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Epigenomes, Volume 2, Issue 1 (March 2018) – 6 articles

Cover Story (view full-size image): While most cells of the same organism contain an identical DNA sequence, what governs the diversity of cell phenotypes is a matter of intense research. A novel epigenetic mark, 5-hydroxymethylcytosine (5hmC), originally described as an intermediate during active DNA-demethylation, is emerging as a stable modified base with unique functions. In this review, we summarize recent evidence suggesting that dynamic distribution of 5hmC could be an acquired "fingerprint" of cell identity during adult progenitor cell differentiation. View this paper
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17 pages, 726 KiB  
Review
Epigenomics of Plant Responses to Environmental Stress
by Suresh Kumar
Epigenomes 2018, 2(1), 6; https://doi.org/10.3390/epigenomes2010006 - 16 Mar 2018
Cited by 41 | Viewed by 11038
Abstract
Genome-wide epigenetic changes in plants are being reported during development and environmental stresses, which are often correlated with gene expression at the transcriptional level. The sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the [...] Read more.
Genome-wide epigenetic changes in plants are being reported during development and environmental stresses, which are often correlated with gene expression at the transcriptional level. The sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as an epigenome. These changes are often responsible for variation in the expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting in the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli, which affect phenotypic plasticity of the organism. Both the epigenetic changes and variation in gene expression might return to the pre-stress state soon after the withdrawal of the stress. However, a part of the epigenetic changes may be retained, which is reported to play a role in acclimatization and adaptation as well as in the evolutionary process. Probable exploitation of epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic resources. This review delineates the importance of epigenomics towards the possible improvement of plant responses to environmental stresses for climate resilient agriculture. Full article
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12 pages, 1612 KiB  
Article
Panobinostat Potentiates Temozolomide Effects and Reverses Epithelial–Mesenchymal Transition in Glioblastoma Cells
by Alejandro Urdiciain, Bárbara Meléndez, Juan A. Rey, Miguel A. Idoate and Javier S. Castresana
Epigenomes 2018, 2(1), 5; https://doi.org/10.3390/epigenomes2010005 - 19 Feb 2018
Cited by 5 | Viewed by 4161
Abstract
Glioblastoma is the most common form of glioma, as well as the most aggressive. Patients suffering from this disease have a very poor prognosis. Surgery, radiotherapy, and temozolomide are the only approved treatments nowadays. Panobinostat is a pan-inhibitor of histone deacetylases (HDACs) that [...] Read more.
Glioblastoma is the most common form of glioma, as well as the most aggressive. Patients suffering from this disease have a very poor prognosis. Surgery, radiotherapy, and temozolomide are the only approved treatments nowadays. Panobinostat is a pan-inhibitor of histone deacetylases (HDACs) that has been shown to break some pathways which play an important role in cancer development. A global intention of using panobinostat as a therapeutic agent against glioblastoma is beginning to be a reality. We have treated the LN405 glioblastoma cell line with temozolomide, panobinostat, and combined treatment, in order to test apoptosis, colony formation, and a possible molecular reversion of the mesenchymal phenotype of the cells to an epithelial one. Our results show that panobinostat decreased N-cadherin levels in the LN405 glioblastoma cell line while it increased the expression of E-cadherin, which might be associated with a mesenchymal–epithelial transition in glioblastoma cells. Colony formation was reduced, and apoptosis was increased with treatments. Our research highlights the importance of panobinostat as a potential adjuvant therapy to be used with temozolomide to treat glioblastoma and the advantages of the combined treatment versus temozolomide alone, which is currently the first-line treatment used to treat this tumor. Full article
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51 pages, 3525 KiB  
Review
From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development
by Izabella Bajusz, Gergő Kovács and Melinda K. Pirity
Epigenomes 2018, 2(1), 4; https://doi.org/10.3390/epigenomes2010004 - 05 Feb 2018
Cited by 11 | Viewed by 8385
Abstract
Originally two types of Polycomb Repressive Complexes (PRCs) were described, canonical PRC1 (cPRC1) and PRC2. Recently, a versatile set of complexes were identified and brought up several dilemmas in PRC mediated repression. These new class of complexes were named as non-canonical PRC1s (ncPRC1s). [...] Read more.
