ArticlePLoS computational biology2016
Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
- Subtle-seq reveals frequent ageing-associated chromosome fragmentation on nucleosome core DNA.Nucleic acids research · 2026Article
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells.International journal of molecular sciences · 2022Article
- Article
- HIV-Proteins-Associated CNS Neurotoxicity, Their Mediators, and Alternative Treatments.Cellular and molecular neurobiology · 2022Review
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- Distinctive regulatory architectures of germline-active and somatic genes inGenome research · 2020Article
- A unified view of the sequence and functional organization of the human RNA polymerase II promoter.Nucleic acids research · 2020Article
- HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis.Genome biology · 2020Article
- Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.Nucleic acids research · 2020Article
- Opposing chromatin remodelers control transcription initiation frequency and start site selection.Nature structural & molecular biology · 2019Article
- Eukaryotic core promoters and the functional basis of transcription initiation.Nature reviews. Molecular cell biology · 2018Review
- Telling Left from Right in Breathing Nucleosomes.Biophysical journal · 2018Article
- The Latest Twists in Chromatin Remodeling.Biophysical journal · 2018Review
- Promoter shape varies across populations and affects promoter evolution and expression noise.Nature genetics · 2017Article
- The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.Nucleic acids research · 2017Article
- A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes.Scientific reports · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters' sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters' primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals.
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