scholarly journals Differential DNA Methylation of the IMMP2L Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay

2021 ◽  
pp. 1-15
Author(s):  
Stanislav A. Vasilyev ◽  
Nikolay A. Skryabin ◽  
Anna A. Kashevarova ◽  
Ekaterina N. Tolmacheva ◽  
Renata R. Savchenko ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Intellectual Disability ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Copy Number Variations ◽  
Incomplete Penetrance ◽  
Cpg Sites ◽  
Transport Chain ◽  
Underlying Mechanisms ◽  
Chromosome 7Q

Most copy number variations (CNVs) in the human genome display incomplete penetrance with unknown underlying mechanisms. One such mechanism may be epigenetic modification, particularly DNA methylation. The <i>IMMP2L</i> gene is located in a critical region for autism susceptibility on chromosome 7q (AUTS1). The level of DNA methylation was assessed by bisulfite sequencing of 87 CpG sites in the <i>IMMP2L</i> gene in 3 families with maternally inherited 7q31.1 microdeletions affecting the <i>IMMP2L</i> gene alone. Bisulfite sequencing revealed comparable levels of DNA methylation in the probands, healthy siblings without microdeletions, and their fathers. In contrast, a reduced DNA methylation index and increased <i>IMMP2L</i> expression were observed in lymphocytes from the healthy mothers compared with the probands. A number of genes were upregulated in the healthy mothers compared to controls and downregulated in probands compared to mothers. These genes were enriched in components of the ribosome and electron transport chain, as well as oxidative phosphorylation and various degenerative conditions. Differential expression in probands and mothers with <i>IMMP2L</i> deletions relative to controls may be due to compensatory processes in healthy mothers with <i>IMMP2L</i> deletions and disturbances of these processes in probands with intellectual disability. The results suggest a possible partial compensation for <i>IMMP2L</i> gene haploinsufficiency in healthy mothers with the 7q31.1 microdeletion by reducing the DNA methylation level. Differential DNA methylation of intragenic CpG sites may affect the phenotypic manifestation of CNVs and explain the incomplete penetrance of chromosomal microdeletions.

scholarly journals Performance comparison and in-silico harmonization of commercial platforms for DNA methylome analysis by targeted bisulfite sequencing

2021 ◽  
Author(s):  
Miljana Tanic ◽  
Ismail Moghul ◽  
Simon Rodney ◽  
Pawan Dhami ◽  
Heli Vaikkinen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Fate ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Cost Effective ◽  
Performance Comparison ◽  
Performance Criteria ◽  
Targeted Bisulfite Sequencing ◽  
Cpg Sites ◽  
Targeted Analysis

Abstract DNA methylation is a key epigenetic modification in the regulation of cell fate and differentiation, and its analysis is gaining increasing importance in both basic and clinical research. Targeted Bisulfite Sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. Here we benchmarked five commercially available TBS platforms, including three hybridization capture-based (Agilent, Roche, and Illumina) and two RRBS-based (Diagenode and NuGen), across 11 samples. A subset of these were also compared to whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed performance with respect to workflow complexity, on/off-target performance, coverage, accuracy, and reproducibility. We find all platforms able to produce usable data but with major differences for some performance criteria, especially in the number and identity of the CpG sites covered, which affects the interoperability of datasets generated on these different platforms. To overcome this limitation, we used imputation and show that it improves the interoperability from an average of 10.35% (0.8M CpG sites) to 97% (7.6M CpG sites). Our study provides cross-validated guidance on which TBS platform to use for different features of the methylome and offers an imputation-based harmonization solution for improved interoperability between platforms, allowing comparative and integrative analysis.

scholarly journals Performance comparison and in-silico harmonisation of commercial platforms for DNA methylome analysis by targeted bisulfite sequencing

2021 ◽  
Author(s):  
Miljana Tanić ◽  
Ismail Moghul ◽  
Simon Rodney ◽  
Pawan Dhami ◽  
Heli Vaikkinen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Fate ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Cost Effective ◽  
Performance Comparison ◽  
Performance Criteria ◽  
Targeted Bisulfite Sequencing ◽  
Cpg Sites ◽  
Targeted Analysis

