ArticleNature2012
Genome-wide structure and organization of eukaryotic pre-initiation complexes.
Article in Nature, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 349 papers, 1 of them a synthesis that pooled it.
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
349 citing papers in PubMed, 1 synthesis or guideline pooled it, 540 citations in OpenAlex.
- Pooled it
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- Sequence-dependent binding modes of INO80 control +1 nucleosome positioning.bioRxiv : the preprint server for biology · 2026Article
- Molecular Acrobats: How CHD Remodelers Shape the Genetic Playground to License Cell Identity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Genetic dissection of transcription start site selection by RNA polymerase II in Saccharomyces cerevisiae.Genetics · 2026Article
- Nucleosome positioning shapes cryptic antisense transcription.PLoS genetics · 2026Article
- Genomic and structural insights into TATA-Binding protein from cestodes.Transcription · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo.Research square · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differencesbioRxiv : the preprint server for biology · 2025Article
- H2A.Z and H3:K56Q Affect Transcription Through Chromatin and Yeast FACT-Dependent Nucleosome Unfolding.International journal of molecular sciences · 2025Article
- Genetic dissection of transcription start site selection by RNA Polymerase II inbioRxiv : the preprint server for biology · 2025Article
- Mot1 regulation of promoter binding by TBP varies with stress and gene expression levels independently of coactivator dependence.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dual roles of DEAD-box RNA helicase Brr2 in genome stability regulation.Nature communications · 2025Article
- Refined mechanism of promoter nucleosome-depleted regions resetting after replication.Nucleic acids research · 2025Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- H2A.Z deposition by the SWR complex is stimulated by polyadenine DNA sequences in nucleosomes.PLoS biology · 2025Article
289 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within promoters and excluded from coding regions. Exonuclease patterns were in agreement with crystallographic models of the PIC, and were sufficiently precise to identify TATA-like elements at so-called TATA-less promoters. These PICs and their transcription start sites were positionally constrained at TFIID-engaged downstream +1 nucleosomes. At TATA-box-containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competition with the PIC, which may allow greater latitude in start-site selection. Our genomic localization of messenger RNA and non-coding RNA PICs reveals that two PICs, in inverted orientation, may occupy the flanking borders of nucleosome-free regions. Their unambiguous detection may help distinguish bona fide genes from transcriptional noise.
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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.