Analysis of Genetic Variation and DNA Methylation Alteration in Autoetraploid and Diploid Rice

2013 ◽  
Vol 19 (4) ◽  
pp. 630-636 ◽  
Author(s):  
Qiong YANG ◽  
Lin QIU ◽  
Ke LUO ◽  
Shengbin TU
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Methylation Alteration ◽  
Diploid Rice

scholarly journals VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association

2021 ◽  
Vol 22 (5) ◽  
pp. 2535
Author(s):  
Pierre-Antoine Dugué ◽  
Chenglong Yu ◽  
Timothy McKay ◽  
Ee Ming Wong ◽  
Jihoon Eric Joo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Genetic Factors ◽  
Disease Association ◽  
Country Of Birth ◽  
Cpg Site ◽  
Multiple Case ◽  
Metastable Epiallele ◽  
Methylation Quantitative Trait Loci

VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

scholarly journals Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits

2018 ◽  
Author(s):  
Eilis Hannon ◽  
Tyler J Gorrie-Stone ◽  
Melissa C Smart ◽  
Joe Burrage ◽  
Amanda Hughes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Common Genetic Variation ◽  
Online Data ◽  
The Relationship ◽  
Methylation Quantitative Trait Loci

ABSTRACTCharacterizing the complex relationship between genetic, epigenetic and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. In this study, we describe the most comprehensive analysis of common genetic variation on DNA methylation (DNAm) to date, using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (P < 6.52x10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified using previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits, using Summary data–based Mendelian Randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression, identifying 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database (http://www.epigenomicslab.com/online-data-resources/) as a resource to the research community.

scholarly journals Genome-Wide Epigenetic Signatures of Adaptive Developmental Plasticity in the Andes

2020 ◽  
Author(s):  
Ainash Childebayeva ◽  
Jaclyn M Goodrich ◽  
Fabiola Leon-Velarde ◽  
Maria Rivera-Chira ◽  
Melisa Kiyamu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
High Altitude ◽  
Developmental Plasticity ◽  
Hypoxia Inducible Factor ◽  
Adaptation To Hypoxia ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Epigenetic Signatures ◽  
Adaptive Developmental Plasticity

Abstract High-altitude adaptation is a classic example of natural selection operating on the human genome. Physiological and genetic adaptations have been documented in populations with a history of living at high altitude. However, the role of epigenetic gene regulation, including DNA methylation, in high-altitude adaptation is not well understood. We performed an epigenome-wide DNA methylation association study based on whole blood from 113 Peruvian Quechua with differential lifetime exposures to high altitude (&gt;2,500) and recruited based on a migrant study design. We identified two significant differentially methylated positions (DMPs) and 62 differentially methylated regions (DMRs) associated with high-altitude developmental and lifelong exposure statuses. DMPs and DMRs were found in genes associated with hypoxia-inducible factor pathway, red blood cell production, blood pressure, and others. DMPs and DMRs associated with fractional exhaled Nitric Oxide (FeNO) also were identified. We found a significant association between EPAS1 methylation and EPAS1 SNP genotypes, suggesting that local genetic variation influences patterns of methylation. Our findings demonstrate that DNA methylation is associated with early developmental and lifelong high-altitude exposures among Peruvian Quechua as well as altitude-adaptive phenotypes. Together these findings suggest that epigenetic mechanisms might be involved in adaptive developmental plasticity to high altitude. Moreover, we show that local genetic variation is associated with DNA methylation levels, suggesting that methylation associated SNPs could be a potential avenue for research on genetic adaptation to hypoxia in Andeans.

scholarly journals An in vitro attempt at precision toxicology reveals the involvement of DNA methylation alteration in ochratoxin A-induced G0/G1 phase arrest

Epigenetics ◽  
2019 ◽  
Vol 15 (1-2) ◽  
pp. 199-214 ◽  
Author(s):  
Boyang Zhang ◽  
Liye Zhu ◽  
Yaqi Dai ◽  
Hongyu Li ◽  
Kunlun Huang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Ochratoxin A ◽  
G1 Phase ◽  
Methylation Alteration ◽  
Phase Arrest ◽  
G1 Phase Arrest

scholarly journals Pleiotropic Effects of Trait-Associated Genetic Variation on DNA Methylation: Utility for Refining GWAS Loci

2017 ◽  
Vol 100 (6) ◽  
pp. 954-959 ◽  
Author(s):  
Eilis Hannon ◽  
Mike Weedon ◽  
Nicholas Bray ◽  
Michael O’Donovan ◽  
Jonathan Mill
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Pleiotropic Effects

scholarly journals Correction: Passive and active DNA methylation and the interplay with genetic variation in gene regulation

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Maria Gutierrez-Arcelus ◽  
Tuuli Lappalainen ◽  
Stephen B Montgomery ◽  
Alfonso Buil ◽  
Halit Ongen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Genetic Variation

scholarly journals Methylomics of nitroxidative stress on precancerous cells reveals DNA methylation alteration at the transition from in situ to invasive cervical cancer

Oncotarget ◽  
2017 ◽  
Vol 8 (39) ◽  
pp. 65281-65291 ◽  
Author(s):  
Po-Hsuan Su ◽  
Yao-Wen Hsu ◽  
Rui-Lan Huang ◽  
Yu-Chun Weng ◽  
Hui-Chen Wang ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Dna Methylation ◽  
Invasive Cervical Cancer ◽  
Methylation Alteration ◽  
Nitroxidative Stress

scholarly journals Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjing Xu ◽  
Yingchun Li ◽  
Yajing Li ◽  
Chun Liu ◽  
Yanxia Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Nucleotide Substitution ◽  
Somatic Hybridization ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Asymmetric Somatic Hybridization ◽  
Genomic Shock ◽  
Flanking Sequences ◽  
Synonymous Codon Usage Bias

Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.

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