ArticlePLoS computational biology2008
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed, 83 citations in OpenAlex.
- PARP1 Exhibits an Enzymatically Inactive Chromatin Binding Mode.bioRxiv : the preprint server for biology · 2026Article
- Differential nucleosome organization in human interphase and metaphase chromosomes.Molecular systems biology · 2026Article
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Differential nucleosome organization in human interphase and metaphase chromosomes.bioRxiv : the preprint server for biology · 2025Article
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- Histone H3 core domain in chromatin with different DNA linker lengths studied byFrontiers in molecular biosciences · 2022Article
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Topological polymorphism of nucleosome fibers and folding of chromatin.Biophysical journal · 2021Review
- Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies.Scientific reports · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Modelling and DNA topology of compact 2-start and 1-start chromatin fibres.Nucleic acids research · 2019Article
- Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays.The Journal of biological chemistry · 2019Article
- Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.Biophysical journal · 2018Review
- Precise genome-wide mapping of single nucleosomes and linkers in vivo.Genome biology · 2018Article
- Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.Molecular biology and evolution · 2016Article
- Nucleosomal arrangement affects single-molecule transcription dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Topological polymorphism of the two-start chromatin fiber.Biophysical journal · 2015Article
- Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription.AIMS biophysics · 2015Article
- Functional roles of nucleosome stability and dynamics.Briefings in functional genomics · 2015Review
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 3 institutions in 4 countries.
Funding
Abstract
The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.
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.