The mammalian genome is partitioned into submegabase-sized chromatin domains. Gene expression is highly regulated within domains, depending on their structure, whereas the chromatin itself is highly dynamic. We observed the movement of single nucleosomes using fluorescent labels (H2B-PA-mCherry; red spots in the background) in nuclei of living human cells. By modeling chromatin as a polymer with a fractal domain structure (lumps of fiber), the movement of nucleosomes was shown to depend on the domain structure they belong to. This means that the measured movement can provide information on how the fiber is packed in living cells. Shinkai et al.
Image Credit: Shinkai et al.
Editorials
Ten Simple Rules for Developing a MOOC
PLOS Computational Biology: published October 20, 2016 | https://doi.org/10.1371/journal.pcbi.1005061
Ten Simple Rules for Digital Data Storage
PLOS Computational Biology: published October 20, 2016 | https://doi.org/10.1371/journal.pcbi.1005097
Education
A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution
PLOS Computational Biology: published October 13, 2016 | https://doi.org/10.1371/journal.pcbi.1005046
Research Articles
AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
PLOS Computational Biology: published October 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005096
A Motor-Gradient and Clustering Model of the Centripetal Motility of MTOCs in Meiosis I of Mouse Oocytes
PLOS Computational Biology: published October 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005102
Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
PLOS Computational Biology: published October 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005140
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions
PLOS Computational Biology: published October 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005051
Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein
PLOS Computational Biology: published October 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005094
Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
PLOS Computational Biology: published October 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005126
Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States
PLOS Computational Biology: published October 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005133
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
PLOS Computational Biology: published October 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005135
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PLOS Computational Biology: published October 19, 2016 | https://doi.org/10.1371/journal.pcbi.1005146
Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections
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Optimized Treatment Schedules for Chronic Myeloid Leukemia
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Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells
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PLOS Computational Biology: published October 21, 2016 | https://doi.org/10.1371/journal.pcbi.1005154
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