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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 18737

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Special Issue Editors

Dr. Zhe Liang

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Guest Editor

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: plant genome; RNA methylation; multi-omics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Hai Du

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Guest Editor

College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
Interests: plant; genomics; systematics; bioinformatics; evolution; RNA-seq analysis; multi-omics; molecular biology of plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In eukaryotes, epigenetics play an essential role in regulating gene expression, which is crucial for cell differentiation and development. With the recent advances in technologies, particular in high-throughput sequencing, the recent decades have seen significant progress being made in terms of the discovery of epigenetic phenomena, the identification of key genes related to epigenetics, methods for the quantification and genome/transcriptome mapping of epigenetic markers, evolutionary and functional analyses of epigenetic genes (family) in virous species, molecular mechanisms for epigenetic regulation, and applications in breeding and medicines. In this Special Issue, we welcome original research or review articles related to all aspect of epigenetics, including DNA methylation, RNA modification, histone modification, non-coding RNA, chromatin remodeling, and 3D genomes.

Dr. Zhe Liang
Prof. Dr. Hai Du
Guest Editors

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Keywords

epigenetics
DNA methylation
RNA modification
histone modification
non-coding RNA
chromatin remodeling
3D genome

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Published Papers (6 papers)

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Research

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19 pages, 4140 KiB

Open AccessArticle

Foliar Application of dsRNA Targeting Endogenous Potato (Solanum tuberosum) Isoamylase Genes ISA1, ISA2, and ISA3 Confers Transgenic Phenotype

by Ido Simon, Zohar Persky, Aviram Avital, Hila Harat, Avi Schroeder and Oded Shoseyov

Int. J. Mol. Sci. 2023, 24(1), 190; https://doi.org/10.3390/ijms24010190 - 22 Dec 2022

Cited by 3 | Viewed by 2077

Abstract

Isoamylase (ISA) is a debranching enzyme found in many plants, which hydrolyzes (1-6)-α-D glucosidic linkages in starch, amylopectin, and β-dextrins, and is thought to be responsible for starch granule formation (ISA1 and ISA2) and degradation (ISA3). Lipid-modified PEI (lmPEI) was synthesized as a carrier for long double-stranded RNA (dsRNA, 250-bp), which targets the three isoamylase isoforms. The particles were applied to the plant via the foliar spray and were differentially effective in suppressing the expressions of ISA1 and ISA2 in the potato leaves, and ISA3 in the tubers. Plant growth was not significantly impaired, and starch levels in the tubers were not affected as well. Interestingly, the treated plants had significantly smaller starch granule sizes as well as increased sucrose content, which led to an early sprouting phenotype. We confirm the proposal of previous research that an increased number of small starch granules could be responsible for an accelerated turnover of glucan chains and, thus, the rapid synthesis of sucrose, and we propose a new relationship between ISA3 and the starch granule size. The implications of this study are in achieving a transgenic phenotype for endogenous plant genes using a systemic, novel delivery system, and foliar applications of dsRNA for agriculture. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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16 pages, 38124 KiB

Open AccessArticle

Novel Roles of RNA m6A Methylation Regulators in the Occurrence of Alzheimer’s Disease and the Subtype Classification

by Min Li, Wenli Cheng, Luyun Zhang, Cheng Zhou, Xinyue Peng, Susu Yu and Wenjuan Zhang

Int. J. Mol. Sci. 2022, 23(18), 10766; https://doi.org/10.3390/ijms231810766 - 15 Sep 2022

Cited by 6 | Viewed by 2898

Abstract

Alzheimer’s disease (AD) is one of the most common forms of dementia, closely related to epigenetic factors. N6-methyladenosine (m6A) is the most abundant RNA modification, affecting the pathogenesis and development of neurodegenerative diseases. This study was the first exploration of the combined role of 25 common m6A RNA methylation regulators in AD through the integrated bioinformatics approaches. The 14 m6A regulators related to AD were selected by analyzing differences between AD patients and normal controls. Based on the selected m6A regulators, AD patients could be well classified into two m6A models using consensus clustering. The two clusters of patients had different immune profiles, and m6A regulators were associated with the components of immune cells. Additionally, there were 19 key AD genes obtained by screening differential genes through weighted gene co-expression network and least absolute shrinkage and selection operator regression analysis, which were highly associated with important m6A regulators during the occurrence of AD. More interestingly, NOTCH2 and NME1 could be potential targets for m6A regulation of AD. Taken together, these findings indicate that dysregulation of m6A methylation affects the occurrence of AD and is vital for the subtype classification and immune infiltration of AD. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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19 pages, 6137 KiB

Open AccessArticle

Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development

by Xiaoyu Huang, Nigara Abuduwaili, Xinting Wang, Miao Tao, Xiaoqian Wang and Gengqing Huang

