Chromatin Organization in Cell Differentiation

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

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 3746

Special Issue Editor

Skeletal Biology and Regenerative Medicine and Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
Interests: functional genomics; chromatin remodelling; epigenetic regulation

Special Issue Information

Dear Colleagues,

Gene expression is regulated by a coordinated interplay between chromatin remodelling, DNA methylation/demethylation, histone modifications and long noncoding RNAs. Temporal changes in gene expression are critical for the commitment of cells to specific cell fates and their ability to differentiate into particular kinds of cells. This Special Issue aims to highlight the latest findings on chromatin architecture, epigenetic changes and transcriptional regulation during development and cell differentiation. Chromatin deregulation often results in developmental disorders; therefore, deciphering the genomic mechanisms that underlie cellular differentiation holds enormous discovery potential for human health and medicine.

We welcome contributions (original research, short communications, reviews and conceptual articles) that offer novel mechanistic and functional insights into gene regulation.

Research areas include, but are not limited to, the following:

  • Epigenetic mechanisms;
  • Chromatin architecture;
  • Nuclear organization;
  • Post-translational modifications;
  • Cell signalling;
  • Gene expression;
  • Systems biology;
  • Gene regulatory networks.

Dr. Dashzeveg Bayarsaihan
Guest Editor

Manuscript Submission Information

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Keywords

  • epigenetic modifications 
  • gene regulatory networks 
  • multi-omics 
  • functional genomics 
  • chromatin remodeling 
  • transcriptomics 
  • proteomics 
  • metabolomics

Published Papers (2 papers)

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Research

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22 pages, 4274 KiB  
Article
Changes in Hox Gene Chromatin Organization during Odontogenic Lineage Specification
by Gokul Gopinathan, Xinmin Zhang, Xianghong Luan and Thomas G. H. Diekwisch
Genes 2023, 14(1), 198; https://doi.org/10.3390/genes14010198 - 12 Jan 2023
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Abstract
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic [...] Read more.
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic progenitors and to explore the effects of elevated levels of HOX. The ChIP-chip data demonstrated high levels of repressive H3K27me3 marks on the HOX gene promoters in ES and cranial neural crest cells when compared to the H3K4me3 marks, while the K4/K27 ratio was less repressive in the odontogenic progenitors, dental follicle, dental pulp, periodontal ligament fibroblasts, alveolar bone osteoblasts, and cementoblasts. The gene expression of multiple HOX genes, especially those from the HOXA and HOXB clusters, was significantly elevated and many times higher in alveolar bone cells than in the dental follicle cells. In addition, the HOX levels in the skeletal osteoblasts were many times higher in the trunk osteoblasts compared to the alveolar bone osteoblasts, and the repressive mark H3K27me3 promoter occupancy was substantially and significantly elevated in the alveolar bone osteoblasts when compared to the trunk osteoblasts. To explore the effect of elevated HOX levels in craniofacial neural crest cells, HOX expression was induced by transfecting cells with the Cdx4 transcription factor, resulting in a significant decrease in the mineralization markers, RUNX2, OSX, and OCN upon HOX elevation. Promoting HOX gene expression in developing teeth using the small molecule EZH2 inhibitor GSK126 resulted in an increased number of patterning events, supernumerary cusp formation, and increased Hoxa4 and Hoxb6 gene expression when compared to the controls. Together, these studies illustrate the profound effects of epigenetic regulatory events at all stages of the differentiation of craniofacial peripheral tissues from the neural crest, including lineage specification, tissue differentiation, and patterning. Full article
(This article belongs to the Special Issue Chromatin Organization in Cell Differentiation)
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Review

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13 pages, 640 KiB  
Review
A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation
by Salvatore Martino, Pietro Salvatore Carollo and Viviana Barra
Genes 2023, 14(5), 1046; https://doi.org/10.3390/genes14051046 - 06 May 2023
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Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through [...] Read more.
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope. Full article
(This article belongs to the Special Issue Chromatin Organization in Cell Differentiation)
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