AbstractDNA methylation is a key epigenetic modification in the regulation of cell fate and differentiation, and its analysis is gaining increasing importance in both basic and clinical research. Targeted Bisulfite Sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. Here we benchmarked five commercially available TBS platforms, including three hybridization capture-based (Agilent, Roche, and Illumina) and two RRBS-based (Diagenode and NuGen), across 16 samples. A subset of these were also compared to whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed performance with respect to workflow complexity, on/off-target performance, coverage, accuracy and reproducibility. We find all platforms able to produce usable data but major differences for some performance criteria, especially in the number and identity of the CpG sites covered, which affects the interoperability of datasets generated on these different platforms. To overcome this limitation, we used imputation and show that it improves the interoperability from an average of 10.35% (0.8M CpG sites) to 97% (7.6M CpG sites). Our study provides cross-validated guidance on which TBS platform to use for different features of the methylome and offers an imputation-based harmonization solution for improved interoperability between platforms, allowing comparative and integrative analysis.

Abstract 428: DNA Methylation of ASC is Associated with Decreased ASC and IL-1β Expression in Heart Failure

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Brittany Butts ◽  
Javed Butler
Keyword(s):  
Heart Failure ◽  
Dna Methylation ◽  
Inflammatory Cytokines ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Inflammasome Activation ◽  
Cpg Sites ◽  
Exon 1 ◽  
Vital Component ◽  
Intron Region

Introduction: Heart failure (HF) is associated with formation and activation of inflammasome, a complex of intracellular interaction proteins that trigger maturation of inflammatory cytokines to initiate inflammatory response. ASC, a vital component of the inflammasome, is controlled through epigenetic modification via methylation of CpG islands surrounding exon 1. Methods: To assess the relationships between DNA methylation of ASC, ASC expression, and inflammatory cytokines IL-1β and IL-18 in HF, stored samples from 155 chronic HF patients (age 56.9±12.0 yr, 64% male, 47% black, and ejection fraction 29.9±14.9) were analyzed. DNA extracted from PMBCs were analyzed by pyrosequencing for percent methylation of seven CpG sites in the intron region preceding exon 1 of the ASC gene. ASC mRNA was quantified via real-time PCR and analyzed as the ratio ASC:GAPDH. Serum ASC, IL-1β, and IL-18 were measured by ELISA. Results: Higher ASC methylation was associated with lower ASC mRNA (r=0-.328, p<0.001) and protein (r=-.464, p<0.001) expression. Lower ASC mRNA expression was associated with lower ASC protein expression (r=0.494, p<0.001). Decreased IL-1β expression was associated with higher ASC methylation (r=-.424, p=0.005) and lower ASC mRNA (r=.619, p<0.001) and ASC protein (r=.433, p<0.001). IL-18 expression was not significantly associated with ASC methylation or expression. Conclusions: Increased ASC methylation was associated with lower IL-1β, likely via decreased ASC gene expression. As ASC is required for inflammasome activation of IL-1β, this study implicates the inflammasome pathway as a driver of inflammation in HF, proving a potential target for novel interventions.

scholarly journals Genome-Wide DNA Methylation Profiling in the Lotus (Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 135 ◽  
Author(s):  
Zhongyuan Lin ◽  
Meihui Liu ◽  
Rebecca Njeri Damaris ◽  
Tonny Maraga Nyong’a ◽  
Dingding Cao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Nelumbo Nucifera ◽  
Flower Formation ◽  
Relationship Analysis ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.

scholarly journals The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

2020 ◽  
Vol 10 (9) ◽  
pp. 3337-3346
Author(s):  
Yijia Zhou ◽  
Funan He ◽  
Weilin Pu ◽  
Xun Gu ◽  
Jiucun Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Germline Mutation ◽  
Developmental Stages ◽  
Rare Variants ◽  
Epigenetic Modification ◽  
Genome Project ◽  
Germline Development ◽  
Cpg Sites ◽  
The Impact

