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Dynamics of 3D Genome Organization
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Dynamics of 3D Genome Organization

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 August 2024 | Viewed by 17231

Special Issue Editors

Dr. Feifei Li

E-Mail
Guest Editor
School of Medicine, South China University of Technology, Guangzhou 510640, China
Interests: genomics; chromatin structure; transcription regulation; phase separation; epigenetics
Dr. Xuepeng Chen

E-Mail Website
Guest Editor
Basic Research Department, Guangzhou National Laboratory, Guangzhou 510320, China
Interests: 3D chromatin structures; gene expression regulation; nervous system development; mammalian embryonic development

Special Issue Information

Dear Colleagues,

Three-dimensional (3D) genome organization provides a physical scaffold and influences all DNA-based biological processes in the nucleus, including RNA transcription, DNA replication, DNA repair, etc. Our understanding of 3D genomes has been deepened by both microscopy- and sequencing-based methods during the past few years and we now know that interphase chromatin in eukaryotic nuclei is folded into multiple layers of hierarchical structures. Recent research has shown that 3D genome organization experiences rearrangement during development, disease and environmental stress, and the dynamics of the 3D genome is important for the progress of these biological processes. In addition, the dynamics of the 3D genome is closely related with the regulation of other epigenetic modifications. More research in the dynamics of the 3D genome organization will not only give us clue for the mechanism of formation and change of chromatin structure but will also deepen our understanding of the roles of the 3D genome. In this Special Issue of Genes, we will highlight the most recent advances in the dynamics of 3D genome organization and its role in various biological process. We are also interested in new experimental and analysis techniques studying chromatin structure. We welcome reviews and original articles in the research area of 3D genome organization.

Dr. Feifei Li
Dr. Xuepeng Chen
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. Genes 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 2600 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

  • 3D genome organization
  • architectural protein
  • A/B compartments
  • topological associated domain
  • DNA loop
  • phase separation
  • transcription regulation
  • epigenome
  • new techniques relating to 3D genome

Published Papers (5 papers)

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Research

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15 pages, 23920 KiB  
Article
Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data
by Muhammad Muzammal Adeel, Khaista Rehman, Yan Zhang, Yibeltal Arega and Guoliang Li
Genes 2022, 13(7), 1170; https://doi.org/10.3390/genes13071170 - 29 Jun 2022
Cited by 2 | Viewed by 3029
Abstract
Complex chromosomal rearrangements such as translocations play a critical role in oncogenesis. Translocation detection is vital to decipher their biological role in activating cancer-associated mechanisms. High-throughput chromosomal conformations capture (Hi-C) data have shown promising progress in unveiling the genome variations in a disease [...] Read more.
Complex chromosomal rearrangements such as translocations play a critical role in oncogenesis. Translocation detection is vital to decipher their biological role in activating cancer-associated mechanisms. High-throughput chromosomal conformations capture (Hi-C) data have shown promising progress in unveiling the genome variations in a disease condition. Until now, multiple structural data (Hi-C)-based methods are available that can detect translocations in cancer genomes. However, the consistency and specificity of Hi-C-based translocation results still need to be validated with conventional methods. This study used Hi-C data of cancerous cell lines, namely lung cancer (A549), Chronic Myelogenous Leukemia (K562), and Acute Monocytic Leukemia (THP-1), to detect the translocations. The results were cross-validated through whole-genome sequencing (WGS) and paired-read analysis. Moreover, PCR amplification validated the presence of translocated reads in different chromosomes. By integrating different data types, we showed that the results of Hi-C data are as reliable as WGS and can be utilized as an assistive method for detecting translocations in the diseased genome. Our findings support the utility of Hi-C technology to detect the translocations and study their effects on the three-dimensional architecture of the genome in cancer condition. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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Review

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17 pages, 1322 KiB  
Review
Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization
by Xiaoli Li, Ziyang An, Wenqing Zhang and Feifei Li
Genes 2023, 14(2), 499; https://doi.org/10.3390/genes14020499 - 15 Feb 2023
Cited by 4 | Viewed by 3154
Abstract
The multi-level spatial chromatin organization in the nucleus is closely related to chromatin activity. The mechanism of chromatin organization and remodeling attract much attention. Phase separation describes the biomolecular condensation which is the basis for membraneless compartments in cells. Recent research shows that [...] Read more.
The multi-level spatial chromatin organization in the nucleus is closely related to chromatin activity. The mechanism of chromatin organization and remodeling attract much attention. Phase separation describes the biomolecular condensation which is the basis for membraneless compartments in cells. Recent research shows that phase separation is a key aspect to drive high-order chromatin structure and remodeling. In addition, chromatin functional compartmentalization in the nucleus which is formed by phase separation also plays an important role in overall chromatin structure. In this review, we summarized the latest work about the role of phase separation in spatial chromatin organization, focusing on direct and indirect effects of phase separation on 3D chromatin organization and its impact on transcription regulation. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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15 pages, 2019 KiB  
Review
Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development
by Longtao Yu, Hengxiang Shen and Xiaowen Lyu
Genes 2022, 13(12), 2382; https://doi.org/10.3390/genes13122382 - 16 Dec 2022
Viewed by 1849
Abstract
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP [...] Read more.
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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15 pages, 1212 KiB  
Review
A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos
by Zhenping Chen and Xuepeng Chen
Genes 2022, 13(10), 1864; https://doi.org/10.3390/genes13101864 - 15 Oct 2022
Cited by 3 | Viewed by 1945
Abstract
The 3D chromatin structure within the nucleus is important for gene expression regulation and correct developmental programs. Recently, the rapid development of low-input chromatin conformation capture technologies has made it possible to study 3D chromatin structures in gametes, zygotes and early embryos in [...] Read more.
The 3D chromatin structure within the nucleus is important for gene expression regulation and correct developmental programs. Recently, the rapid development of low-input chromatin conformation capture technologies has made it possible to study 3D chromatin structures in gametes, zygotes and early embryos in a variety of species, including flies, vertebrates and mammals. There are distinct 3D chromatin structures within the male and female gametes. Following the fertilization of male and female gametes, fertilized eggs undergo drastic epigenetic reprogramming at multi levels, including the 3D chromatin structure, to convert the terminally differentiated gamete state into the totipotent state, which can give rise to an individual. However, to what extent the 3D chromatin structure reorganization is evolutionarily conserved and what the underlying mechanisms are for the tremendous reorganization in early embryos remain elusive. Here, we review the latest findings on the 3D chromatin structure reorganization during embryogenesis, and discuss the convergent and divergent reprogramming patterns and key molecular mechanisms for the 3D chromatin structure reorganization from gametes to embryos in different species. These findings shed light on how the 3D chromatin structure reorganization contribute to embryo development in different species. The findings also indicate the role of the 3D chromatin structure on the acquisition of totipotent developmental potential. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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19 pages, 1758 KiB  
Review
CTCF and Its Partners: Shaper of 3D Genome during Development
by Xiaoyue Sun, Jing Zhang and Chunwei Cao
Genes 2022, 13(8), 1383; https://doi.org/10.3390/genes13081383 - 02 Aug 2022
Cited by 9 | Viewed by 6224
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners [...] Read more.
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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