ArticleNucleic acids research2014
Fuzziness and noise in nucleosomal architecture.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
- Deep learning-based non-invasive profiling of tumor transcriptomes from cell-free DNA for precision oncology.bioRxiv : the preprint server for biology · 2026Article
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- The PCNA-Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance.Science advances · 2024Article
- A study of strong nucleosomes in the human genome.iScience · 2022Article
- Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin.Journal of molecular biology · 2021Review
- Survey of the Arc Epigenetic Landscape in Normal Cognitive Aging.Molecular neurobiology · 2020Article
- Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning.Frontiers in cell and developmental biology · 2020Article
- Absolute nucleosome occupancy map for theGenome research · 2019Article
- Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.Nucleic acids research · 2019Article
- Directed Nucleosome Sliding during the Formation of the Simian Virus 40 Particle Exposes DNA Sequences Required for Early Transcription.Journal of virology · 2019Article
- Spt6 Association with RNA Polymerase II Directs mRNA Turnover During Transcription.Molecular cell · 2018Article
- The implication of DNA bending energy for nucleosome positioning and sliding.Scientific reports · 2018Article
- CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.Bioinformatics (Oxford, England) · 2017Article
- Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.Methods in molecular biology (Clifton, N.J.) · 2017Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Nucleosome architecture throughout the cell cycle.Scientific reports · 2016Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- Autonomous actions of the human growth hormone long-range enhancer.Nucleic acids research · 2015Article
- 'Memory and molecular turnover,' 30 years after inception.Epigenetics & chromatin · 2014Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleosome organization plays a key role in the regulation of gene expression. However, despite the striking advances in the accuracy of nucleosome maps, there are still severe discrepancies on individual nucleosome positioning and how this influences gene regulation. The variability among nucleosome maps, which precludes the fine analysis of nucleosome positioning, might emerge from diverse sources. We have carefully inspected the extrinsic factors that may induce diversity by the comparison of microccocal nuclease (MNase)-Seq derived nucleosome maps generated under distinct conditions. Furthermore, we have also explored the variation originated from intrinsic nucleosome dynamics by generating additional maps derived from cell cycle synchronized and asynchronous yeast cultures. Taken together, our study has enabled us to measure the effect of noise in nucleosome occupancy and positioning and provides insights into the underlying determinants. Furthermore, we present a systematic approach that may guide the standardization of MNase-Seq experiments in order to generate reproducible genome-wide nucleosome patterns.
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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.