ArticleBiochemistry2014
Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes.FEMS microbiology reviews · 2024Review
- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase.Nucleic acids research · 2023Article
- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates forbioRxiv : the preprint server for biology · 2023Article
- Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions withFrontiers in molecular biosciences · 2023Article
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Promoter Architecture Differences amongmSystems · 2021Article
- Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter.Journal of bacteriology · 2021Article
- Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor.MicrobiologyOpen · 2020Article
- DNA template sequence control of bacterial RNA polymerase escape from the promoter.Nucleic acids research · 2018Article
- Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.Molecular cell · 2015Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Base flipping in open complex formation at bacterial promoters.Biomolecules · 2015Review
- Differential role of base pairs on gal promoters strength.Journal of molecular biology · 2015Article
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2 authors.
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Abstract
Promoter melting by bacterial RNA polymerase is a key step in transcription initiation. We used a next generation sequencing (NGS) based approach to analyze in parallel promoter melting of all 4096 sequence variants of the 6 bp -10 promoter element. We used NGS read count for each sequence of a promoter library containing a randomized -10 sequence as an observable to determine relative enrichment of -10 element sequence variants at different time points of the promoter melting reaction. The analysis reinforced the dominating role of consensus bases at positions -11 and -7, demonstrated an enhanced preference for A at -11 among sequences exhibiting the fastest melting kinetics, and showed higher overall importance of the T at -7 compared to the A at -11 for efficient promoter melting. Sequences lacking the consensus bases at -7 or -11 could still melt fast if they contained compensatory base patterns at other positions. We observed a significant correlation between the duplex melting energy of -10 element and the kinetics of promoter melting that became more pronounced when the dominating base-specific interactions with RNAP were diminished. These observations indicate that promoter melting kinetics is determined by a combination of base-specific effects/interactions and sequence-dependent stability of DNA duplex with the former playing a dominating role. Our data show that NGS can provide a reliable, quantitative readout for a highly parallel analysis of DNA template sequence dependence of activities of proteins that bind or operate on a DNA template.
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