Int. J. Mol. Sci. 2022, 23(17), 9887; https://doi.org/10.3390/ijms23179887 - 31 Aug 2022

Cited by 5 | Viewed by 2048

Abstract

N6-methyladenosine (m⁶A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m⁶A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m⁶A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m⁶A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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16 pages, 3697 KiB

Open AccessArticle

Dynamic Alteration Profile and New Role of RNA m6A Methylation in Replicative and H₂O₂-Induced Premature Senescence of Human Embryonic Lung Fibroblasts

by Fan Wu, Luyun Zhang, Caiyun Lai, Xinyue Peng, Susu Yu, Cheng Zhou, Bo Zhang and Wenjuan Zhang

Int. J. Mol. Sci. 2022, 23(16), 9271; https://doi.org/10.3390/ijms23169271 - 17 Aug 2022

Cited by 10 | Viewed by 3245

Abstract

N6-methyladenosine (m6A) methylation is one of the most common RNA modifications, regulating RNA fate at the posttranscriptional level, and is closely related to cellular senescence. Both models of replicative and premature senescence induced by hydrogen peroxide (H₂O₂) were used to detect m6A regulation during the senescence of human embryonic lung fibroblasts (HEFs). The ROS level accumulated gradually with senescence, leading to normal replicative senescence. H₂O₂-treated cells had dramatically increased ROS level, inducing the onset of acute premature senescence. Compared with replicative senescence, ROS changed the expression profiles for m6A-related enzymes and binding proteins, including higher levels of METTL3, METTL14, WTAP, KIAA1429, and FTO, and lower levels of METTL16, ALKBH5, YTHDC1, and YTHDF1/2/3 in the premature senescence persistence group, respectively. Meanwhile, senescent cells decreased total m6A content and RNA methylation enzymes activity, regardless of replicative or premature senescence. Moreover, specific m6A methylation levels regulated the expression of SIRT3, IRS2, and E2F3 between replicative and premature senescence separately. Taken together, differential m6A epitranscription microenvironment and the targeted genes can be used as epigenetic biomarkers to cell senescence and the related diseases, offering new clues for the prevention and intervention of cellular senescence. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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13 pages, 22452 KiB

Open AccessArticle

Interaction Analysis between the Arabidopsis Transcription Repressor VAL1 and Transcription Coregulators SIN3-LIKEs (SNLs)

by Chuanyou Chen, Xia Gong, Yan Li, Haitao Li, Haitao Zhang, Li Liu, Dacheng Liang and Wenya Yuan

Int. J. Mol. Sci. 2022, 23(13), 6987; https://doi.org/10.3390/ijms23136987 - 23 Jun 2022

Cited by 5 | Viewed by 2423

Abstract

VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE1 (VAL1) encodes a DNA-binding B3 domain protein and plays essential roles in seed maturation and flowering transition by repressing genes through epigenetic silencing in Arabidopsis. SWI-INDEPENDENT3 (SIN3)-LIKEs (SNLs), which encode scaffold proteins for the assembly of histone deacetylase complexes and have six SIN3 homologues (SNL1–SNL6) in Arabidopsis thaliana, directly repress gene expression to regulate seed maturation and flowering transition. However, it remains unclear whether VAL1 and SNLs work together in repressing the expression of related genes. In this study, yeast two-hybrid and firefly luciferase complementation imaging assays revealed that VAL1 interacts with SNLs, which can be attributed to its own zinc-finger CW (conserved Cys (C) and Trp (W) residues) domain and the PAH (Paired Amphipathic Helices) domains of SNLs. Furthermore, pull-down experiments confirmed that the CW domain of VAL1 interacts with both intact protein and the PAH domains of SNLs proteins, and the co-immunoprecipitation assays also confirmed the interaction between VAL1 and SNLs. In addition, quantitative real-time PCR (qRT-PCR) analysis showed that VAL1 and SNLs were expressed in seedlings, and transient expression assays showed that VAL1 and SNLs were localized in the nucleus. Considered together, these results reveal that VAL1 physically interacts with SNLs both in vitro and in vivo, and suggest that VAL1 and SNLs may work together to repress the expression of genes related to seed maturation and flowering transition in Arabidopsis. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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Review

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23 pages, 1433 KiB

Open AccessReview

A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms

by Ekaterina P. Kalabusheva, Anastasia S. Shtompel, Alexandra L. Rippa, Sergey V. Ulianov, Sergey V. Razin and Ekaterina A. Vorotelyak

Int. J. Mol. Sci. 2023, 24(6), 5603; https://doi.org/10.3390/ijms24065603 - 15 Mar 2023

Cited by 5 | Viewed by 3894

Abstract

Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure. Full article

(This article belongs to the Special Issue Recent Advances in Epigenetics)

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