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Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli

Author

Listed:
  • Yichao Han

    (Washington University in St. Louis)

  • Wanji Li

    (Washington University in St. Louis)

  • Alden Filko

    (Washington University in St. Louis)

  • Jingyao Li

    (Washington University in St. Louis)

  • Fuzhong Zhang

    (Washington University in St. Louis
    Washington University in St. Louis
    Washington University in St. Louis)

Abstract

Elucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. We perform PPTP-seq for E. coli growing in three different media. The PPTP-seq data reveal robust steady-state promoter activities under most single TF knockdown conditions. PPTP-seq also enables identifications of, to the best of our knowledge, previously unknown TF autoregulatory responses and complex transcriptional control on one-carbon metabolism. We further find context-dependent promoter regulation by multiple TFs whose relative binding strengths determined promoter activities. Additionally, PPTP-seq reveals different promoter responses in different growth media, suggesting condition-specific gene regulation. Overall, PPTP-seq provides a powerful method to examine genome-wide transcriptional regulatory networks and can be potentially expanded to reveal gene expression responses to other genetic elements.

Suggested Citation

  • Yichao Han & Wanji Li & Alden Filko & Jingyao Li & Fuzhong Zhang, 2023. "Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41572-4
    DOI: 10.1038/s41467-023-41572-4
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    References listed on IDEAS

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    1. Jason Fontana & David Sparkman-Yager & Ian Faulkner & Ryan Cardiff & Cholpisit Kiattisewee & Aria Walls & Tommy G. Primo & Patrick C. Kinnunen & Hector Garcia Martin & Jesse G. Zalatan & James M. Caro, 2024. "Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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