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High-depth spatial transcriptome analysis by photo-isolation chemistry

Author

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  • Mizuki Honda

    (Graduate School of Medical Sciences, Kyushu University
    Kyoto University Graduate School of Medicine)

  • Shinya Oki

    (Graduate School of Medical Sciences, Kyushu University
    Kyoto University Graduate School of Medicine)

  • Ryuichi Kimura

    (Kyoto University Graduate School of Medicine)

  • Akihito Harada

    (Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University)

  • Kazumitsu Maehara

    (Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University)

  • Kaori Tanaka

    (Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University)

  • Chikara Meno

    (Graduate School of Medical Sciences, Kyushu University)

  • Yasuyuki Ohkawa

    (Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University)

Abstract

In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions.

Suggested Citation

  • Mizuki Honda & Shinya Oki & Ryuichi Kimura & Akihito Harada & Kazumitsu Maehara & Kaori Tanaka & Chikara Meno & Yasuyuki Ohkawa, 2021. "High-depth spatial transcriptome analysis by photo-isolation chemistry," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24691-8
    DOI: 10.1038/s41467-021-24691-8
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    Cited by:

    1. Misa Minegishi & Takahiro Kuchimaru & Kaori Nishikawa & Takayuki Isagawa & Satoshi Iwano & Kei Iida & Hiromasa Hara & Shizuka Miura & Marika Sato & Shigeaki Watanabe & Akifumi Shiomi & Yo Mabuchi & Hi, 2023. "Secretory GFP reconstitution labeling of neighboring cells interrogates cell–cell interactions in metastatic niches," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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