ArticleMolecular cell2015
Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.
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 55 papers.
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Who cites it
55 citing papers in PubMed, 81 citations in OpenAlex.
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- Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria.Nucleic acids research · 2025Article
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.Nucleic acids research · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis by Taq polymerase involves nick-translation.Scientific reports · 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
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Structural and mechanistic basis of reiterative transcription initiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- XACT-seq: A photocrosslinking-based technique for detection of the RNA polymerase active-center position relative to DNA inSTAR protocols · 2021Article
- Quantitative Control for Stoichiometric Protein Synthesis.Annual review of microbiology · 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
- Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.Nature communications · 2021Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.Nature communications · 2021Article
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8 authors at 2 institutions in 2 countries.
Funding
Abstract
We report the development of a next-generation sequencing-based technology that entails construction of a DNA library comprising up to at least 4(7) (∼ 16,000) barcoded sequences, production of RNA transcripts, and analysis of transcript ends and transcript yields (massively systematic transcript end readout, "MASTER"). Using MASTER, we define full inventories of transcription start sites ("TSSomes") of Escherichia coli RNA polymerase for initiation at a consensus core promoter in vitro and in vivo; we define the TSS-region DNA sequence determinants for TSS selection, reiterative initiation ("slippage synthesis"), and transcript yield; and we define effects of DNA topology and NTP concentration. The results reveal that slippage synthesis occurs from the majority of TSS-region DNA sequences and that TSS-region DNA sequences have profound, up to 100-fold, effects on transcript yield. The results further reveal that TSSomes depend on DNA topology, consistent with the proposal that TSS selection involves transcription-bubble expansion ("scrunching") and transcription-bubble contraction ("anti-scrunching").
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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.