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. 2022 Sep 2;13:5159. doi: 10.1038/s41467-022-32829-5

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — A Model development combined promoter design, barcoded oligopool synthesis, library cloning & culturing, and next-generation sequencing to measure the transcription start site distribution and transcription rate of each promoter variant. B The interaction strengths between RNAP/σ⁷⁰ and promoter DNA control transcription initiation rates. 14206 promoter variants were designed to quantify how sequence modifications affect each interaction. Sequence design criteria are shown. C The frequencies of observed transcription start sites are shown for each set of promoter variants. The star indicates the predominant start site. The inset schematic shows the system architecture, the locations of the promoter and barcode variants, and the cDNA architecture after library preparation. D The transcription rates’ dynamic ranges are shown for each set of promoter variants, considering only the predominant start site. Con: UP element promoter variants with consensus hexamers. Anti: UP element promoter variants with anti-consensus hexamers. Data are provided in Supplementary Data 1.