A comparative analysis of DNA methylation in diploid and tetraploid apple (Malus × domestica Borkh.)

DNA methylation is one of the major epigenetic modifications. It is very important to the regulation of gene expression. Methylation-sensitive amplification polymorphism (MSAP) profiling was applied to a diploid apple cultivar and its derived autotetraploid in order to characterize the level and pattern of DNA methylation at the two different ploidies. The frequency of methylated restriction sites was very similar between the two types (28.0% vs 27.3%), implying that polyploidization had a low effect on the global level of DNA methylation. However, with respect to the pattern of methylation, the frequency of hemi-methylated sites was higher in the tetraploid. When the transcription level of three genes encoding DNA methyltransferase was investigated in various tissues, it was established that MET1 transcript abundance was the lowest of the three genes throughout the plant, while that of DRM2 was high in the leaf, flower and fruit, as was that of CTM3 in the fruit. Polyploidization had no discernible effect on the transcription level of any of the three genes.

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Study on the Heterosis of the First Generation of Hybrid between Chinese and Korean Populations of Scapharca broughtonii using Methylation-Sensitive Amplification Polymorphism (MSAP)

Journal of Molecular Biology Research ◽

10.5539/jmbr.v5n1p56 ◽

2015 ◽

Vol 5 (1) ◽

pp. 56

Author(s):

Hailin Sun ◽

Yanxin Zheng ◽

Chunnuan Zhao ◽

Tao Yu ◽

Jianguo Lin

Keyword(s):

Dna Methylation ◽

First Generation ◽

Cytosine Methylation ◽

Shell Height ◽

Regulation Of Gene Expression ◽

Patinopecten Yessoensis ◽

Chinese Populations ◽

Scapharca Broughtonii ◽

Methylation Sensitive Amplification Polymorphism ◽

Methylation Ratio

DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, the author assessed the extent and pattern of cytosine methylation in the Scapharca broughtonii genome using the technique of methylation-sensitive amplified polymorphism (MSAP).The results showed that, DNA methylation rate was negatively related to the shell length, the gross weight and the weight of soft body, but positively related to the shell broadness and the shell height; there was significantly different between the parents and the offspring: 31.6% of 5'-CCGG sites in the Patinopecten yessoensis of Korean populations genome were cytosine methylated, and in the Patinopecten yessoensis of Chinese populations were 33%, the methylation rates of F1 was 29.98%; four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid, increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. It indicated that the alteration of methylation resulted from cross-breeding, and the inbreeding did not change the methylation ratio and patterns; The DNA cytosine methylation has a relationship with the heterosis.

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DNA methylation in lowbush blueberry (Vaccinium angustifolium Ait.) propagated by softwood cutting and tissue culture

Canadian Journal of Plant Science ◽

10.1139/cjps-2017-0297 ◽

2018 ◽

Vol 98 (5) ◽

pp. 1035-1044 ◽

Cited By ~ 7

Author(s):

Juran C. Goyali ◽

Abir U. Igamberdiev ◽

Samir C. Debnath

Keyword(s):

Dna Methylation ◽

Tissue Culture ◽

Growth Conditions ◽

Vaccinium Angustifolium ◽

Lowbush Blueberry ◽

Restriction Sites ◽

Methylation Sensitive Amplification Polymorphism ◽

Softwood Cutting

Plant DNA methylation is one of the frequent epigenetic variations induced by tissue culture. Global DNA methylation was evaluated in lowbush blueberry (Vaccinium angustifolium Ait.) wild clone QB9C and cultivar Fundy propagated by conventional softwood cutting (SC) and tissue culture (TC) using the methylation-sensitive amplification polymorphism (MSAP) technique. In all, 106 and 107 DNA fragments were amplified using 16 selective primer combinations in SC plants of QB9C and Fundy, respectively. In micropropagated QB9C and Fundy plants, there were 105 and 109 amplified fragments, respectively. Overall, 25% of restriction sites were methylated at the cytosine nucleotide in QB9C plants propagated by SC compared with 19% in Fundy. In contrast, a total of 29% and 20% of restriction sites were methylated at cytosine in micropropagated QB9C and Fundy plants, respectively. Tissue culture plants demonstrated higher methylation events than SC plants in both genotypes. Previously, methylation polymorphism has been detected in TC plants but not in SC counterparts. Different patterns of DNA methylation and polymorphism in the plants propagated in in vitro and in vivo conditions suggest the possibility of involvement of these fragments in the processes of regulating plant growth and development under prevailing growth conditions.

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Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice

Plants ◽

10.3390/plants9091088 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1088

Author(s):

Sung-Il Lee ◽

Jae Wan Park ◽

Soon-Jae Kwon ◽

Yeong Deuk Jo ◽

Min Jeong Hong ◽

...

Keyword(s):

Dna Methylation ◽

Gamma Rays ◽

Genome Stability ◽

Dna Methyltransferase ◽

Combined Treatment ◽

Regulation Of Gene Expression ◽

Mutation Breeding ◽

Dependent Manner ◽

Dna Methyltransferase Inhibitors ◽

Epigenetic Diversity

DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.

