scholarly journals Epigenome-Wide DNA Methylation Analysis of Monozygotic Twins Discordant for Diurnal Preference

2015 ◽  
Vol 18 (6) ◽  
pp. 662-669 ◽  
Author(s):  
Chloe C. Y. Wong ◽  
Michael J. Parsons ◽  
Kathryn J. Lester ◽  
Joe Burrage ◽  
Thalia C. Eley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Circadian Clock ◽  
Monozygotic Twins ◽  
Enrichment Analysis ◽  
Genome Wide ◽  
Analysis Strategy ◽  
Diurnal Preference ◽  
Significant Enrichment ◽  
Longitudinal Twin Study ◽  
Mz Twins

Diurnal preference is an individual's preference for daily activities and sleep timing and is strongly correlated with the underlying circadian clock and the sleep-wake cycle validating its use as an indirect circadian measure in humans. Recent research has implicated DNA methylation as a mechanism involved in the regulation of the circadian clock system in humans and other mammals. In order to evaluate the extent of epigenetic differences associated with diurnal preference, we examined genome-wide patterns of DNA methylation in DNA from monozygotic (MZ) twin-pairs discordant for diurnal preference. MZ twins were selected from a longitudinal twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. Fifteen pairs of MZ twins were identified in which one member scored considerably higher on the Horne–Ostberg Morningness–Eveningness Questionnaire (MEQ) than the other. Genome-wide DNA methylation patterns were assessed in twins’ buccal cell DNA using the Illumina Infinium HumanMethylation450 BeadChips. Quality control and data pre-processing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. Our data indicate that DNA methylation differences are detectable in MZ twins discordant for diurnal preference. Moreover, downstream gene ontology (GO) enrichment analysis on the top-ranked diurnal preference associated DMPs revealed significant enrichment of pathways that have been previously associated with circadian rhythm regulation, including cell adhesion processes and calcium ion binding.

scholarly journals Monozygotic Twins Discordant for Immunoglobulin A Nephropathy Display Differences in DNA Methylation and Gene Expression

2020 ◽  
pp. 1-10
Author(s):  
Min Wei ◽  
Sijun Meng ◽  
Sufang Shi ◽  
Lijun Liu ◽  
Xujie Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Profiles ◽  
Immunoglobulin A ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
Mz Twins

<b><i>Introduction:</i></b> Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis. It involves both genetic and environmental factors, among which DNA methylation, the most studied epigenetic modification, was shown to play a role. Here, we assessed genome-wide DNA methylation and gene expression profiles in 2 pairs of IgAN-discordant monozygotic (MZ) twins, in order to characterize methylation changes and their potential influences on gene expression in IgAN. <b><i>Methods:</i></b> Genome-wide DNA methylation and gene expression profiles were evaluated in peripheral blood mononuclear cells obtained from 2 IgAN-discordant MZ twins. Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected, and an integrated analysis was performed. Finally, functional enrichment analysis was done for DMR-associated genes and DEGs. <b><i>Results:</i></b> Totally 521 DMRs were detected for 2 IgAN-discordant MZ twins. Among them, 9 DMRs were found to be mapped to genes that differentially expressed in 2 MZ twins, indicating the potential regulatory mechanisms of expression for these 9 genes (<i>MNDA</i>, <i>DYSF</i>, <i>IL1R2</i>, <i>TLR6</i>, <i>TREML2</i>, <i>TREM1</i>, <i>IL32</i>, <i>S1PR5</i>, and <i>ADGRE3</i>) in IgAN. Biological process analysis of them showed that they were mostly involved in the immune system process. Functional enrichment analysis of DEGs and DMR-associated genes both identified multiple pathways relevant to inflammatory and immune responses. And DMR-associated genes were significantly enriched in terms related to T-cell function. <b><i>Conclusions:</i></b> Our findings indicate that changes in DNA methylation patterns were involved in the pathogenesis of IgAN. Nine target genes detected in our study may provide new ideas for the exploration of molecular mechanisms of IgAN.

Genome-wide analysis of sperm DNA methylation from monozygotic twin bulls

2017 ◽  
Vol 29 (4) ◽  
pp. 838 ◽  
Author(s):  
Habib A. Shojaei Saadi ◽  
Éric Fournier ◽  
Christian Vigneault ◽  
Patrick Blondin ◽  
Janice Bailey ◽  
...  
Keyword(s):  
Complex Traits ◽  
Semen Quality ◽  
Enrichment Analysis ◽  
Monozygotic Twin ◽  
Progeny Testing ◽  
Dna Methylome ◽  
Genome Wide ◽  
Sperm Dna ◽  
Significant Enrichment ◽  
Mz Twins

Monozygotic (MZ) twins are of great interest to elucidate the contributions of pre- and postnatal environmental factors on epigenetics in the expression of complex traits and diseases. Progeny testing recently revealed that MZ twin bulls do not necessarily lead to identical genetic merit estimates (i.e. breeding values). Therefore, to explain differences in offspring productivity of MZ twin bulls despite their identical genetic backgrounds, we hypothesised that paternal sperm epigenomes vary between MZ twin bulls. In the present study, semen characteristics and global sperm DNA methylome were profiled for four pairs of MZ twin bulls. Some MZ twin pairs had divergent semen quality (sperm morphology, motility and viability). Comparative genome-wide DNA methylome surveys were performed using methyl-sensitive enrichment and microarray identification. Between 2% and 10% of all probes (400 000) were differentially methylated between MZ twin pairs. In addition, there were 580 loci differentially methylated across all pairs of MZ twins. Furthermore, enrichment analysis indicated a significant enrichment for fertility associated quantitative trait loci (P = 0.033). In conclusion, differences in the sperm epigenome may contribute to incongruous diverging performances of daughters sired by bulls that are MZ twins.

