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2025/08/27

Yawako Kawaguchi won the Best Oral Presentation Award

Yawako W. Kawaguchi, a postdoctoral researcher in Molecular Life History Laboratory (Kuraku Lab), received the Best Oral Presentation Award at the 27th Annual Meeting of the Japanese Society for Evolutionary Studies, Japan. The meeting was held at Nagahama Institute of Bio-Science and Technology (Nagahama, Shiga Prefecture) from August 20 to 23, 2025.

▶ Awarded presentation title: Dynamics of Genome Structural Evolution in Vertebrates

▶ SESJ2025 (the 27th Annual Meeting of Society of Evolutionary Studies)

▶ Kuraku Group • Molecular Life History Laboratory

左から岩里コース長、南さん、飯田さん、鳩山さん

Yawako W. Kawaguchi

2025/08/25

TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data

Press release

Advanced Genomics Center

TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.

Shunichi Kosugi, Chikashi Terao 

Genome Biology 26, Article number: 246 (2025) DOI:10.1186/s13059-025-03718-z

Press release (In Japanese only)

Tandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed a computational tool, TRsv, to distinguish and detect TR-CNVs, SVs, and short indels using long reads. In evaluation with simulated and real datasets, TRsv outperformed existing tools for detection of TR-CNVs and indels, and performed equally well for detection of SVs. We demonstrated genome-wide detection of TR-CNVs, including variants associated with gene expression, disease, and quantitative traits, using 160 long-read whole genome sequencing data and TRsv.

Fig. 1: TRsv distinguishes different types of insertions observed within tandem repeat regions

Within tandem repeat (TR) regions, TR insertions consisting of the same repeat unit as the TR region (GCC in the example figure) are often observed, but insertions consisting of different repeat units (non-TR repeat insertions) and insertions without repeats (non-repeat insertions) are also frequently observed. TRsv distinguishes and identifies these different types of insertions.

Fig. 2: TRsv identifies TR-CNVs associated with expression of disease-associated genes

The correlations between the sizes of TR-CNVs and gene expression levels were tested using 6 x 104 TR-CNVs detected with TRsv and 160 long read whole genome sequencing data and 59 matched RNA-seq data. The associated genes were fractionated into 5 equal fractions from 5 to 1 in order of correlation strength (horizontal axis). The proportion of disease-associated genes in each fraction was calculated, and the ratio of the content of each fraction to the content of disease-associated genes in the fraction with correlation strength 1 (odds ratio) was plotted for each disease (vertical axis). As a control, odds ratios for a randomly selected set of 800 genes from 20,000 human genes are shown. The black lines on the bars indicate standard errors. This result indicates that the expression of genes involved in many diseases is regulated by TR-CNVs and suggest that disease development is affected by TR-CNVs.

2025/08/05

Inducible NMDA Receptor Knockdown Reveals a Maintenance Phase in Dendritic Refinement of Barrel Cortex Neurons　

Press release

Iwasato Group / Laboratory of Mammalian Neural Circuits

Inducible NMDA Receptor Knockdown Reveals a Maintenance Phase in Dendritic Refinement of Barrel Cortex Neurons

Ayane Nihashi, Naoki Nakagawa, Takuya Sato, Mariko Yamamoto, Luwei Wang, Rieko Ajima, Yumiko Saga, Yumiko Yoshimura, Masato T. Kanemaki, Takuji Iwasato*
* Corresponding Author

iScience (2025) DOI:10.1016/j.isci.2025.113229

Press release (In Japanese only)

The temporal mechanisms of activity-dependent dendritic patterning during postnatal development remain unclear because appropriate technology is lacking. Here, we demonstrate that the auxin-inducible degron 2 technology enables the rapid knockdown of target proteins at specific time points in the postnatal mouse brain. When N-methyl-D-aspartate-type glutamate receptor (NMDAR) depletion was induced from postnatal day (P)3, barrel cortex layer 4 spiny stellate neurons (barrel cells) failed to form strong asymmetry and a high tree-length variance in the dendritic patterns. Intriguingly, these unique dendritic patterns of barrel cells formed by P6 were rapidly canceled by NMDAR depletion from P6 but not from P12. NMDAR depletion from P6 also extinguished the existing Golgi apparatus’ lateral polarity. These results suggest that the barrel cells’ dendritic refinement involves not only formation but also “maintenance” of specific dendritic patterns during early postnatal development, in which NMDARs play a critical role, likely by regulating the Golgi polarity.


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