Originally two types of Polycomb Repressive Complexes (PRCs) were described, canonical PRC1 (cPRC1) and PRC2. Recently, a versatile set of complexes were identified and brought up several dilemmas in PRC mediated repression. These new class of complexes were named as non-canonical PRC1s (ncPRC1s). Both cPRC1s and ncPRC1s contain Ring finger protein (RING1, RNF2) and Polycomb group ring finger catalytic (PCGF) core, but in ncPRCs, RING and YY1 binding protein (RYBP), or YY1 associated factor 2 (YAF2), replaces the Chromobox (CBX) and Polyhomeotic (PHC) subunits found in cPRC1s. Additionally, ncPRC1 subunits can associate with versatile accessory proteins, which determine their functional specificity. Homozygous null mutations of the ncPRC members in mice are often lethal or cause infertility, which underlines their essential functions in mammalian development. In this review, we summarize the mouse knockout phenotypes of subunits of the six major ncPRCs. We highlight several aspects of their discovery from fly to mice and emerging role in target recognition, embryogenesis and cell-fate decision making. We gathered data from stem cell mediated in vitro differentiation assays and genetically engineered mouse models. Accumulating evidence suggests that ncPRC1s play profound role in mammalian embryogenesis by regulating gene expression during lineage specification of pluripotent stem cells. Full article
(This article belongs to the Special Issue Polycomb and Trithorax Group of Proteins in Development and Disease)
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20 pages, 1609 KiB  
Perspective
5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell
by Szilvia Ecsedi, Jesús Rafael Rodríguez-Aguilera and Héctor Hernandez-Vargas
Epigenomes 2018, 2(1), 3; https://doi.org/10.3390/epigenomes2010003 - 30 Jan 2018
Cited by 12 | Viewed by 11536
Abstract
Recently described as the sixth base of the DNA macromolecule, the precise role of 5-hydroxymethylcytosine (5hmC) is the subject of debate. Early studies indicate that it is functionally distinct from cytosine DNA methylation (5mC), and there is evidence for 5hmC being a stable [...] Read more.
Recently described as the sixth base of the DNA macromolecule, the precise role of 5-hydroxymethylcytosine (5hmC) is the subject of debate. Early studies indicate that it is functionally distinct from cytosine DNA methylation (5mC), and there is evidence for 5hmC being a stable derivate of 5mC, rather than just an intermediate of demethylation. Moreover, 5hmC events correlate in time and space with key differentiation steps in mammalian cells. Such events span the three embryonic germ layers and multiple progenitor cell subtypes, suggesting a general mechanism. Because of the growing understanding of the role of progenitor cells in disease origin, we attempted to provide a detailed summary on the currently available literature supporting 5hmC as a key player in adult progenitor cell differentiation. This summary consolidates the emerging role for 5hmC in defining cellular fate. Full article
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2 pages, 633 KiB  
Editorial
Acknowledgement to Reviewers of Epigenomes in 2017
by Epigenomes Editorial Office
Epigenomes 2018, 2(1), 2; https://doi.org/10.3390/epigenomes2010002 - 27 Jan 2018
Viewed by 2912
Abstract
Peer review is an essential part in the publication process, ensuring that Epigenomes maintains high quality standards for its published papers. [...]
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24 pages, 8141 KiB  
Review
Drosophila DNA-Binding Proteins in Polycomb Repression
by Maksim Erokhin, Pavel Georgiev and Darya Chetverina
Epigenomes 2018, 2(1), 1; https://doi.org/10.3390/epigenomes2010001 - 16 Jan 2018
Cited by 17 | Viewed by 8880
Abstract
The formation of individual gene expression patterns in different cell types is required during differentiation and development of multicellular organisms. Polycomb group (PcG) proteins are key epigenetic regulators responsible for gene repression, and dysregulation of their activities leads to developmental abnormalities and diseases. [...] Read more.
The formation of individual gene expression patterns in different cell types is required during differentiation and development of multicellular organisms. Polycomb group (PcG) proteins are key epigenetic regulators responsible for gene repression, and dysregulation of their activities leads to developmental abnormalities and diseases. PcG proteins were first identified in Drosophila, which still remains the most convenient system for studying PcG-dependent repression. In the Drosophila genome, these proteins bind to DNA regions called Polycomb response elements (PREs). A major role in the recruitment of PcG proteins to PREs is played by DNA-binding factors, several of which have been characterized in detail. However, current knowledge is insufficient for comprehensively describing the mechanism of this process. In this review, we summarize and discuss the available data on the role of DNA-binding proteins in PcG recruitment to chromatin. Full article
(This article belongs to the Special Issue Polycomb and Trithorax Group of Proteins in Development and Disease)
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