ArticleProceedings of the National Academy of Sciences of the United States of America2011
Nucleosome positioning in a model of active chromatin remodeling enzymes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Chromatin remodelers: a concise introduction for biophysicists.Biophysical reviews · 2024Review
- Article
- Nucleosome Assembly and DisassemblyFrontiers in cell and developmental biology · 2021Article
- On the role of transcription in positioning nucleosomes.PLoS computational biology · 2021Article
- Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties.Nucleic acids research · 2020Article
- Metabolism, Epigenetics, and Causal Inference in Heart Failure.Trends in endocrinology and metabolism: TEM · 2020Review
- Theory of Active Chromatin Remodeling.Physical review letters · 2019Article
- ChIPulate: A comprehensive ChIP-seq simulation pipeline.PLoS computational biology · 2019Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- The Latest Twists in Chromatin Remodeling.Biophysical journal · 2018Review
- Major Determinants of Nucleosome Positioning.Biophysical journal · 2018Review
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.Nucleic acids research · 2014Article
- Chromosome positioning from activity-based segregation.Nucleic acids research · 2014Article
- Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence.Nucleic acids research · 2014Article
- Toward a unified physical model of nucleosome patterns flanking transcription start sites.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants.Physical review. E, Statistical, nonlinear, and soft matter physics · 2013Article
- Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.Open biology · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Accounting for enzyme-mediated active sliding, disassembly, and sequence-dependent positioning of nucleosomes, we simulate nucleosome occupancy over cell-cycle-scale times using a stochastic kinetic model. We show that ATP-dependent active nucleosome sliding and nucleosome removal processes are essential to obtain in vivo-like nucleosome positioning. While active sliding leads to dense nucleosome filling, sliding events alone cannot ensure sequence-dependent nucleosome positioning: Active nucleosome removal is the crucial remodeling event that drives positioning. We also show that remodeling activity changes nucleosome dynamics from glassy to liquid-like, and that remodeling dramatically influences exposure dynamics of promoter regions.
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.