ArticleProceedings of the National Academy of Sciences of the United States of America2016
Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Global kinetic mechanism describing single nucleotide incorporation for RNA polymerase I reveals fast UMP incorporation.Biophysical chemistry · 2024Article
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes.FEMS microbiology reviews · 2024Review
- An Improved Method for Eliminating or Creating Intragenic Bacterial Promoters.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- Structural and mechanistic basis of σ-dependent transcriptional pausing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans.Microbiology spectrum · 2022Article
- Methylation Motifs in Promoter Sequences May Contribute to the Maintenance of a ConservedMicroorganisms · 2021Article
- RNA polymerase spoiled for choice as transcription begins.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Promoter-sequence determinants and structural basis of primer-dependent transcription initiation inProceedings 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
- Transcription closed and open complex formation coordinate expression of genes with a shared promoter region.Journal of the Royal Society, Interface · 2019Article
- MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.Genome biology · 2019Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- Application of Biolayer Interferometry (BLI) for Studying Protein-Protein Interactions in Transcription.Journal of visualized experiments : JoVE · 2019Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
- Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli.Biochemistry · 2019Article
- Promoter RNA sequencing (PRSeq) for the massive and quantitative promoter analysis in vitro.Scientific reports · 2019Article
- Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.Nature communications · 2018Article
- Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example.The Journal of chemical physics · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein-DNA interactions with the downstream part of the nontemplate strand of the transcription bubble ("core recognition element," CRE). Here, we investigated whether sequence-specific RNAP-CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP-CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP-CRE interactions on TSS selection in vitro and in vivo for a library of 4(7) (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP-CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5' merodiploid native-elongating-transcript sequencing, 5' mNET-seq, we assessed effects of RNAP-CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP-CRE interactions determine TSS selection. Our findings establish RNAP-CRE interactions are a functional determinant of TSS selection. We propose that RNAP-CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).
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