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Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

Journal of Applied Genetics ◽

10.1007/s13353-021-00609-4 ◽

2021 ◽

Author(s):

Agata Tyczewska ◽

Joanna Gracz-Bernaciak ◽

Jakub Szymkowiak ◽

Tomasz Twardowski

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Zea Mays ◽

Expression Patterns ◽

Regulation Of Gene Expression ◽

Differential Susceptibility ◽

Inbred Lines ◽

Specific Gene ◽

Genes Encoding ◽

Shock Proteins

AbstractDNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

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CBFB-MYH11 Fusion Sequesters RUNX1 in Cytoplasm to Prevent DNMT3A Recruitment to Target Genes in AML

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.675424 ◽

2021 ◽

Vol 9 ◽

Author(s):

Peng Liu ◽

Jin-Pin Liu ◽

Si-Jia Sun ◽

Yun Gao ◽

Yingjie Ai ◽

...

Keyword(s):

Dna Methylation ◽

Fusion Protein ◽

Dna Methyltransferase ◽

Target Genes ◽

Gene Mutations ◽

Loss Of Function ◽

Dna Hypomethylation ◽

Multiple Cancer ◽

Genes Encoding ◽

Related Transcription Factor

A growing number of human diseases have been found to be associated with aberrant DNA methylation, including cancer. Mutations targeting genes encoding DNA methyltransferase (DNMT), TET family of DNA demethylases, and isocitrate dehydrogenase (IDH1, IDH2) that produce TET inhibitory metabolite, 2-hyoxyglutarate (2-HG), are found in more than half of acute myeloid leukemia (AML). To gain new insights into the regulation of DNA de/methylation and consequence of its alteration in cancer development, we searched for genes which are mutated in a manner that is linked with gene mutations involved in DNA de/methylation in multiple cancer types. We found that recurrent CBFB-MYH11 fusions, which result in the expression of fusion protein comprising core-binding factor β (CBFB) and myosin heavy chain 11 (MYH11) and are found in 6∼8% of AML patients, occur mutually exclusively with DNMT3A mutations. Tumors bearing CBFB-MYH11 fusion show DNA hypomethylation patterns similar to those with loss-of-function mutation of DNMT3A. Expression of CBFB-MYH11 fusion or inhibition of DNMT3A similarly impairs the methylation and expression of target genes of Runt related transcription factor 1 (RUNX1), a functional partner of CBFB. We demonstrate that RUNX1 directly interacts with DNMT3A and that CBFB-MYH11 fusion protein sequesters RUNX1 in the cytoplasm, thereby preventing RUNX1 from interacting with and recruiting DNMT3A to its target genes. Our results identify a novel regulation of DNA methylation and provide a molecular basis how CBFB-MYH11 fusion contributes to leukemogenesis.

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DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells

The Journal of Cell Biology ◽

10.1083/jcb.200610062 ◽

2007 ◽

Vol 176 (5) ◽

pp. 565-571 ◽

Cited By ~ 131

Author(s):

Fabio Spada ◽

Andrea Haemmer ◽

David Kuch ◽

Ulrich Rothbauer ◽

Lothar Schermelleh ◽

...

Keyword(s):

Dna Methylation ◽

Dna Methyltransferase ◽

Regulation Of Gene Expression ◽

Human Cells ◽

Nuclear Antigen ◽

Replication Machinery ◽

Catalytically Active ◽

Methylation Patterns ◽

Proliferating Cell

DNA methylation plays a central role in the epigenetic regulation of gene expression in vertebrates. Genetic and biochemical data indicated that DNA methyltransferase 1 (Dnmt1) is indispensable for the maintenance of DNA methylation patterns in mice, but targeting of the DNMT1 locus in human HCT116 tumor cells had only minor effects on genomic methylation and cell viability. In this study, we identified an alternative splicing in these cells that bypasses the disrupting selective marker and results in a catalytically active DNMT1 protein lacking the proliferating cell nuclear antigen–binding domain required for association with the replication machinery. Using a mechanism-based trapping assay, we show that this truncated DNMT1 protein displays only twofold reduced postreplicative DNA methylation maintenance activity in vivo. RNA interference–mediated knockdown of this truncated DNMT1 results in global genomic hypomethylation and cell death. These results indicate that DNMT1 is essential in mouse and human cells, but direct coupling of the replication of genetic and epigenetic information is not strictly required.

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DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423603112 ◽

2015 ◽

Vol 112 (3) ◽

pp. 911-916 ◽

Cited By ~ 14

Author(s):

Xuehua Zhong ◽

Christopher J. Hale ◽

Minh Nguyen ◽

Israel Ausin ◽

Martin Groth ◽

...

