DNA methylation related gene expression and morphophysiological response to abiotic stresses in Arabidopsis thaliana

AbstractThis study aimed to evaluate the effect of in ovo feeding (IOF) of vitamin C at embryonic age 11 (E11) on post-hatch performance, immune status and DNA methylation-related gene expression in broiler chickens. A total of 240 Arbor Acres breeder eggs (63 (sem 0·5) g) were randomly divided into two groups: normal saline and vitamin C (VC) groups. After incubation, newly hatched chicks from each group were randomly divided into six replicates with ten chicks per replicate. Hatchability, average daily feed intake (D21–42 and D1–42), and average daily gain and feed conversion ratio (D1–21) were improved by vitamin C treatment (P < 0·05). IOF of vitamin C increased vitamin C content (D1), total antioxidant capacity (D42), IgA (D1), IgM (D1 and D21), stimulation index for T lymphocyte (D35) and lysozyme activity (D21) in plasma (P < 0·05). On D21, vitamin C increased the splenic expression of IL-4 and DNMT1 and decreased IL-1β, Tet2, Tet3 and Gadd45β expression (P < 0·05). On D42, vitamin C increased the splenic expression of IL-4 and DNMT3A and decreased IFN-γ, Tet3, MBD4 and TDG expression (P < 0·05). In conclusion, the vitamin C via in ovo injection can be absorbed by broiler’s embryo and IOF of vitamin C at E11 improves the post-hatch performance and immune status and, to some extent, the antioxidant capacity of broiler chickens. The expression of enzyme-related DNA methylation and demethylation indicates that the level of DNA methylation may increase in spleen in the VC group and whether the fluctuating expression of pro- and anti-inflammatory cytokines is related to DNA methylation change remained to be further investigated.

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

International Journal of Molecular Sciences ◽

10.3390/ijms21124476 ◽

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.

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The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

Bioinformatics ◽

10.1093/bioinformatics/bty1053 ◽

2018 ◽

Vol 35 (16) ◽

pp. 2718-2723 ◽

Cited By ~ 3

Author(s):

Tamir Tuller ◽

Alon Diament ◽

Avital Yahalom ◽

Assaf Zemach ◽

Shimshi Atar ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Arabidopsis Thaliana ◽

Gene Expression Regulation ◽

Developmental Pathways ◽

Cop9 Signalosome ◽

Supplementary Information ◽

Loss Of Function ◽

Genome Wide ◽

High Level

Abstract Motivation The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. Supplementary information Supplementary data are available at Bioinformatics online.

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Overexpression of the Activated Disease Resistance 1-like1 (ADR1-L1) Gene Results in a Dwarf Phenotype and Activation of Defense-Related Gene Expression in Arabidopsis thaliana

Journal of Plant Biology ◽

10.1007/s12374-011-9153-z ◽

2011 ◽

Vol 54 (3) ◽

pp. 172-179 ◽

Cited By ~ 7

Author(s):

Hiroaki Kato ◽

Takuhiro Shida ◽

Yoshibumi Komeda ◽

Tamao Saito ◽

Atsushi Kato

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Disease Resistance ◽

Related Gene ◽

Dwarf Phenotype ◽

Defense Related Gene

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The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

10.1101/362905 ◽

2018 ◽

Author(s):

Komivi Dossa ◽

Marie Ali Mmadi ◽

Rong Zhou ◽

Qi Zhou ◽

Mei Yang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Abiotic Stresses ◽

Cytosine Methylation ◽

De Novo ◽

Recovery Phase ◽

Epigenetic Mechanism ◽

Drought Tolerant ◽

Sesame Genotypes ◽

Methylation Patterns

AbstractDNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.

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