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

Yichao Han, Wanji Li, Alden Filko, Jingyao Li and Fuzhong Zhang ()
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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

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-41572-4

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