ArticleMolecular cell2015
Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.
Article in Molecular cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Promoter contacts by TFB and TFEα during archaeal transcription initiation.Transcription · 2026Article
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin.Nucleic acids research · 2024Article
- Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes.FEMS microbiology reviews · 2024Review
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Structural and mechanistic basis of σ-dependent transcriptional pausing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural and mechanistic basis of reiterative transcription initiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Use of an unnatural amino acid to map helicase/DNA interfaces via photoactivated crosslinking.Methods in enzymology · 2022Article
- XACT-seq: A photocrosslinking-based technique for detection of the RNA polymerase active-center position relative to DNA inSTAR protocols · 2021Article
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Pathway of Hsp70 interactions at the ribosome.Nature communications · 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
- Diverse and unified mechanisms of transcription initiation in bacteria.Nature reviews. Microbiology · 2021Review
- XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.Molecular cell · 2020Article
- Stepwise Promoter Melting by Bacterial RNA Polymerase.Molecular cell · 2020Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa.Molecular microbiology · 2019Article
- Function of a strand-separation pin element in the PriA DNA replication restart helicase.The Journal of biological chemistry · 2019Article
- Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA.Nucleic acids research · 2018Article
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7 authors.
Funding
Abstract
RNA polymerase binds tightly to DNA to recognize promoters with high specificity but then releases these contacts during the initial stage of transcription. We report a site-specific crosslinking approach to map the DNA path in bacterial transcription intermediates at amino acid and nucleotide resolution. After validating the approach by showing that the DNA path in open complexes (RPO) is the same as in high-resolution X-ray structures, we define the path following substrate addition in "scrunched" complexes (RPITC). The DNA bulges that form within the transcription bubble in RPITC are positioned differently on the two strands. Our data suggest that the non-template strand bulge is extruded into solvent in complexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand tunnel, exerting stress on interactions between the β flap, β' clamp, and σ3.2. We propose that this stress contributes to σ3.2 displacement from the RNA exit channel, facilitating promoter escape.
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