scholarly journals The Metabolism of 5-methylcytosine Residues in DNA

2018 ◽  
pp. 383-389
Author(s):  
R. MURÍN ◽  
M. ABDALLA ◽  
N. MURÍNOVÁ ◽  
J. HATOK ◽  
D. DOBROTA
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Spatial Pattern ◽  
Promoter Region ◽  
Opposite Effect ◽  
Methylation Pattern ◽  
Molecular Processes ◽  
Biochemical Processes ◽  
Dna Methylation Pattern ◽  
Silence Gene

The fundamental biochemical processes of 5-methylcytosine (5-mC) synthesis, maintenance, conversion and removal determine the time and spatial pattern of DNA methylation. This has a strong effect on a plethora of physiological aspects of cellular metabolism. While the presence of 5-mC within the promoter region can silence gene expression, its derivative – 5-hydroxymethylcytosine exerts an opposite effect. Dysregulations in the metabolism of 5-mC lead to an altered DNA methylation pattern which is linked with a disrupted epigenome, and are considered to play a significant part in the etiology of several human diseases. A summary of recent knowledge about the molecular processes participating in DNA methylation pattern shaping is provided here.

Assessment of DNA methylation pattern under drought stress using methylation-sensitive randomly amplified polymorphism analysis in rice

2020 ◽  
Vol 18 (4) ◽  
pp. 222-230
Author(s):  
Harihar Sapna ◽  
Narasimha Ashwini ◽  
Sampangiramareddy Ramesh ◽  
Karaba N. Nataraja
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Promoter Region ◽  
Dna Analysis ◽  
Water Status ◽  
Cpg Islands ◽  
Methylation Pattern ◽  
Epigenetic Mechanism ◽  
Polymorphism Analysis ◽  
Dna Methylation Pattern

AbstractDNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

scholarly journals DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Ramesh S. Bhat ◽  
J. Rockey ◽  
Kenta Shirasawa ◽  
I. S. Tilak ◽  
M. P. Brijesh Patil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Methylation Pattern ◽  
Chromosome 17 ◽  
Foliar Disease ◽  
Genome Wide ◽  
Arachis Hypogaea L ◽  
Dna Sequence Polymorphism ◽  
Dna Methylation Pattern ◽  
Resistant Genotypes

Abstract Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (3,05,37,376) of DNA methylation followed by CpG (3,03,56,066) and CHH (1,59,93,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (4,62,94,063) than the A sub-genome (3,04,15,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. A few genes showed altered methylation and expression between the parent and its EMS-derived mutant. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM). Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression, indicating the application of these epialleles in peanut breeding.

scholarly journals DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
R. S. Bhat ◽  
J. Rockey ◽  
Kenta Shirasawa ◽  
I. S. Tilak ◽  
M. P. Brijesh Patil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Methylation Pattern ◽  
Chromosome 17 ◽  
Foliar Disease ◽  
Genome Wide ◽  
Arachis Hypogaea L ◽  
Dna Sequence Polymorphism ◽  
Dna Methylation Pattern ◽  
Resistant Genotypes

Abstract Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.

scholarly journals DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Ramesh S. Bhat ◽  
J. Rockey ◽  
Kenta Shirasawa ◽  
I. S. Tilak ◽  
M. P. Brijesh Patil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Methylation Pattern ◽  
Chromosome 17 ◽  
Foliar Disease ◽  
Genome Wide ◽  
Arachis Hypogaea L ◽  
Dna Sequence Polymorphism ◽  
Dna Methylation Pattern ◽  
Resistant Genotypes

Abstract Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.

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