ArticleProceedings of the National Academy of Sciences of the United States of America2010
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
58 citing papers in PubMed, 85 citations in OpenAlex.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- How is polyadenylation restricted to 3'-untranslated regions?Yeast (Chichester, England) · 2024Review
- Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Sumoylation is Largely Dispensable for Normal Growth but Facilitates Heat Tolerance in Yeast.Molecular and cellular biology · 2023Article
- Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by the separation of core and tail Mediator modules.G3 (Bethesda, Md.) · 2022Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing.Genome biology · 2021Article
- Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters.PLoS genetics · 2021Article
- The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.International journal of molecular sciences · 2021Review
- Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases.Nucleic acids research · 2020Article
- Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase.PLoS genetics · 2020Article
- A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats.Current genetics · 2019Article
- Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Identification of Two Distinct Classes of the Human INO80 Complex Genome-Wide.G3 (Bethesda, Md.) · 2018Article
- Chemically induced proximity in biology and medicine.Science (New York, N.Y.) · 2018Review
- Precise genome-wide mapping of single nucleosomes and linkers in vivo.Genome biology · 2018Article
- Mechanism of Apoptosis Induction by Mycoplasmal Nuclease MGA_0676 in Chicken Embryo Fibroblasts.Frontiers in cellular and infection microbiology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of pol II, but rather involves a distinct mechanism linked to 3'-end formation.
Indexed as
Identifiers
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.