ArticleNucleic acids research2017
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 47 citations in OpenAlex.
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events.International journal of molecular sciences · 2024Review
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- A transient intermediate RNA structure underlies the regulatory function of theRNA (New York, N.Y.) · 2023Article
- Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level.Nucleic acids research · 2023Article
- Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.Nature communications · 2023Article
- Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.Nature communications · 2022Article
- Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems.Communications biology · 2022Article
- Monitoring RNA dynamics in native transcriptional complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Preparation and Characterization of Internally Modified DNA Templates for Chemical Transcription Roadblocking.Bio-protocol · 2021Article
- Transcription complexes as RNA chaperones.Transcription · 2021Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Chemical roadblocking of DNA transcription for nascent RNA display.The Journal of biological chemistry · 2020Article
- Nucleobase mutants of a bacterial preQThe Journal of biological chemistry · 2020Article
- DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.Bioinformatics (Oxford, England) · 2019Article
- A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control.Nature chemical biology · 2019Article
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.