No consistent daily variation in DNA methylation detected in Populus nigra leaves by methylation-sensitive amplification polymorphism analysis

Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino is a diploid plant belonging to the Asteraceae family, with typical capitula composed of female ray florets and bisexual disc florets. The differentiation and development of these two types of florets have long been important research focuses; however, the potential epigenetic mechanisms governing these processes have not been elucidated. In the present study, methylation-sensitive amplification polymorphism method was used to trace the dynamic changes of DNA methylation during capitulum development in C. lavandulifolium. DNA methylation patterns and levels were detected in the whole capitula during seven developmental stages, and the obtained results revealed that DNA demethylation was dominant during this process. In addition, DNA methylation patterns and levels showed significant differences between ray and disc florets. Moreover, the expression patterns of candidate genes potentially involved in the development processes of two types of florets were analyzed by real-time quantitative reverse transcription polymerase chain reaction, and correlation analysis indicated that the expression levels of ClPI, ClAG2, ClSEP1, ClCYC2c, ClCYC2d, and ClCYC2e were highly correlated with DNA methylation levels. These results indicate that DNA methylation may be involved in the differentiation and development of ray and disc florets. This study provides epigenetic insights into the capitulum development in C. lavandulifolium.

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Methylation-sensitive Amplified Polymorphism Analysis of DNA Methylation in Arabidopsis Under Mannitol Treatment

CHINESE BULLETIN OF BOTANY ◽

10.3724/sp.j.1259.2011.00285 ◽

2011 ◽

Vol 46 (3) ◽

pp. 285-292 ◽

Cited By ~ 3

Author(s):

Du Yaqiong ◽

Wang Zicheng

Keyword(s):

Dna Methylation ◽

Polymorphism Analysis

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

Czech Journal of Genetics and Plant Breeding ◽

10.17221/55/2016-cjgpb ◽

2017 ◽

Vol 53 (No. 2) ◽

pp. 63-68

Author(s):

P. He ◽

L. Cheng ◽

H. Li ◽

H. Wang ◽

L. Li

Keyword(s):

Dna Methylation ◽

Dna Methyltransferase ◽

Regulation Of Gene Expression ◽

Transcript Abundance ◽

Global Level ◽

Transcription Level ◽

Discernible Effect ◽

Restriction Sites ◽

Genes Encoding ◽

Methylation Sensitive Amplification Polymorphism

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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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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Ultraviolet B Radiation Triggers DNA Methylation Change and Affects Foraging Behavior of the Clonal Plant Glechoma longituba

Frontiers in Plant Science ◽

10.3389/fpls.2021.633982 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jiaxin Quan ◽

Vít Latzel ◽

Dan Tie ◽

Yuhan Zhang ◽

Zuzana Münzbergová ◽

...

Keyword(s):

Dna Methylation ◽

Foraging Behavior ◽

Clonal Plants ◽

Ultraviolet B ◽

Light Environment ◽

Polymorphism Analysis ◽

Epigenetic Variation ◽

Heterogeneous Environment ◽

Distributed Resources ◽

Glechoma Longituba

Clonal plants in heterogeneous environments can benefit from their habitat selection behavior, which enables them to utilize patchily distributed resources efficiently. It has been shown that such behavior can be strongly influenced by their memories on past environmental interactions. Epigenetic variation such as DNA methylation was proposed to be one of the mechanisms involved in the memory. Here, we explored whether the experience with Ultraviolet B (UV-B) radiation triggers epigenetic memory and affects clonal plants’ foraging behavior in an UV-B heterogeneous environment. Parental ramets of Glechoma longituba were exposed to UV-B radiation for 15 days or not (controls), and their offspring ramets were allowed to choose light environment enriched with UV-B or not (the species is monopodial and can only choose one environment). Sizes and epigenetic profiles (based on methylation-sensitive amplification polymorphism analysis) of parental and offspring plants from different environments were also analyzed. Parental ramets that have been exposed to UV-B radiation were smaller than ramets from control environment and produced less and smaller offspring ramets. Offspring ramets were placed more often into the control light environment (88.46% ramets) than to the UV-B light environment (11.54% ramets) when parental ramets were exposed to UV-B radiation, which is a manifestation of “escape strategy.” Offspring of control parental ramets show similar preference to the two light environments. Parental ramets exposed to UV-B had lower levels of overall DNA methylation and had different epigenetic profiles than control parental ramets. The methylation of UV-B-stressed parental ramets was maintained among their offspring ramets, although the epigenetic differentiation was reduced after several asexual generations. The parental experience with the UV-B radiation strongly influenced foraging behavior. The memory on the previous environmental interaction enables clonal plants to better interact with a heterogeneous environment and the memory is at least partly based on heritable epigenetic variation.

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Integrative analysis of genome-wide DNA methylation and single-nucleotide polymorphism identified ACSM5 as a suppressor of lumbar ligamentum flavum hypertrophy

Arthritis Research & Therapy ◽

10.1186/s13075-021-02625-5 ◽

2021 ◽

Vol 23 (1) ◽

Author(s):

Yanlin Cao ◽

Yenan Zhan ◽

Sujun Qiu ◽

Zhong Chen ◽

Kaiqin Gong ◽

...

Keyword(s):

Dna Methylation ◽

Single Nucleotide Polymorphism ◽

Ligamentum Flavum ◽

Global Analysis ◽

Integrated Analysis ◽

Polymorphism Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome

Abstract Background Hypertrophy of ligamentum flavum (HLF) is a common lumbar degeneration disease (LDD) with typical symptoms of low back pain and limb numbness owing to an abnormal pressure on spinal nerves. Previous studies revealed HLF might be caused by fibrosis, inflammatory, and other bio-pathways. However, a global analysis of HLF is needed severely. Methods A genome-wide DNA methylation and single-nucleotide polymorphism analysis were performed from five LDD patients with HLF and five LDD patients without HLF. Comprehensive integrated analysis was performed using bioinformatics analysis and the validated experiments including Sanger sequencing, methylation-specific PCR, qPCR and ROC analysis. Furthermore, the function of novel genes in ligamentum flavum cells (LFCs) was detected to explore the molecular mechanism in HLF through knock down experiment, overexpression experiment, CCK8 assay, apoptosis assay, and so on. Results We identified 69 SNP genes and 735 661 differentially methylated sites that were enriched in extracellular matrix, inflammatory, and cell proliferation. A comprehensive analysis demonstrated key genes in regulating the development of HLF including ACSM5. Furthermore, the hypermethylation of ACSM5 that was mediated by DNMT1 led to downregulation of ACSM5 expression, promoted the proliferation and fibrosis, and inhibited the apoptosis of LFCs. Conclusion This study revealed that DNMT1/ACSM5 signaling could enhance HLF properties in vitro as a potential therapeutic strategy for HLF.

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