MONTH

2024年9月

2024年9月22日
2024年9月22日

A protocol for DNA/RNA/IF-seqFISH image analysis has been published in Methods Mol. Biol.!

The image analysis protocol for DNA/RNA/IF-seqFISH has been published in Methods Mol. Biol. (Computational Methods for 3D Genome Analysis, edited by Ryuichi Nakato)! https://link.springer.com/protocol/10.1007/978-1-0716-4136-1_24#DOI Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH DataHiroaki Ohishi & Hiroshi Ochiai AbstractImaging-based spatial multi-omics technologies enable the analysis of higher-order genomic structures, gene transcription, and the localization of proteins and posttranslational modifications (PTMs) at the single-allele level. This allows for detailed observation of biological phenomena, including transcription machinery within cells and tissues. This chapter provides an in-depth explanation of the principles behind these technologies, focusing on DNA/RNA/immunofluorescence (IF) sequential fluorescence in situ hybridization (seqFISH). The chapter also offers a comprehensive, step-by-step image analysis protocol, covering aspects such as image preprocessing, spot detection, and data visualization. For practical use, complete Jupyter Notebook codes are available on GitHub (https://github.com/Ochiai-Lab/seqFISH_analysis).

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2024年9月12日
2024年9月12日

A collaborative study with the Mat Francois lab (Centenary Institute, The University of Sydney) has been published on bioRxiv!

This research focuses on the complex molecular mechanisms required for stem cells to self-renew, shedding light on the dynamics of the SOX2 transcription factor. Using single-molecule tracking technology combined with the STREAMING-tag transcriptional reporter system, we visualized in real-time how SOX2 clusters form at the Nanog gene locus and their relationship to transcription bursts in embryonic stem cells. The study reveals that SOX2 clustering occurs at different timings from transcription bursts, highlighting distinct roles for SOX2 at various stages of the transcription cycle. https://www.biorxiv.org/content/10.1101/2024.09.10.612363v1 Anti-phase clustering of regulatory factors shapes gene bursting Bitong Li, Yew Yan Wong, Neftali Flores-Rodriguez, Tara Davidson, Matthew S Graus, Valeriia Smialkovska, Hiroaki Ohishi, Angelika Feldmann, Hiroshi Ochiai, Mathias Francois AbstractThe ability of stem cells to divide and self-renew depends on a complex choreography of molecular events that maintain the transcriptional oscillation of pluripotency genes. Only a handful of transcription factors (TFs) are necessary to preserve […]