ArticleNature2013
Genomic organization of human transcription initiation complexes.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 41 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed, 80 citations in OpenAlex.
- Genome-wide analysis of TFIIB's role in termination of transcription.Research square · 2024Article
- Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle.Biochimica et biophysica acta. Proteins and proteomics · 2024Article
- Article
- Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes.Computational and structural biotechnology journal · 2023Article
- Beyond the canonical role of TFIIB in eukaryotic transcription.Current genetics · 2022Review
- Inferring primase-DNA specific recognition using a data driven approach.Nucleic acids research · 2021Article
- Systematic interrogation of human promoters.Genome research · 2019Article
- Encoding activities of non-coding RNAs.Theranostics · 2018Review
- Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription.The EMBO journal · 2017Article
- Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.Nucleic acids research · 2017Article
- Genome annotation for clinical genomic diagnostics: strengths and weaknesses.Genome medicine · 2017Review
- Article
- Article
- Identifying transcription start sites and active enhancer elements using BruUV-seq.Scientific reports · 2015Article
- cncRNAs: Bi-functional RNAs with protein coding and non-coding functions.Seminars in cell & developmental biology · 2015Review
- Perspectives on Unidirectional versus Divergent Transcription.Molecular cell · 2015Article
- Gene looping facilitates TFIIH kinase-mediated termination of transcription.Scientific reports · 2015Article
- Article
- ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.Nature biotechnology · 2015Article
- Getting up to speed with transcription elongation by RNA polymerase II.Nature reviews. Molecular cell biology · 2015Review
Corrections and comments
- Retraction · 2014-09-18Error in Methods · Unreliable Results and/or Conclusions ·
- Commented on by
- Retracted
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The human genome is pervasively transcribed, yet only a small fraction is coding. Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcription factor IIB (TFIIB) and RNA polymerase (Pol) II. Using ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing), we identify approximately 160,000 transcription initiation complexes across the human K562 genome, and more in other cancer genomes. Only about 5% associate with messenger RNA genes. The remainder associates with non-polyadenylated non-coding transcription. Regardless, Pol II moves into a transcriptionally paused state, and TBP and TFIIB remain at the promoter. Remarkably, the vast majority of locations contain the four core promoter elements- upstream TFIIB recognition element (BREu), TATA, downstream TFIIB recognition element (BREd), and initiator element (INR)-in constrained positions. All but the INR also reside at Pol III promoters, where TBP makes similar contacts. This comprehensive and high-resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events from yeast to humans at Pol II/III TATA-containing/TATA-less coding and non-coding genes.
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What OpenQuestion holds
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.