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Epigenomes, Volume 1, Issue 2 (September 2017)

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Research

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Open AccessArticle Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana
Epigenomes 2017, 1(2), 8; doi:10.3390/epigenomes1020008
Received: 15 April 2017 / Revised: 12 June 2017 / Accepted: 15 June 2017 / Published: 29 June 2017
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Abstract
Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine
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Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics. Full article
(This article belongs to the Special Issue Plant Epigenome Dynamics)
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Open AccessArticle Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley
Epigenomes 2017, 1(2), 9; doi:10.3390/epigenomes1020009
Received: 25 April 2017 / Revised: 15 June 2017 / Accepted: 20 June 2017 / Published: 27 June 2017
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Abstract
Terminal drought stress during grain filling is the major abiotic factor that limits crop yield in barley. The mother plant acclimates to the environment and perceives signals that result in a change of the physiological state within the grain and therefore affect the
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Terminal drought stress during grain filling is the major abiotic factor that limits crop yield in barley. The mother plant acclimates to the environment and perceives signals that result in a change of the physiological state within the grain and therefore affect the seed development and germination of the next generation. Small regulatory RNAs have been described to be involved in plant drought stress response by suppressing the respective target genes. Based on their origin and function, these small RNAs are classified as micro RNAs (miRNA), short interfering RNAs (siRNA) or heterochromatic small interfering RNA (hc-siRNA). In addition, 24mer sized hc-siRNAs are associated with RNA directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). The analysis of hc-siRNA by small RNA sequencing in barley caryopses after imposition of terminal drought stress allowed the identification of stress specific 24mers. Based on the sequence homology of the siRNAs to the promoter region of CYTOKININ-OXIDASE 2.1 (HvCKX2.1), this putative target gene was selected for further investigation. Terminal drought stress leads to an increased level of DNA methylation at the HvCKX2.1 promoter and the seeds derived from drought stressed plants showed faster shoot emergence. Accumulation of cytokinin ribosides, which are the known substrates of cytokinin-oxidase, can explain the observed phenotype of faster shoot emergence from seeds of drought stressed mother plants. Analysis of transgenic plants with modulated levels of abscisic acid (ABA) in the grain confirmed the ABA/drought stress responsive ProHvCKX2.1 methylation and correlation with shoot emergence speed. Full article
(This article belongs to the Special Issue Plant Epigenome Dynamics)
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Open AccessArticle Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review
Epigenomes 2017, 1(2), 13; doi:10.3390/epigenomes1020013
Received: 3 July 2017 / Revised: 5 September 2017 / Accepted: 8 September 2017 / Published: 13 September 2017
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Abstract
Large-scale transcriptome and methylome data analyses obtained by high-throughput technologies have been enabling the identification of novel imprinted genes. We investigated genome-wide DNA methylation patterns in multiple human tissues, using a high-resolution microarray to uncover hemimethylated CpGs located in promoters overlapping CpG islands,
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Large-scale transcriptome and methylome data analyses obtained by high-throughput technologies have been enabling the identification of novel imprinted genes. We investigated genome-wide DNA methylation patterns in multiple human tissues, using a high-resolution microarray to uncover hemimethylated CpGs located in promoters overlapping CpG islands, aiming to identify novel candidate imprinted genes. Using our approach, we recovered ~30% of the known human imprinted genes, and a further 168 candidates were identified, 61 of which with at least three hemimethylated CpGs shared by more than two tissue types. Thirty-four of these candidate genes are members of the protocadherin cluster on 5q31.3; in mice, protocadherin genes have non-imprinted random monoallelic expression, which might also be the case in humans. Among the remaining 27 genes, ZNF331 was recently validated as an imprinted gene, and six of them have been reported as candidates, supporting our prediction. Five candidates (CCDC166, ARC, PLEC, TONSL, and VPS28) map to 8q24.3, and might constitute a novel imprinted cluster. Additionally, we performed a comprehensive compilation of known human and mice imprinted genes from literature and databases, and a comparison among high-throughput imprinting studies in humans. The screening for hemimethylated CpGs shared by multiple human tissues, together with the extensive review, appears to be a useful approach to reveal candidate imprinted genes. Full article
(This article belongs to the Special Issue Biological Methylation in Development and Cancer)
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Review

