ArticleGenome research2010
A novel strategy of transcription regulation by intragenic nucleosome ordering.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 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
43 citing papers in PubMed.
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Review
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin inProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks.Biophysical journal · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Nucleosome positions alone can be used to predict domains in yeast chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The implication of DNA bending energy for nucleosome positioning and sliding.Scientific reports · 2018Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions.Biophysical journal · 2017Article
- Dynamics of Nucleosome Positioning Maturation following Genomic Replication.Cell reports · 2016Article
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- Epigenomics and the structure of the living genome.Genome research · 2015Review
- Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.PLoS computational biology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5' gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5' and 3' gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a "crystal-like" array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly compacted nucleosomes. This adaptability confers "bi-stable" properties to chromatin and is a key to its dynamics. Compared to crystal-like genes, bi-stable genes present higher transcriptional plasticity, higher sensitivity to chromatin regulators, higher H3 turnover rate, and lower H2A.Z enrichment. The results strongly suggest that transcription elongation is facilitated by higher chromatin compaction. The data allow us to propose a new paradigm of transcriptional control mediated by the stability and the level of compaction of the intragenic chromatin architecture and open new ways for investigating eukaryotic gene expression regulation.
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.