2023-09-19 ワシントン大学セントルイス校
◆この技術により、数百の転写因子(TFs)が働く数千のプロモーターに対する遺伝子制御を1つの実験で調査し、約200,000のTF-プロモーター相互作用を明らかにできるようになりました。
◆これにより、バクテリアなどの単純な生物の遺伝子調節ネットワークを包括的に理解でき、バイオテクノロジーや医学などの分野に革命をもたらす可能性があります。
<関連情報>
- https://engineering.wustl.edu/news/2023/Unveiling-the-hidden-world-of-gene-regulation.html
- https://www.nature.com/articles/s41467-023-41572-4
CRISPRによる制御因子の改変に対するゲノムワイドなプロモーター応答から、大腸菌における制御ネットワークが明らかになる Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Yichao Han,Wanji Li,Alden Filko,Jingyao Li & Fuzhong Zhang
Nature Communications Published:16 September 2023
DOI:https://doi.org/10.1038/s41467-023-41572-4
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.
