scholarly journals Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Rohini Garg ◽  
VVS Narayana Chevala ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Stress Response ◽  
Salinity Stress ◽  
Rice Cultivars ◽  
Methylation Patterns

scholarly journals Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars

2019 ◽  
Author(s):  
Mohan Singh Rajkumar ◽  
Rama Shankar ◽  
Rohini Garg ◽  
Mukesh Jain
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Abiotic Stress ◽  
Stress Response ◽  
Salinity Stress ◽  
Stress Responses ◽  
Rice Cultivars ◽  
Abiotic Stress Response ◽  
Methylation Patterns

AbstractDNA methylation is an epigenetic mark that controls gene expression in response to internal and environmental cues. In this study, we sought to understand the role of DNA methylation in response to desiccation and salinity stresses in three rice cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) via bisulphite sequencing. We identified DNA methylation patterns in different genomic/genic regions and analysed their correlation with gene expression. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. However, methylation in other sequence contexts and genic regions was negatively correlated with gene expression. DNA methylation was found to be most dynamic in CHH context under stress condition(s) in the rice cultivars. The expression profiles of genes involved in de-novo methylation were correlated with methylation dynamics. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stress, respectively, were correlated with higher expression of abiotic stress response related genes. Our results suggest an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. This study provides useful resource of DNA methylomes that can be integrated with other data to understand abiotic stress response in rice.HighlightBisulphite sequencing revealed single base resolution DNA methylation, and cultivar-specific differential methylation patterns and correlation with gene expression that control desiccation and salinity stress response in the rice cultivars.

Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance

2013 ◽  
Vol 12 (2) ◽  
pp. 253-264 ◽  
Author(s):  
Mukesh Jain ◽  
Kanhu Charan Moharana ◽  
Rama Shankar ◽  
Romika Kumari ◽  
Rohini Garg
Keyword(s):  
Stress Response ◽  
Salinity Stress ◽  
Dna Polymorphisms ◽  
Rice Cultivars ◽  
Functional Relevance

Abstract 40: Disturbed Flow Alters Genomewide DNA Methylation Patterns, Regulating Endothelial Gene Expression and Atherosclerosis

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Jessilyn Dunn ◽  
Haiwei Qiu ◽  
Soyeon Kim ◽  
Daudi Jjingo ◽  
Ryan Hoffman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Western Diet ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Endothelial Gene Expression

Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. We found that d-flow induced expression of DNMT1, but not DNMT3a or DNMT3b, in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) compared to unidirectional laminar shear in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two atherosclerosis models using ApoE-/- mice (western diet for 3 months and the partial carotid ligation model with western diet for 3 weeks). To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and transcript microarray using endothelial-enriched gDNA and RNA, respectively, obtained from the partially-ligated left common carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA exposed to s-flow) of mice treated with 5Aza or vehicle. D-flow induced DNA hypermethylation in 421 gene promoters, which was significantly prevented by 5Aza in 335 genes. Systems biological analyses using the RRBS and the transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated by d-flow but rescued by 5Aza treatment. Of those, five genes contain hypermethylated cAMP-response-elements in their promoters, including the transcription factors HoxA5 and Klf3. Their methylation status could serve as a mechanosensitive master switch in endothelial gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

scholarly journals TET2 coactivates gene expression through demethylation of enhancers

2018 ◽  
Vol 4 (11) ◽  
pp. eaau6986 ◽  
Author(s):  
Lu Wang ◽  
Patrick A. Ozark ◽  
Edwin R. Smith ◽  
Zibo Zhao ◽  
Stacy A. Marshall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Regulation Of Gene Expression ◽  
Estrogen Receptor Α ◽  
Dna Demethylation ◽  
Estrogen Response ◽  
Dna Base ◽  
Modified Dna ◽  
Global Increase ◽  
Methylation Patterns

The tet methylcytosine dioxygenase 2 (TET2) enzyme catalyzes the conversion of the modified DNA base 5-methylcytosine to 5-hydroxymethylcytosine. TET2 is frequently mutated or dysregulated in multiple human cancers, and loss of TET2 is associated with changes in DNA methylation patterns. Here, using newly developed TET2-specific antibodies and the estrogen response as a model system for studying the regulation of gene expression, we demonstrate that endogenous TET2 occupies active enhancers and facilitates the proper recruitment of estrogen receptor α (ERα). Knockout of TET2 by CRISPR-CAS9 leads to a global increase of DNA methylation at enhancers, resulting in attenuation of the estrogen response. We further identified a positive feedback loop between TET2 and ERα, which further requires MLL3 COMPASS at these enhancers. Together, this study reveals an epigenetic axis coordinating a transcriptional program through enhancer activation via DNA demethylation.

