ArticleGenome research2017
Genome-wide uniformity of human 'open' pre-initiation complexes.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Mechanisms of MCM2-7 helicase activation and initial DNA melting at near base-pair resolution.Nature communications · 2026Article
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- PEGR: a flexible management platform for reproducible epigenomic and genomic research.Genome biology · 2022Article
- Promoter-proximal elongation regulates transcription in archaea.Nature communications · 2021Article
- Collaboration through chromatin: motors of transcription and chromatin structure.Journal of molecular biology · 2021Review
- Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces.Cell reports · 2021Article
- Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.Genome biology · 2020Article
- TFIID Enables RNA Polymerase II Promoter-Proximal Pausing.Molecular cell · 2020Article
- Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions.Nature communications · 2020Article
- R-Loops Promote Antisense Transcription across the Mammalian Genome.Molecular cell · 2019Article
- Determinants of promoter and enhancer transcription directionality in metazoans.Nature communications · 2018Article
- Eukaryotic core promoters and the functional basis of transcription initiation.Nature reviews. Molecular cell biology · 2018Review
- Molecular mechanisms driving transcriptional stress responses.Nature reviews. Genetics · 2018Review
- Insights from resolving protein-DNA interactions at near base-pair resolution.Briefings in functional genomics · 2018Review
- The punctilious RNA polymerase II core promoter.Genes & development · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5' ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome.
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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.