researchers believe tomoseqr can advance the understanding of genetic diseases and the development of targeted treatments. Its accessibility promotes interdisciplinary research, potentially leading to faster scientific breakthroughs.
* Matsuzawa R, Kawahara D, Kashima M, Hirata H, Ozaki H (2025) tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography. PLoS ONE 20(1)