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User-friendly software enables easy estimation of 3D gene expression distribution

Researchers at University of Tsukuba have developed "tomoseqr"—a new software tool that enables easy estimation of the three-dimensional (3D) spatial distribution of gene expression. Tomoseqr is and has been integrated into Bioconductor—a widely used international platform for life science software. This innovative tool will potentially help researchers identify key genes involved in organism development, disease mechanisms, and regenerative biology. The study is in the journal PLOS ONE.

Understanding the 3D spatial distribution of gene expression—in which a gene is active or inactive within biological tissue—is essential for uncovering gene functions. One method for estimating this distribution is RNA tomography, involving preparing frozen tissue sections along three orthogonal axes, performing RNA sequencing (gene expression analysis) on each section, and superimposing the expression data to reconstruct a 3D gene expression map. However, processing this data requires advanced programming skills, making it challenging for researchers without computational expertise.

Researchers have now developed tomoseqr—a user-friendly software designed to estimate 3D spatial gene expression distribution. Tomoseqr features an intuitive graphical user interface that simplifies the creation of tissue morphology data and enables visualization of 3D gene expression models. The software is freely available, making this complex analysis accessible to a broad research community.

By applying tomoseqr to gene expression data from zebrafish, researchers successfully reproduced known gene expression patterns, confirming the accuracy of the software. Moreover, they analyzed approximately 18,000 genes in planarians—a model organism known for its regenerative capabilities—and mapped the 3D spatial distribution of each gene expression. This data-driven approach also identified genes with remarkable spatial fluctuations, suggesting their potential roles in biological functions such as tissue regeneration.

Notably, tomoseqr has been adopted by Bioconductor, a globally recognized platform for life science software, allowing researchers across various fields to leverage its capabilities for 3D gene expression analysis. This tool will potentially drive advancements in developmental biology, disease research, and regenerative medicine, expanding opportunities for scientific discovery.