scholarly journals Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

2021 ◽  
Author(s):  
Jincheng Long ◽  
James Walker ◽  
Wenjing She ◽  
Billy Aldridge ◽  
Hongbo Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Nurse Cell ◽  
De Novo ◽  
Epigenetic Inheritance ◽  
Genome Integrity ◽  
Nurse Cells ◽  
Male Germline ◽  
Methylation Patterns

AbstractThe plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and facilitates meiosis. Why reprogramming is limited to the germline and how specific genes are chosen is unknown. Here, we demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by germline-specific siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the tapetum-specific chromatin remodeler CLASSY3. Remarkably, tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Finally, we demonstrate that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal that tapetal niRNAs are sufficient to reconstitute germline methylation patterns and drive extensive, functional methylation reprogramming analogous to piRNA-mediated reprogramming in animal germlines.

scholarly journals DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

2021 ◽  
Author(s):  
Carlos A. M. Cardoso-Junior ◽  
Boris Yagound ◽  
Isobel Ronai ◽  
Emily J. Remnant ◽  
Klaus Hartfelder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Honey Bee ◽  
Differential Gene Expression ◽  
Social Contexts ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Differential Gene ◽  
Honey Bee Workers ◽  
Methylation Patterns

AbstractIntragenic DNA methylation, also called gene body methylation, is an evolutionarily-conserved epigenetic mechanism in animals and plants. In social insects, gene body methylation is thought to contribute to behavioral plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in a subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.

P2019 Adipocyte gene expression and DNA methylation patterns differ significantly between lean and obese pigs

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 46-46
Author(s):  
M. J. Jacobsen ◽  
J. H. Havgaard ◽  
C. M. Junker Mentzel ◽  
P. M. Sørensen ◽  
S. Pundhir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Methylation Patterns

scholarly journals Changes in DNA Methylation and Gene Expression of Insulin and Obesity-Related Gene PIK3R1 after Roux-en-Y Gastric Bypass

2020 ◽  
Vol 21 (12) ◽  
pp. 4476
Author(s):  
Marcela A S Pinhel ◽  
Natália Y Noronha ◽  
Carolina F Nicoletti ◽  
Vanessa AB Pereira ◽  
Bruno AP de Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Weight Loss ◽  
Gastric Bypass ◽  
Related Gene ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genetically Determined ◽  
Methylation Patterns ◽  
Weight Loss Interventions

Weight regulation and the magnitude of weight loss after a Roux-en-Y gastric bypass (RYGB) can be genetically determined. DNA methylation patterns and the expression of some genes can be altered after weight loss interventions, including RYGB. The present study aimed to evaluate how the gene expression and DNA methylation of PIK3R1, an obesity and insulin-related gene, change after RYGB. Blood samples were obtained from 13 women (35.9 ± 9.2 years) with severe obesity before and six months after surgical procedure. Whole blood transcriptome and epigenomic patterns were assessed by microarray-based, genome-wide technologies. A total of 1966 differentially expressed genes were identified in the pre- and postoperative periods of RYGB. From these, we observed that genes involved in obesity and insulin pathways were upregulated after surgery. Then, the PIK3R1 gene was selected for further RT-qPCR analysis and cytosine-guanine nucleotide (CpG) sites methylation evaluation. We observed that the PI3KR1 gene was upregulated, and six DNA methylation CpG sites were differently methylated after bariatric surgery. In conclusion, we found that RYGB upregulates genes involved in obesity and insulin pathways.

scholarly journals DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 137 ◽  
Author(s):  
Shenglin Liu ◽  
Anne Aagaard ◽  
Jesper Bechsgaard ◽  
Trine Bilde
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sequence Data ◽  
Social Spider ◽  
The Social ◽  
Genome Bisulfite Sequencing ◽  
Differential Gene ◽  
Methylation Patterns ◽  
Comparative Phylogenetic Analysis

Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.

scholarly journals A comparison of gene expression and DNA methylation patterns across tissues and species

2020 ◽  
Vol 30 (2) ◽  
pp. 250-262 ◽  
Author(s):  
Lauren E. Blake ◽  
Julien Roux ◽  
Irene Hernando-Herraez ◽  
Nicholas E. Banovich ◽  
Raquel Garcia Perez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Methylation Patterns
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