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Biology
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Chromatin Dynamics
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Chromatin Dynamics

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 65267

Special Issue Editors

Dr. Ian Cowell

E-Mail Website
Guest Editor
Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
Interests: DNA topoisomerase; transcription
Prof. Dr. Caroline A. Austin

E-Mail Website
Guest Editor
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK
Interests: DNA Topoisomerase II; topoisomerase protein structure

Special Issue Information

Dear Colleagues,

Genomic DNA is packaged into chromatin, an arrangement that might seem to obstruct nuclear processes such as transcription, replication and DNA repair whose molecular machineries require access to specific genomic locations. However, it is now clear that the dynamic nature of chromatin is central to how these processes are ordered and regulated. The dynamic structural and spatial organization of chromatin embraces topics such as the structure, function and dynamics of nucleosomes, the role of histone variants, chromatin topology and supercoiling, chromatin remodeling machines, aspects of DNA repair, chromatin loops and long-distance chromatin interactions and the function of enhancers, insulators and other regulatory elements. This volume aims to cover recent progress in our understanding in this area.

Dr. Ian G. Cowell
Prof. Dr. Caroline A. Austin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Chromatin dynamics
  • chromatin
  • nucleosomes
  • gene regulation
  • DNA repair
  • chromatin remodeling

Published Papers (2 papers)

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Research

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15 pages, 2084 KiB  
Article
Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin
by Renáta Rusková and Dušan Račko
Biology 2021, 10(2), 130; https://doi.org/10.3390/biology10020130 - 07 Feb 2021
Cited by 6 | Viewed by 59888
Abstract
We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers. Different levels of negative supercoiling are controlled by varying imposed friction between the cohesin ring and the [...] Read more.
We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers. Different levels of negative supercoiling are controlled by varying imposed friction between the cohesin ring and the chromatin fiber. The speed of generation of negative supercoiling by RNA polymerase associated with TOP1 is kept constant and corresponds to 10 rotations per second. The model was tested by coarse-grained molecular simulations for a wide range of frictions between 2 to 200 folds of that of generic fiber and the surrounding medium. The higher friction allowed for the accumulation of higher levels of supercoiling, while the resulting extrusion rate also increased. The obtained extrusion rates for the given range of investigated frictions were between 1 and 10 kbps, but also a saturation of the rate at high frictions was observed. The calculated contact maps indicate a qualitative improvement obtained at lower levels of supercoiling. The fits of mathematical equations qualitatively reproduce the loop sizes and levels of supercoiling obtained from simulations and support the proposed mechanism of entropically driven extrusion. The cohesin ring is bound on the fibers pseudo-topologically, and the model suggests that the topological binding is not necessary. Full article
(This article belongs to the Special Issue Chromatin Dynamics)
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Review

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21 pages, 1728 KiB  
Review
Mass Spectrometry to Study Chromatin Compaction
by Stephanie Stransky, Jennifer Aguilan, Jake Lachowicz, Carlos Madrid-Aliste, Edward Nieves and Simone Sidoli
Biology 2020, 9(6), 140; https://doi.org/10.3390/biology9060140 - 26 Jun 2020
Cited by 2 | Viewed by 4648
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and [...] Read more.
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease. Full article
(This article belongs to the Special Issue Chromatin Dynamics)
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