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

Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Jieru Li, Yuko Sato, Manabu Shintani, Hitoshi Owada, Yasuyuki Ohkawa, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura () and Hiroshi Ochiai ()
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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
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
Hiroshi Ochiai: Hiroshima University

Nature Communications, 2022, vol. 13, issue 1, 1-19

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-35286-2

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