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Open AccessReview DNA Methylation in Rice and Relevance for Breeding
Epigenomes 2017, 1(2), 10; doi:10.3390/epigenomes1020010
Received: 3 June 2017 / Revised: 27 June 2017 / Accepted: 30 June 2017 / Published: 4 July 2017
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Abstract
The challenge of sustaining food security in the context of global changes is at the heart of plant research. Environmental stresses, in particular, are known to impact genome stability and epigenetic mechanisms. Epigenetic pathways are well characterized in plants, particularly in the dicotyledon
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The challenge of sustaining food security in the context of global changes is at the heart of plant research. Environmental stresses, in particular, are known to impact genome stability and epigenetic mechanisms. Epigenetic pathways are well characterized in plants, particularly in the dicotyledon model plant Arabidopsis thaliana, but an increasing number of epigenetic and epigenomic studies are also performed on rice (Oryza sativa). Rice represents a major food crop of worldwide importance and is also a good model for monocotyledons owing to its relatively small genome size and fully sequenced well-annotated genome. Today, the main regulators of DNA methylation are identified in rice. Moreover, compared to Arabidopsis, rice has an important evolutionary history due to human selection since its domestication. DNA methylation may be involved in both adaptation and agronomic performances and thus, a better understanding of epigenetic regulations in rice should contribute to improving the adaptation of crops to a changing environment. In this review, we expose the current knowledge on DNA methylation in rice and future perspectives to be considered. Full article
(This article belongs to the Special Issue Plant Epigenome Dynamics)
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Open AccessReview Epitranscriptome and FMRP Regulated mRNA Translation
Epigenomes 2017, 1(2), 11; doi:10.3390/epigenomes1020011
Received: 18 May 2017 / Revised: 14 July 2017 / Accepted: 17 July 2017 / Published: 21 July 2017
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Abstract
An important regulatory mechanism affecting mRNA translation involves various covalent modifications of RNA, which establish distinct epitranscriptomic signatures that actively influence various physiological processes. Dendritic translation in mammalian neurons is a potent target for RNA modification-based regulation. In this mini-review, we focus on
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An important regulatory mechanism affecting mRNA translation involves various covalent modifications of RNA, which establish distinct epitranscriptomic signatures that actively influence various physiological processes. Dendritic translation in mammalian neurons is a potent target for RNA modification-based regulation. In this mini-review, we focus on the effect of potential RNA modifications on the spatiotemporal regulation of the dendritic translation of mRNAs, which are targeted by two important neuronal translational co-regulators, namely TDP-43 and Fragile X Mental Retardation Protein (FMRP). Full article
(This article belongs to the Special Issue Epigenetics of the Nervous System)
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Open AccessReview The Role of Epigenetics on Dental Implant Therapy: A Systematic Review
Epigenomes 2017, 1(2), 12; doi:10.3390/epigenomes1020012
Received: 19 May 2017 / Revised: 14 August 2017 / Accepted: 28 August 2017 / Published: 31 August 2017
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Abstract
Abstract: Cell phenotype is influenced by the linear sequence of bases and by epigenetic changes. Despite the huge number of implants placed every year, epigenetic mechanisms controlling peri-implant processes remain unexplored. The purpose of this systematic qualitative review was to investigate the
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Abstract: Cell phenotype is influenced by the linear sequence of bases and by epigenetic changes. Despite the huge number of implants placed every year, epigenetic mechanisms controlling peri-implant processes remain unexplored. The purpose of this systematic qualitative review was to investigate the available articles dealing with the relationships between DNA methylations, histone modifications, or micro-RNA (miRNA) production and implant therapy. A large variety of different surfaces were evaluated based on their osteogenic stimulation of osteoblasts. Dental implant treatments like potassium hydroxide (KOH) alkali-etching, electrolytic etching, ionization, functionalization with miRNAs or anti-miRNAs, or osteogenic peptides enhanced osteoblast differentiation and gene activation by regulating miRNA production. Zirconia and anatase coating inhibited the activation of osteogenic genes. Epigenetic changes on peri-implant cells induced by smoking still remain unclear. Due to the heterogeneity of methodologies, a meta-analysis was not possible. Even if it is impossible to define which implant surface was best to genetically stimulate osteogenesis, there is evidence that implant surface features can upregulate or downregulate genes related to osseointegration. Full article
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