A Genome-Wide Scan of DNA Methylation Markers for Distinguishing Monozygotic Twins

2015 ◽  
Vol 18 (6) ◽  
pp. 670-679 ◽  
Author(s):  
Qingqing Du ◽  
Guijun Zhu ◽  
Guangping Fu ◽  
Xiaojing Zhang ◽  
Lihong Fu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
G Protein ◽  
Dna Typing ◽  
Monozygotic Twins ◽  
G Protein Signaling ◽  
Protein Signaling ◽  
Genome Wide ◽  
A Genome ◽  
Mz Twins ◽  
Genome Wide Scan

Identification of individuals within pairs of monozygotic (MZ) twins remains unresolved using common forensic DNA typing technology. For some criminal cases involving MZ twins as suspects, the twins had to be released due to inability to identify which of the pair was the perpetrator. In this study, we performed a genome-wide scan on whole blood-derived DNA from four pairs of healthy phenotypically concordant MZ twins using the methylated DNA immunoprecipitation sequencing technology to identify candidate DNA methylation markers with capacity to distinguish MZ twins within a pair. We identified 38 differential methylation regions showing within-pair methylation differences in all four MZ pairs. These are all located in CpG islands, 17 of which are promoter-associated, 17 are intergenic islands, and four are intragenic islands. Genes associated with these markers are related with cell proliferation, differentiation, and growth and development, including zinc finger proteins, PRRX2, RBBP9, or are involved in G-protein signaling, such as the regulator of G-protein signaling 16. Further validation studies on additional MZ twins are now required to evaluate the broader utility of these 38 markers for forensic use.

scholarly journals A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins

2020 ◽  
Vol 14 ◽  
Author(s):  
Mette Soerensen ◽  
Dominika Marzena Hozakowska-Roszkowska ◽  
Marianne Nygaard ◽  
Martin J. Larsen ◽  
Veit Schwämmle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cognitive Functioning ◽  
Association Study ◽  
Gene Expression Data ◽  
Monozygotic Twins ◽  
Later Life ◽  
Expression Data ◽  
Genome Wide ◽  
A Genome

scholarly journals Gene set enrichment analysis for genome-wide DNA methylation data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jovana Maksimovic ◽  
Alicia Oshlack ◽  
Belinda Phipson
Keyword(s):  
Dna Methylation ◽  
Enrichment Analysis ◽  
R Package ◽  
Gene Set Enrichment Analysis ◽  
Methylation Array ◽  
Gene Set ◽  
Genome Wide ◽  
Genome Methylation ◽  
Unbiased Gene ◽  
Gene Set Testing

AbstractDNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions. GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis. Benchmarking analyses demonstrate GOmeth outperforms other approaches, and GOregion is the first method for gene set testing of differentially methylated regions. Both methods are publicly available in the missMethyl Bioconductor R package.

T.N.3 A GENOME-WIDE DNA METHYLATION STUDY IN MONOZYGOTIC TWINS DISCORDANT FOR PRIMARY BILIARY CIRRHOSIS

2010 ◽  
Vol 42 ◽  
pp. S16
Author(s):  
A. Lleo ◽  
M.R. Martin ◽  
L. Zammataro ◽  
M.J. Mayo ◽  
N. Bach ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Primary Biliary Cirrhosis ◽  
Monozygotic Twins ◽  
Biliary Cirrhosis ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tong Wang ◽  
Weijing Wang ◽  
Weilong Li ◽  
Haiping Duan ◽  
Chunsheng Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Pulmonary Function ◽  
Monozygotic Twins ◽  
Linear Mixed Effect Model ◽  
Sequencing Analysis ◽  
Mixed Effect ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. Methods The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. Results We identified 112 CpG sites with the level of P < 1 × 10–4 which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. Conclusion Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.

scholarly journals EWAS of Monozygotic Twins Implicate a Role of mTOR Pathway in Pathogenesis of Tic Spectrum Disorder

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1510
Author(s):  
Mathis Hildonen ◽  
Amanda M. Levy ◽  
Christine Søholm Hansen ◽  
Jonas Bybjerg-Grauholm ◽  
Axel Skytthe ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Monozygotic Twins ◽  
Neuropsychiatric Disorders ◽  
Monozygotic Twin ◽  
Mtor Pathway ◽  
Spectrum Disorder ◽  
Genetic Components ◽  
Genome Wide ◽  
Chronic Tic Disorder ◽  
Mtor Signalling

Tic spectrum disorder (TSD) is an umbrella term which includes Gilles de la Tourette syndrome (GTS) and chronic tic disorder (CTD). They are considered highly heritable, yet the genetic components remain largely unknown. In this study we aimed to investigate disease-associated DNA methylation differences to identify genes and pathways which may be implicated in TSD aetiology. For this purpose, we performed an exploratory analysis of the genome-wide DNA methylation patterns in whole blood samples of 16 monozygotic twin pairs, of which eight were discordant and six concordant for TSD, while two pairs were asymptomatic. Although no sites reached genome-wide significance, we identified several sites and regions with a suggestive significance, which were located within or in the vicinity of genes with biological functions associated with neuropsychiatric disorders. The two top genes identified (TSC1 and CRYZ/TYW3) and the enriched pathways and components (phosphoinosides and PTEN pathways, and insulin receptor substrate binding) are related to, or have been associated with, the PI3K/AKT/mTOR pathway. Genes in this pathway have previously been associated with GTS, and mTOR signalling has been implicated in a range of neuropsychiatric disorders. It is thus possible that altered mTOR signalling plays a role in the complex pathogenesis of TSD.

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