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 free to use 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.

Tsukuba, Japan—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.

Considerably, researchers 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.

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This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number JP22K15127 to MK, JP22K17992 to HO, and JST-Mirai Program Grant Number JPMJMI20G7 to HO.

Original Paper

Title of original paper:

tomoseqr: a Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography

Journal:

PLOS One

DOI:

10.1371/journal.pone.0311296

Correspondence

Associate Professor OZAKI Haruka
Center for Artificial Intelligence Research (C-AIR) / Institute of Medicine, University of Tsukuba

MATSUZAWA Ryosuke
Doctral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba

Associate Professor KASHIMA Makoto
Department of Biomolecular Science, Faculty of Science, Toho University

Related Link

Institute of Medicine
Center for Artificial Intelligence Research
Doctral Program in Medical Sciences