Science Tokyo creates mouse model for visualizing gene transcription sites

A research group led by Professor Hiroshi Kimura of the Cell Biology Center, Institute of Integrated Research, Institute of Science Tokyo, Professor Yoshihiro Baba and Professor Yasuyuki Ohkawa of the Medical Institute of Bioregulation at Kyushu University, and Professor Masahito Ikawa of the Research Institute for Microbial Diseases at the University of Osaka announced on September 25 that they have developed a new mouse model that enables observation of transcription sites in living cells. They found that the locations and movements of transcription sites vary considerably depending on tissue type and cell differentiation state. The findings are expected to advance understanding of gene transcription regulation mechanisms and contribute to drug discovery and therapeutic development. The results were published in the Journal of Molecular Biology on August 13.

Cell characteristics are determined by gene function. For genes to function, they must undergo "transcription," a process in which RNA is synthesized using the gene as a template. This reaction is carried out by RNA polymerase II, an enzyme.

While numerous RNA polymerase II molecules exist within cells, only about 20% are actually engaged in transcription. Because RNA polymerase II undergoing transcription is phosphorylated, it can be specifically detected using antibodies that bind specifically to phosphorylated forms. Conventional methods require immunostaining for antibody detection, necessitating chemical fixation of tissues and cells.

The research group had previously succeeded in revealing the dynamics of transcription sites in human cultured cells by developing intracellular antibodies capable of detecting phosphorylated RNA polymerase II with fluorescence in living cells.

In this study, the research group created mice that express this fluorescent antibody throughout the body.

When cells from various tissues of these mice were observed using super-resolution fluorescence microscopy, the researchers successfully visualized sites where genes were actively being transcribed in real time. Transcription sites numbered from a few hundred to thousands.

In immune cells within the spleen, including B cells that produce antibodies, T cells, and neutrophils that phagocytose bacteria, the number of transcription sites varied considerably depending on cell type.

Examining the movement of transcription sites revealed that they were relatively immobile in liver and pancreatic cells but moved quite actively in fibroblast cells isolated from embryos. This is thought to reflect the fact that in proliferating cells, the genes being used change constantly and chromatin (a higher-order structure consisting of nucleosomes, which are composed of approximately 150 base pairs of DNA and histone proteins) remains relatively relaxed, whereas in differentiated cells, the genes used are limited, resulting in overall chromatin condensation.

Additionally, in testes of male mice, changes in transcription status were observed as spermatogenesis progressed.

Combined with aging and disease model mice, this approach is expected to find applications in understanding disease onset mechanisms and evaluating drug efficacy.

Kimura commented: "We can now observe in real time where genetic information is transcribed from DNA to RNA in living tissues. While this report focuses on mice, the approach is fundamentally applicable to any organism. A challenge is that we cannot identify which genes are being transcribed, but moving forward, we aim to address this issue while advancing our understanding of mechanisms underlying gene expression during development, differentiation, and responses to stimuli. I am grateful to the many collaborators involved in this research and for the research funding support."

Journal Information
Publication: Journal of Molecular Biology
Title: Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues
DOI: 10.1016/j.jmb.2025.169395