Abstract DNA methylation is a dynamic epigenetic modification found in most eukaryotic genomes. It is known to lead to a high CpG to TpG mutation rate. However, the relationship between the methylation dynamics in germline development and the germline mutation rate remains unexplored. In this study, we used whole genome bisulfite sequencing (WGBS) data of cells at 13 stages of human germline development and rare variants from the 1000 Genome Project as proxies for germline mutations to investigate the correlation between dynamic methylation levels and germline mutation rates at different scales. At the single-site level, we found a significant correlation between methylation and the germline point mutation rate at CpG sites during germline developmental stages. Then we explored the mutability of methylation dynamics in all stages. Our results also showed a broad correlation between the regional methylation level and the rate of C &gt; T mutation at CpG sites in all genomic regions, especially in intronic regions; a similar link was also seen at all chromosomal levels. Our findings indicate that the dynamic DNA methylome during human germline development has a broader mutational impact than is commonly assumed.

scholarly journals DNA methylation patterns of β-globin cluster in β-thalassemia patients

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiuqin Bao ◽  
Yangjin Zuo ◽  
Diyu Chen ◽  
Cunyou Zhao
Keyword(s):  
Dna Methylation ◽  
Cord Blood ◽  
Methylation Level ◽  
Epigenetic Modification ◽  
Fetal Hemoglobin ◽  
Cpg Sites ◽  
Hbf Level ◽  
Globin Promoter ◽  
Methylation Patterns ◽  
Normal Controls

Abstract Background Reactivation of fetal hemoglobin (HbF, α2γ2) holds a therapeutic target for β-thalassemia and sickle cell disease. Although many HbF regulators have been identified, the methylation patterns in β-globin cluster driving the fetal-to-adult hemoglobin switch remains to be determined. Results Here, we evaluated DNA methylation patterns of the β-globin cluster from peripheral bloods of 105 β0/β0 thalassemia patients and 44 normal controls. We also recruited 15 bone marrows and 4 cord blood samples for further evaluation. We identified that the CpG sites in the locus control region (LCR) DNase I hypersensitive site 4 and 3 (HS4-3) regions, and γ- and β-globin promoters displayed hypomethylation in β0/β0-thalassemia patients, especially for the patients with high HbF level, as compared with normal controls. Furthermore, hypomethylations in most of CpG sites of the HS4-3 core regions were also observed in bone marrows (BM) of β0/β0-patients compared with normal controls; and methylation level of γ-globin promoter -50 and + 17 CpG sites showed lower methylation level in patients with high HbF level compared with those with low HbF level and a negative correlation with HbF level among β0-thalassemia patients. Finally, γ-globin promoter + 17 and + 50 CpG sites also displayed significant hypomethylation in cord blood (CB) tissues compared with BM tissues from normal controls. Conclusions Our findings revealed methylation patterns in β-globin cluster associated with β0 thalassemia disease and γ-globin expression, contributed to understand the epigenetic modification in β0 thalassemia patients and provided candidate targets for the therapies of β-hemoglobinopathies.

