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Positioning of Nucleosomes 2.0
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Positioning of Nucleosomes 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 4874

Special Issue Editor

Dr. Tobias Straub

E-Mail Website
Guest Editor
Biomedical Center - Bioinformatics, Ludwig-Maximilians-Universität München, Munich, Germany
Interests: functional genomics; biostatistis; chromatin biology; metabolism; open science; translational life science; digital health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nucleosomes consisting of core histone proteins with about 150 bp DNA wrapped around are the building blocks of chromatin. Their relative positioning along the DNA is thought to have strong impact on transcription factor binding and DNA templated processes. Furthermore, the ensemble configuration characterised by the spacing of consecutive nucleosomes influences the steric organisation of the chromatin fibre. There is great interest in elucidating the principles that both fix nucleosomes at specific sites and relocate them for regulating genome activity. Biochemical in vitro assays, functional analyses at specific genomic target sites, genome-wide nucleosome mapping and high dimensional bioinformatic analyses constitute a plethora of approaches that further our knowledge on the interplay between nucleosome positions, DNA sequence, histone variants and modifications and the functional state of the genome.

This Special Issue, “Nucleosome positioning”, will cover a selection of recent research topics and current review articles in the field of chromatin biology with a specific focus on the rules and processes that define the positions of nucleosomes as well as their functional implications.

Potential topics include, but are not limited to:

  • Nucleosome positioning sequences
  • Nucleosome positions & histone modifications / variants
  • Nucleosome remodeler defining nucleosome positions
  • Nucleosomal arrays
  • Mapping nucleosome positions
  • Gene expression regulation by nucleosome positioning
  • Nucleosome positioning and genome integrity

Dr. Tobias Straub
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Related Special Issue

Published Papers (3 papers)

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Research

21 pages, 3197 KiB  
Article
Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler
by Corinna Lieleg, Ana Novacic, Sanja Musladin, Andrea Schmid, Gözde Güçlüler Akpinar, Slobodan Barbaric and Philipp Korber
Int. J. Mol. Sci. 2023, 24(5), 4949; https://doi.org/10.3390/ijms24054949 - 03 Mar 2023
Viewed by 1450
Abstract
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, [...] Read more.
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes. Full article
(This article belongs to the Special Issue Positioning of Nucleosomes 2.0)
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16 pages, 10643 KiB  
Article
DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells
by Guoqing Liu, Zhi Zhang, Biyu Dong and Jia Liu
Int. J. Mol. Sci. 2022, 23(22), 14488; https://doi.org/10.3390/ijms232214488 - 21 Nov 2022
Viewed by 1397
Abstract
Chromatin architecture is orchestrated, and plays crucial roles during the developmental process by regulating gene expression. In embryonic stem cells (ESCs), three types of chromatin states, including active, repressive and poised states, were previously identified and characterized with specific chromatin modification marks and [...] Read more.
Chromatin architecture is orchestrated, and plays crucial roles during the developmental process by regulating gene expression. In embryonic stem cells (ESCs), three types of chromatin states, including active, repressive and poised states, were previously identified and characterized with specific chromatin modification marks and different transcription activity, but it is largely unknown how nucleosomes are organized in these chromatin states. In this study, by using a DNA deformation energy model, we investigated the sequence-dependent nucleosome organization within the chromatin states in mouse ESCs. The results revealed that: (1) compared with poised genes, active genes are characterized with a higher level of nucleosome occupancy around their transcription start sites (TSS) and transcription termination sites (TTS), and both types of genes do not have a nucleosome-depleted region at their TTS, contrasting with the MNase-seq based result; (2) based on our previous DNA bending energy model, we developed an improved model capable of predicting both rotational positioning and nucleosome occupancy determined by a chemical mapping approach; (3) DNA bending-energy-based analyses demonstrated that the fragile nucleosomes positioned at both gene ends could be explained largely by enhanced rotational positioning signals encoded in DNA, but nucleosome phasing around the TSS of active genes was not determined by sequence preference; (4) the nucleosome occupancy landscape around the binding sites of some developmentally important transcription factors known to bind with different chromatin contexts, was also successfully predicted; (5) the difference of nucleosome occupancy around the TSS between CpG-rich and CpG-poor promoters was partly captured by our sequence-dependent model. Taken together, by developing an improved deformation-energy-based model, we revealed some sequence-dependent properties of the nucleosome arrangements in regions of distinct chromatin states in mouse ESCs. Full article
(This article belongs to the Special Issue Positioning of Nucleosomes 2.0)
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13 pages, 1715 KiB  
Article
Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns
by Erinija Pranckeviciene, Sergey Hosid, Indiras Maziukas and Ilya Ioshikhes
Int. J. Mol. Sci. 2022, 23(9), 4869; https://doi.org/10.3390/ijms23094869 - 28 Apr 2022
Viewed by 1515
Abstract
Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, [...] Read more.
Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms. Full article
(This article belongs to the Special Issue Positioning of Nucleosomes 2.0)
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