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ATP-dependent Chromatin Remodeler
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ATP-dependent Chromatin Remodeler

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

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 30357

Special Issue Editor

Prof. Dr. Blaine Bartholomew

E-Mail Website
Guest Editor
Department of Epigenetics & Molecular Carcinogenesis, UT MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA
Interests: chromatin; chromatin remodeling; transcription; enhancers; nucleosomes

Special Issue Information

Dear Colleagues,

One of the major types of epigenetic factors is the large family of ATP-dependent chromatin remodeling complexes that reorganize chromatin by moving nucleosomes on DNA, disassembling and reassembling nucleosomes, or dynamically exchanging into chromatin different histone variants such as histone H2A.Z. Recent advances in high resolution cryo-electron microscopy have provided critical insights into the mechanisms of chromatin remodeling that also complement biochemical approaches used for this purpose. Advances in genomics/next generation DNA sequencing and molecular genetics has revealed that these chromatin remodelers are important in development and differentiation and when mutated can become the molecular basis for several diseases including cancer. In this issue, we will examine the convergence of these two distinct areas and how they inform us as to the importance and roles of these factors for regulating the epigenome and its impact on human diseases.

Prof. Blaine Bartholomew
Guest Editor

Manuscript Submission Information

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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
  • nuclear organization and architecture
  • chromatin dynamics
  • nucleosome
  • histone variants
  • genomics
  • epigenomics
  • chromatin remodeling
  • transcription regulation
  • genomic integrity and maintenance

Published Papers (5 papers)

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Review

15 pages, 2802 KiB  
Review
At the Crossroad of Gene Regulation and Genome Organization: Potential Roles for ATP-Dependent Chromatin Remodelers in the Regulation of CTCF-Mediated 3D Architecture
by Aktan Alpsoy, Surbhi Sood and Emily C. Dykhuizen
Biology 2021, 10(4), 272; https://doi.org/10.3390/biology10040272 - 27 Mar 2021
Cited by 8 | Viewed by 9751
Abstract
In higher order organisms, the genome is assembled into a protein-dense structure called chromatin. Chromatin is spatially organized in the nucleus through hierarchical folding, which is tightly regulated both in cycling cells and quiescent cells. Assembly and folding are not one-time events in [...] Read more.
In higher order organisms, the genome is assembled into a protein-dense structure called chromatin. Chromatin is spatially organized in the nucleus through hierarchical folding, which is tightly regulated both in cycling cells and quiescent cells. Assembly and folding are not one-time events in a cell’s lifetime; rather, they are subject to dynamic shifts to allow changes in transcription, DNA replication, or DNA damage repair. Chromatin is regulated at many levels, and recent tools have permitted the elucidation of specific factors involved in the maintenance and regulation of the three-dimensional (3D) genome organization. In this review/perspective, we aim to cover the potential, but relatively unelucidated, crosstalk between 3D genome architecture and the ATP-dependent chromatin remodelers with a specific focus on how the architectural proteins CTCF and cohesin are regulated by chromatin remodeling. Full article
(This article belongs to the Special Issue ATP-dependent Chromatin Remodeler)
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20 pages, 1078 KiB  
Review
Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship
by Benjamin J. Patty and Sarah J. Hainer
Biology 2020, 9(8), 213; https://doi.org/10.3390/biology9080213 - 07 Aug 2020
Cited by 17 | Viewed by 5035
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an [...] Read more.
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions. Full article
(This article belongs to the Special Issue ATP-dependent Chromatin Remodeler)
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23 pages, 3081 KiB  
Review
Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast
by Hemant K. Prajapati, Josefina Ocampo and David J. Clark
Biology 2020, 9(8), 190; https://doi.org/10.3390/biology9080190 - 25 Jul 2020
Cited by 18 | Viewed by 5551
Abstract
Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent [...] Read more.
Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides. Full article
(This article belongs to the Special Issue ATP-dependent Chromatin Remodeler)
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18 pages, 1766 KiB  
Review
Regulation of the Mammalian SWI/SNF Family of Chromatin Remodeling Enzymes by Phosphorylation during Myogenesis
by Teresita Padilla-Benavides, Pablo Reyes-Gutierrez and Anthony N. Imbalzano
Biology 2020, 9(7), 152; https://doi.org/10.3390/biology9070152 - 03 Jul 2020
Cited by 2 | Viewed by 4980
Abstract
Myogenesis is the biological process by which skeletal muscle tissue forms. Regulation of myogenesis involves a variety of conventional, epigenetic, and epigenomic mechanisms that control chromatin remodeling, DNA methylation, histone modification, and activation of transcription factors. Chromatin remodeling enzymes utilize ATP hydrolysis to [...] Read more.
Myogenesis is the biological process by which skeletal muscle tissue forms. Regulation of myogenesis involves a variety of conventional, epigenetic, and epigenomic mechanisms that control chromatin remodeling, DNA methylation, histone modification, and activation of transcription factors. Chromatin remodeling enzymes utilize ATP hydrolysis to alter nucleosome structure and/or positioning. The mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) family of chromatin remodeling enzymes is essential for myogenesis. Here we review diverse and novel mechanisms of regulation of mSWI/SNF enzymes by kinases and phosphatases. The integration of classic signaling pathways with chromatin remodeling enzyme function impacts myoblast viability and proliferation as well as differentiation. Regulated processes include the assembly of the mSWI/SNF enzyme complex, choice of subunits to be incorporated into the complex, and sub-nuclear localization of enzyme subunits. Together these processes influence the chromatin remodeling and gene expression events that control myoblast function and the induction of tissue-specific genes during differentiation. Full article
(This article belongs to the Special Issue ATP-dependent Chromatin Remodeler)
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9 pages, 834 KiB  
Review
Structural Insights into the Evolutionarily Conserved BAF Chromatin Remodeling Complex
by Ryan D. Marcum, Alexis A. Reyes and Yuan He
Biology 2020, 9(7), 146; https://doi.org/10.3390/biology9070146 - 30 Jun 2020
Cited by 3 | Viewed by 4234
Abstract
The switch/sucrose nonfermentable (SWI/SNF) family of proteins acts to regulate chromatin accessibility and plays an essential role in multiple cellular processes. A high frequency of mutations has been found in SWI/SNF family subunits by exome sequencing in human cancer, and multiple studies support [...] Read more.
The switch/sucrose nonfermentable (SWI/SNF) family of proteins acts to regulate chromatin accessibility and plays an essential role in multiple cellular processes. A high frequency of mutations has been found in SWI/SNF family subunits by exome sequencing in human cancer, and multiple studies support its role in tumor suppression. Recent structural studies of yeast SWI/SNF and its human homolog, BAF (BRG1/BRM associated factor), have provided a model for their complex assembly and their interaction with nucleosomal substrates, revealing the molecular function of individual subunits as well as the potential impact of cancer-associated mutations on the remodeling function. Here we review the structural conservation between yeast SWI/SNF and BAF and examine the role of highly mutated subunits within the BAF complex. Full article
(This article belongs to the Special Issue ATP-dependent Chromatin Remodeler)
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