1 Whole-genome bisulfite sequencing of bovine gametes and invivo-produced pre-implantation embryos

2019 ◽  
Vol 31 (1) ◽  
pp. 126
Author(s):  
J. E. Duan ◽  
Z. Jiang ◽  
F. Alqahtani ◽  
I. Mandoiu ◽  
H. Dong ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Epigenetic Regulation ◽  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Differentially Methylated Regions ◽  
Whole Genome Bisulfite Sequencing ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Dynamic changes in DNA methylation are crucial in the epigenetic regulation of mammalian embryogenesis. Global DNA methylation studies in the bovine, however, remain mostly at the immunostaining level. We adopted the single-cell whole-genome bisulfite sequencing method to characterise stage-specific genome-wide DNA methylation in bovine sperm, individual oocytes derived invivo and invitro, and invivo-developed embryos at the 2-, 4-, 8-, and 16-cell stages. This method allowed us to theoretically cover all CpG sites in the genome using a limited number of cells from single embryos. Pools of 20 sperm were selected from a bull with proven fertility. Single oocytes (n=6) and embryos (n=4 per stage) were collected from Holstein cows (n=10). Single-cell whole-genome bisulfite sequencing libraries were prepared and sequenced using the Illumina HiSEqn 4000 platform (Illumina, San Diego, CA, USA). Sequencing reads were filtered and aligned to the bovine reference genome (UMD 3.1.1) using Bismark (Krueger and Andrews 2011Bioinformatics27, 1571-1572, DOI: 10.1093/bioinformatics/btr167).A 300-bp tile-based method was applied to bin the genome into consecutive windows to facilitate comparison across samples. The DNA methylation level was calculated as the fraction of read counts of the total number of cytosines (methylated) in the total read counts of reported cytosines and thymines (methylated and unmethylated), only if more than 3 CpG sites were covered in this tile. Gamete-specific differentially methylated regions were identified when DNA methylation levels were greater than 75% in one type of gamete and less than 25% in the other with false discovery rate-corrected Fisher’s exact test P-values of less than 0.05. The major wave of genome-wide DNA demethylation was complete at the 8-cell stage when de novo methylation became prominent. Sperm and oocytes had numerous differentially methylated regions that were enriched in intergenic regions. Differentially methylated regions were also identified between invivo- and invitro-matured oocytes. Moreover, X chromosome methylation followed the global dynamic patterns. Virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, using our RNA sequencing data generated from the same developmental stages (Jiang et al. 2014 BMC Genomics 15, 756; DOI: 10.1186/1471-2164-15-756), we revealed an inverse correlation between gene expression and promoter methylation. Our study provides the first fully comprehensive analysis of the global dynamics of DNA methylation in bovine gametes and single early embryos using single-cell whole-genome bisulfite sequencing. These data provide insights into the critical features of the methylome of bovine embryos and serve as an important reference for embryos produced by assisted reproduction, such as IVF and cloning, and a model for human early embryo epigenetic regulation.

scholarly journals Genome-Wide DNA Methylation Comparison between Brassica napus Genic Male Sterile Line and Restorer Line

2018 ◽  
Vol 19 (9) ◽  
pp. 2689 ◽  
Author(s):  
Zhixin Wang ◽  
Xiangping Wu ◽  
Zengxiang Wu ◽  
Hong An ◽  
Bin Yi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Male Sterility ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Differentially Methylated Region ◽  
Male Sterile ◽  
Male Sterile Line ◽  
Floral Buds ◽  
Global Comparison ◽  
Genome Wide

DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during plant development. However, few studies have determined the DNA methylation profiles of male-sterile rapeseed. Here, we conducted a global comparison of DNA methylation patterns between the rapeseed genic male sterile line 7365A and its near-isogenic fertile line 7365B by whole-genome bisulfite sequencing (WGBS). Profiling of the genome-wide DNA methylation showed that the methylation level in floral buds was lower than that in leaves and roots. Besides, a total of 410 differentially methylated region-associated genes (DMGs) were identified in 7365A relative to 7365B. Traditional bisulfite sequencing polymerase chain reaction (PCR) was performed to validate the WGBS data. Eleven DMGs were found to be involved in anther and pollen development, which were analyzed by quantitative PCR. In particular, Bnams4 was hypo-methylated in 7365A, and its expression was up-regulated, which might affect other DMGs and thus control the male sterility. This study provided genome-wide DNA methylation profiles of floral buds and important clues for revealing the molecular mechanism of genic male sterility in rapeseed.

scholarly journals 0027 Adolescent Sleep Timing And Dietary Patterns In Relation To Dna Methylation Of Core Clock Genes

