High-depth spatial transcriptome analysis by photo-isolation chemistry

• Honda, Mizuki

  Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University; Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine

• Oki, Shinya

  Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University; Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine

• Kimura, Ryuichi

  Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine

• Harada, Akihito

  Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University

• Maehara, Kazumitsu

  Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University

• Tanaka, Kaori

  Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University

• Meno, Chikara

  Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University

• Ohkawa, Yasuyuki

  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.

Journal

• Nature Communications

  Nature Communications 12 2021

  Springer Nature

Keywords

• Reverse transcription polymerase chain reaction
• Transcriptomics

Details

• CRID: 1050852271184975360
• NII Article ID: 120007141968
• HANDLE: 2433/264604
• ISSN: 20411723
• Text Lang: en
• Article Type: journal article
• Data Source:
  • IRDB
  • CiNii Articles