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STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity

Author

Listed:
  • Hiroaki Ohishi

    (Hiroshima University)

  • Seiru Shimada

    (Hiroshima University)

  • Satoshi Uchino

    (Tokyo Institute of Technology)

  • Jieru Li

    (Memorial Sloan Kettering Cancer Center)

  • Yuko Sato

    (Tokyo Institute of Technology
    Tokyo Institute of Technology)

  • Manabu Shintani

    (Hiroshima University)

  • Hitoshi Owada

    (Hiroshima University)

  • Yasuyuki Ohkawa

    (Kyushu University)

  • Alexandros Pertsinidis

    (Memorial Sloan Kettering Cancer Center)

  • Takashi Yamamoto

    (Hiroshima University)

  • Hiroshi Kimura

    (Tokyo Institute of Technology
    Tokyo Institute of Technology)

  • Hiroshi Ochiai

    (Hiroshima University)

Abstract

Transcription is a dynamic process. To detect the dynamic relationship among protein clusters of RNA polymerase II and coactivators, gene loci, and transcriptional activity, we insert an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site. By optimizing the individual elements, we develop the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNA polymerase II and BRD4 are observed proximal to the transcription start site of Nanog when the gene is transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 tend to be located near the transcription start site, even without transcription activity. Thus, the STREAMING-tag system reveals the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding transcriptional regulation in living cells.

Suggested Citation

  • Hiroaki Ohishi & Seiru Shimada & Satoshi Uchino & Jieru Li & Yuko Sato & Manabu Shintani & Hitoshi Owada & Yasuyuki Ohkawa & Alexandros Pertsinidis & Takashi Yamamoto & Hiroshi Kimura & Hiroshi Ochiai, 2022. "STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35286-2
    DOI: 10.1038/s41467-022-35286-2
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    References listed on IDEAS

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    1. Timothy A. Daugird & Yu Shi & Katie L. Holland & Hosein Rostamian & Zhe Liu & Luke D. Lavis & Joseph Rodriguez & Brian D. Strahl & Wesley R. Legant, 2024. "Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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