SLEEP ◽  
2019 ◽  
Vol 42 (Supplement_1) ◽  
pp. A11-A11
Author(s):  
Erica C Jansen ◽  
Dana Dolinoy ◽  
Ronald D Chervin ◽  
Karen E Peterson ◽  
Louise M O'Brien ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dietary Patterns ◽  
Dietary Habits ◽  
Clock Genes ◽  
Epigenetic Modification ◽  
Shift Workers ◽  
Wake Time ◽  
Cpg Sites ◽  
Sleep Timing ◽  
Increased Risk

Abstract Introduction Mistimed sleep/wake and eating patterns put adult shift workers at increased risk for chronic disease, and epigenetic modification of core clock genes has been proposed as a mechanism. Although not as extreme as shift workers, adolescents often have delayed sleep timing. Our aim was to assess whether sleep midpoints in adolescents are associated with DNA methylation of circadian genes. A secondary aim was to examine associations between dietary patterns and circadian gene methylation. Methods The study population included 142 Mexican youth (average age 14.0 (SD=2.0) years, 49% male) enrolled in a cohort study. Average sleep midpoint (between bed time and wake time) over 7 days was estimated with actigraphy. Diet was assessed with a semi-quantitative food frequency questionnaire, and three dietary patterns were derived from principal components analysis (a vegetable-based pattern, a meat and starch-based pattern, and a breakfast pattern). DNA methylation was quantified in blood leukocytes with the Infinium MethylatinEPIC BeadChip. We selected 166 loci (CpG sites) within CpG islands of core ‘clock’ genes known to regulate circadian rhythms (CLOCK, BMAL, PER1, PER2, PER3, CRY1, CRYI2, RORA, RORB, REV-VERBA, REV-VERBB). Linear regression was used to analyze associations between sleep midpoint or dietary patterns and logit-transformed percent methylation at the 166 CpG sites. All models were adjusted for sex and age. Results The average midpoint was 3:41 AM (SD=1 hr 15 min); average bed time was 11:29 PM (SD=68 min) and average wake time was 7:53 AM (SD=97 min). Sleep midpoint was positively associated with DNA methylation of CpG sites from the genes REV-VERBA and RORB at the Bonferroni-corrected significance level of p&lt;0.005. The breakfast dietary pattern (rich in eggs, milk, and bread) was inversely associated with DNA methylation at RORA (P=0.003). Conclusion Sleep timing and dietary habits are associated with DNA methylation of core clock genes in adolescents. Epigenetic modification of clock genes could in part underlie relationships between sleep, diet, and metabolic health among adolescents. Support (If Any) Dr. Jansen is supported by the NIH/NHLBI grant 5T32HL110952-05.

scholarly journals Impact of Infrasound on Methylation Status of Genome in Testes of Rats

2007 ◽  
Vol 26 (2) ◽  
pp. 143-147
Author(s):  
Li Rui-Man ◽  
Zhuang Zhi-Qiang ◽  
Yao Hai-Tao ◽  
Pei Zhao-Hui ◽  
Chen Jing-Zao
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Control Groups ◽  
Methyltransferase Activity ◽  
Dynamic Changes ◽  
Time Points ◽  
Cpg Sites ◽  
Underlying Mechanisms

To probe into the changes induced by infrasonic exposure on the methylation status of the genome in testes and underlying mechanisms, we inspected the percentage of unmethylated CpG sites (an index for DNA methylation level) and DNA methyltransferase activity in testes of SD rats exposed to infrasound of 8Hz at 90dB or 130dB for 1, 7, 14 and 21 days (2h/d). Compared to control groups at the same time points, significantly decreased DNA methylation level and methyltransferase activity were observed in all but experimental groups of ld and 21d at 90dB ( p<0.05). Compared to 90dB groups at the same time points, DNA methylation level and DNA methyltransferase activity at 130dB decreased more significantly ( p<0.05). The patterns of dynamic changes on the percentage of unmethylated CpG sites and methyltransferase activity at 130dB were different from those at 90dB. The results indicated that infrasonic exposure induced epigenetic changes in testes of rats, which depended on parameters of infrasonic exposure.

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