Drought Stress Induces Differential DNA Methylation Shift at Symmetric and Asymmetric Cytosine Sites in the Promoter Region of ZmEXPB2 Gene in Maize

β-expansin 2 (EXPB2) gene induces drought tolerance in different plant species including maize. Different epigenetic mechanisms like DNA methylation, histone modification and RNA interference affect the gene activities under stress conditions. DNA methylation, an important epigenetic mechanism, could be involved in the regulation of ZmEXPB2 gene under drought stress in maize. Plants of drought sensitive variety „Jalal‟ were grown till 4th leaf stage under well-watered conditions. At 5th leaf stage, plants were divided in two groups i.e., well-watered (100% water holding capacity) or drought stress (0% water holding capacity for 15 days). Plants subjected to drought stress showed clear signs of stress by significant decrease in fresh weight of whole plant, 6th leaf length, stunted secondary root growth and increased primary root length. DNA methylation profile of three regions (denoted as -1.7 k, -1.3 k and -0.8 k) in the promoter of ZmEXPB2 gene, of root DNA, were evaluated. Under well-watered conditions, heterogeneity in DNA methylation profile along the promoter sequence was observed. Regions -1.7 k and -1.3 k were methylated whereas the region -0.8 k was nonmethylated. After the comparison of DNA methylation profile of well-watered and drought stress plants, no change in -1.7 k and -0.8 k regions was observed. However, the -1.3k region had significant decrease in the DNA methylation at symmetric cytosine sites i.e., cytosine-guanine (CG) dinucleotides and cytosine-adenine/cytosine/thymine-guanine (CHG where H = A, C or T) trinucleotide and significant increase at asymmetric cytosine sites (CHH) under the stress condition. In addition, significant increase in the gene expression of ZmEXPB2 under drought was also observed. In conclusion, drought stress conditions induce DNA hypomethylation at CG, and CHG sites and DNA hypermethylation at CHH sites in the middle region of the promoter of ZmEXPB2 gene. This shift can be associated with the up regulation of ZmEXPB2 gene which in turn increased primary root length as a plant stress response mechanism. © 2021 Friends Science Publishers

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Integrated analysis of DNA methylation profile in HLA-G gene and imaging in coronary heart disease

European Heart Journal ◽

10.1093/ehjci/ehaa946.1255 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

G Benincasa ◽

C Schiano ◽

T Infante ◽

M Franzese ◽

R Casale ◽

...

Keyword(s):

Dna Methylation ◽

Coronary Heart Disease ◽

Heart Disease ◽

Cpg Island ◽

Methylation Profile ◽

Integrated Analysis ◽

Funding Source ◽

Relevant Parameter ◽

Cardiac Computed Tomography Angiography ◽

Dna Methylation Profile

Abstract Aims Immune endothelial inflammation, underlie coronary heart disease (CHD) related phenotypes, could provide new insight into the pathobiology of the disease. We investigated DNA methylation level of the unique CpG island of HLA-G gene in CHD patients and evaluated the correlation with cardiac computed tomography angiography (CCTA) features. Methods Thirty-two patients that underwent CCTA for suspected CHD were enrolled for this study. Obstructive CHD group included fourteen patients, in which there was a stenosis greater than or equal to 50% in one or more of the major coronary arteries detected; whereas subjects with Calcium (Ca) Score=0, uninjured coronaries and with no obstructive CHD were considered as control subjects (Ctrls) (n=18). For both groups, DNA methylation profile of the whole 5'UTR-CpG island of HLA-G was measured. The plasma soluble HLA-G (sHLA-G) levels were detected in all subjects by specific ELISA assay. Statistical analysis was performed using R software. Results For the first time, our study reported that 1) a significant hypomethylation characterized three specific fragments (B, C and F) of the 5'UTR-CpG island (p=0.05) of HLA-G gene in CHD patients compared to Ctrl group; 2) hypomethylation level of one specific fragment positively correlated with coronary Ca score, a relevant parameter of CCTA (p<0.05) between two groups. Conclusions Our results showed that reduced levels of circulating HLA-G molecules could derive from epigenetic marks inducing hypomethylation of specific regions into 5'UTR-CpG island of HLA-G gene in CHD patients with obstructive coronary stenosis vs non critical stenosis group. Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): Italian Minister of Health

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DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

Communications Biology ◽

10.1038/s42003-020-01469-0 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Vanessa Lakis ◽

◽

Rita T. Lawlor ◽

Felicity Newell ◽

Ann-Marie Patch ◽

...

Keyword(s):

Dna Methylation ◽

Neuroendocrine Tumors ◽

Methylation Profile ◽

Pancreatic Neuroendocrine Tumors ◽

Wild Type ◽

Genomic Information ◽

Chromosome 11 ◽

Dna Methylation Profile ◽

Methylation Patterns ◽

Recurrent Patterns

AbstractHere we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.

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DNA methylation profile of genes involved in inflammation and autoimmunity correlates with vascular function in morbidly obese adults

Epigenetics ◽

10.1080/15592294.2021.1876285 ◽

2021 ◽

pp. 1-17

Author(s):

Mohamed M. Ali ◽

Dina Naquiallah ◽

Maryam Qureshi ◽

Mohammed Imaduddin Mirza ◽

Chandra Hassan ◽

...