Keyword(s):

Dna Methylation ◽

Rna Polymerase ◽

Noncoding Rna ◽

Dna Methyltransferase ◽

Transcript Abundance ◽

Transcriptional Elongation ◽

Rna Transcripts ◽

Pol V ◽

Genome Defense ◽

Eukaryotic Organisms

DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a pathway that also involves the plant-specific RNA Polymerase V (Pol V). Additionally, the Arabidopsis genome encodes an evolutionarily conserved but catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has moderate effects on global DNA methylation and small RNA abundance and that DRM3 physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin occupancy is increased at many sites in the genome. These findings suggest that DRM3 acts to promote Pol V transcriptional elongation or assist in the stabilization of Pol V transcripts. This work sheds further light on the mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation.

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Transcriptome Profiling Reveals Transcriptional Regulation by DNA Methyltransferase Inhibitor 5-Aza-2′-Deoxycytidine Enhancing Red Pigmentation in Bagged “Granny Smith” Apples (Malus domestica)

International Journal of Molecular Sciences ◽

10.3390/ijms19103133 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3133 ◽

Cited By ~ 4

Author(s):

Changqing Ma ◽

Bowen Liang ◽

Bo Chang ◽

Li Liu ◽

Jiuying Yan ◽

...

Keyword(s):

Dna Methylation ◽

Malus Domestica ◽

Dna Methyltransferase ◽

Transcriptome Profiling ◽

Anthocyanin Content ◽

Dna Methyltransferase Inhibitor ◽

Fruit Skin ◽

Red Color ◽

Genes Encoding ◽

And Control

The red color of apples (Malus domestica) is an attractive trait for consumers. The green skinned “Granny Smith” cultivar develops red pigmentation after bagging treatment. DNA methylation plays an important role in various developmental processes in plants. To explore the possible functions of DNA methylation in the pigmentation of bagged “Granny Smith” apples, we first analyzed the anthocyanin content of fruit skin following treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC). The results revealed an increase in anthocyanin content in bagged fruits following 5-aza-dC treatment, while no anthocyanins were detected in unbagged fruits. In addition, 8482 differentially expressed genes between 5-aza-dC-treated and control groups were identified in bagged fruits by RNA sequencing, including genes encoding transcription factors, enzymes related to anthocyanin accumulation, and methylases. Changes in the expression of these genes may be responsible for 5-aza-dC-induced red pigmentation in bagged fruits of “Granny Smith”. The findings provide novel evidence for the involvement of DNA methylation in the red pigmentation of non-red-skinned apples.

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DNA methylation in satellite repeats disorders

Essays in Biochemistry ◽

10.1042/ebc20190028 ◽

2019 ◽

Vol 63 (6) ◽

pp. 757-771 ◽

Cited By ~ 4

Author(s):

Claire Francastel ◽

Frédérique Magdinier

Keyword(s):

Dna Methylation ◽

Human Genome ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Repeats ◽

Tremendous Progress ◽

Genes Encoding ◽

Dna Elements ◽

Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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Profile of copper-associated DNA methylation and its association with incident acute coronary syndrome

Clinical Epigenetics ◽

10.1186/s13148-021-01004-w ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Pinpin Long ◽

Qiuhong Wang ◽

Yizhi Zhang ◽

Xiaoyan Zhu ◽

Kuai Yu ◽

...

Keyword(s):

Dna Methylation ◽

Acute Coronary Syndrome ◽

Methylation Level ◽

Meta Analysis ◽

Regulation Of Gene Expression ◽

Density Lipoprotein ◽

Blood Leukocytes ◽

Coronary Syndrome ◽

A Genome ◽

Increased Risk

Abstract Background Acute coronary syndrome (ACS) is a cardiac emergency with high mortality. Exposure to high copper (Cu) concentration has been linked to ACS. However, whether DNA methylation contributes to the association between Cu and ACS is unclear. Methods We measured methylation level at > 485,000 cytosine-phosphoguanine sites (CpGs) of blood leukocytes using Human Methylation 450 Bead Chip and conducted a genome-wide meta-analysis of plasma Cu in a total of 1243 Chinese individuals. For plasma Cu-related CpGs, we evaluated their associations with the expression of nearby genes as well as major cardiovascular risk factors. Furthermore, we examined their longitudinal associations with incident ACS in the nested case-control study. Results We identified four novel Cu-associated CpGs (cg20995564, cg18608055, cg26470501 and cg05825244) within a 5% false discovery rate (FDR). DNA methylation level of cg18608055, cg26470501, and cg05825244 also showed significant correlations with expressions of SBNO2, BCL3, and EBF4 gene, respectively. Higher DNA methylation level at cg05825244 locus was associated with lower high-density lipoprotein cholesterol level and higher C-reactive protein level. Furthermore, we demonstrated that higher cg05825244 methylation level was associated with increased risk of ACS (odds ratio [OR], 1.23; 95% CI 1.02–1.48; P = 0.03). Conclusions We identified novel DNA methylation alterations associated with plasma Cu in Chinese populations and linked these loci to risk of ACS, providing new insights into the regulation of gene expression by Cu-related DNA methylation and suggesting a role for DNA methylation in the association between copper and ACS.

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