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RIViT-seq enables systematic identification of regulons of transcriptional machineries

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  • Hiroshi Otani

    (Lawrence Berkeley National Laboratory
    Lawrence Berkeley National Laboratory)

  • Nigel J. Mouncey

    (Lawrence Berkeley National Laboratory
    Lawrence Berkeley National Laboratory)

Abstract

Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.

Suggested Citation

  • Hiroshi Otani & Nigel J. Mouncey, 2022. "RIViT-seq enables systematic identification of regulons of transcriptional machineries," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31191-w
    DOI: 10.1038/s41467-022-31191-w
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    1. Yujin Jeong & Ji-Nu Kim & Min Woo Kim & Giselda Bucca & Suhyung Cho & Yeo Joon Yoon & Byung-Gee Kim & Jung-Hye Roe & Sun Chang Kim & Colin P. Smith & Byung-Kwan Cho, 2016. "The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)," Nature Communications, Nature, vol. 7(1), pages 1-11, September.
    2. S. D. Bentley & K. F. Chater & A.-M. Cerdeño-Tárraga & G. L. Challis & N. R. Thomson & K. D. James & D. E. Harris & M. A. Quail & H. Kieser & D. Harper & A. Bateman & S. Brown & G. Chandra & C. W. Che, 2002. "Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)," Nature, Nature, vol. 417(6885), pages 141-147, May.
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