Keyword(s):

Dna Methylation ◽

Vascular Function ◽

Methylation Profile ◽

Morbidly Obese ◽

Obese Adults ◽

Dna Methylation Profile

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Non-TZF Protein AtC3H59/ZFWD3 Is Involved in Seed Germination, Seedling Development, and Seed Development, Interacting with PPPDE Family Protein Desi1 in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22094738 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4738

Author(s):

Hye-Yeon Seok ◽

Hyungjoon Bae ◽

Taehyoung Kim ◽

Syed Muhammad Muntazir Mehdi ◽

Linh Vu Nguyen ◽

...

Keyword(s):

Seed Germination ◽

Seed Development ◽

Zinc Finger ◽

Root Length ◽

Primary Root ◽

Seedling Development ◽

Ccch Zinc Finger ◽

Family Protein ◽

Wd40 Domain ◽

Primary Root Length

Despite increasing reports on the function of CCCH zinc finger proteins in plant development and stress response, the functions and molecular aspects of many non-tandem CCCH zinc finger (non-TZF) proteins remain uncharacterized. AtC3H59/ZFWD3 is an Arabidopsis non-TZF protein and belongs to the ZFWD subfamily harboring a CCCH zinc finger motif and a WD40 domain. In this study, we characterized the biological and molecular functions of AtC3H59, which is subcellularly localized in the nucleus. The seeds of AtC3H59-overexpressing transgenic plants (OXs) germinated faster than those of wild type (WT), whereas atc3h59 mutant seeds germinated slower than WT seeds. AtC3H59 OX seedlings were larger and heavier than WT seedlings, whereas atc3h59 mutant seedlings were smaller and lighter than WT seedlings. Moreover, AtC3H59 OX seedlings had longer primary root length than WT seedlings, whereas atc3h59 mutant seedlings had shorter primary root length than WT seedlings, owing to altered cell division activity in the root meristem. During seed development, AtC3H59 OXs formed larger and heavier seeds than WT. Using yeast two-hybrid screening, we isolated Desi1, a PPPDE family protein, as an interacting partner of AtC3H59. AtC3H59 and Desi1 interacted via their WD40 domain and C-terminal region, respectively, in the nucleus. Taken together, our results indicate that AtC3H59 has pleiotropic effects on seed germination, seedling development, and seed development, and interacts with Desi1 in the nucleus via its entire WD40 domain. To our knowledge, this is the first report to describe the biological functions of the ZFWD protein and Desi1 in Arabidopsis.

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Overlapping DNA methylation profile between placentas with trisomy 16 and early-onset preeclampsia

Placenta ◽

10.1016/j.placenta.2014.01.001 ◽

2014 ◽

Vol 35 (3) ◽

pp. 216-222 ◽

Cited By ~ 16

Author(s):

J.D. Blair ◽

S. Langlois ◽

D.E. McFadden ◽

W.P. Robinson

Keyword(s):

Dna Methylation ◽

Early Onset ◽

Methylation Profile ◽

Trisomy 16 ◽

Dna Methylation Profile ◽

Early Onset Preeclampsia

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Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile

PLoS ONE ◽

10.1371/journal.pone.0192499 ◽

2018 ◽

Vol 13 (3) ◽

pp. e0192499 ◽

Cited By ~ 4

Author(s):

Somaye Dehghanizadeh ◽

Vahid Khoddami ◽

Timothy L. Mosbruger ◽

Sue S. Hammoud ◽

Kornelia Edes ◽

...

Keyword(s):

Dna Methylation ◽

Methylation Profile ◽

Braf V600e ◽

Serrated Polyp ◽

Dna Methylation Profile

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Methylome and transcriptome analyses of soybean response to bean pyralid larvae

BMC Genomics ◽

10.1186/s12864-021-08140-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wei-Ying Zeng ◽

Yu-Rong Tan ◽

Sheng-Feng Long ◽

Zu-Dong Sun ◽

Zhen-Guang Lai ◽

...

Keyword(s):

Dna Methylation ◽

Protein Biosynthesis ◽

Cell Structure ◽

Methylation Profile ◽

Primary Metabolism ◽

Global Methylation ◽

Genome Wide ◽

Differentially Methylated Genes ◽

Dna Methylation Profile ◽

Soybean Resistance

Abstract Background Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far. Results Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82–178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing. Conclusions Genome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.

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Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation

10.21203/rs.3.rs-20344/v2 ◽

2020 ◽

Author(s):

Yuanmei Wang ◽

Liying Liu ◽

Min Li ◽

Lili Lin ◽

Pengcheng Su ◽

...

Keyword(s):

Dna Methylation ◽

Signaling Pathway ◽

Salmonella Enterica ◽

Methylation Profile ◽

Control Group ◽

Poultry Production ◽

Salmonella Enterica Serovar Enteritidis ◽

Genome Wide ◽

Differentially Methylated Genes ◽

Dna Methylation Profile

Abstract Background: Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study.Results: There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean Reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8,946 differentially methylated genes (3,639 hypo-methylated genes, 5,307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated.Conclusions: The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.

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