Hypomethylation of mitochondrial D-loop and ND6 with increased mitochondrial DNA copy number in the arsenic-exposed population

Toxicology ◽  
2018 ◽  
Vol 408 ◽  
pp. 54-61 ◽  
Author(s):  
Tamalika Sanyal ◽  
Pritha Bhattacharjee ◽  
Sandip Bhattacharjee ◽  
Pritha Bhattacharjee
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Dna Copy Number ◽  
Mitochondrial Dna Copy Number ◽  
Exposed Population ◽  
D Loop

Rare instances of non-random dropout with the monochrome multiplex qPCR assay for mitochondrial DNA copy number

2021 ◽  
Author(s):  
Stephanie Y Yang ◽  
Charles E Newcomb ◽  
Stephanie L Battle ◽  
Anthony YY Hsieh ◽  
Hailey L Chapman ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Dna Copy Number ◽  
Loop Primer ◽  
Mitochondrial Dna Copy Number ◽  
D Loop

Mitochondrial DNA copy number (mtDNA-CN) is a proxy for mitochondrial function and has been of increasing interest to the mitochondrial research community. There are several ways to measure mtDNA-CN, ranging from whole genome sequencing to qPCR. A recent article from the Journal of Molecular Diagnostics described a novel method for measuring mtDNA-CN that is both inexpensive and reproducible. However, we show that certain individuals, particularly those with very low qPCR mtDNA measurements, show poor concordance between qPCR and whole genome sequencing measurements. After examining whole genome sequencing data, this seems to be due to polymorphisms within the D-loop primer region. Non-concordant mtDNA-CN was observed in all instances of polymorphisms at certain positions in the D-loop primer regions, however, not all positions are susceptible to this effect. In particular, these polymorphisms appear disproportionately in individuals with the L, T, and U mitochondrial haplogroups, indicating non-random dropout.

scholarly journals Mitochondrial DNA methylation and copy number predict body composition in a young female population

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Laura Bordoni ◽  
Vanessa Smerilli ◽  
Cinzia Nasuti ◽  
Rosita Gabbianelli
Keyword(s):  
Dna Methylation ◽  
Body Composition ◽  
Mitochondrial Dna ◽  
Copy Number ◽  
Buccal Swab ◽  
Dna Copy Number ◽  
Female Population ◽  
Mitochondrial Dna Copy Number ◽  
Buccal Swabs ◽  
D Loop

Abstract Background Since both genomic and environmental factors are involved in obesity etiology, several studies about the influence of adiposity on both nuclear DNA and mitochondrial DNA methylation patterns have been carried out. Nevertheless, few evidences exploring the usage of buccal swab samples to study mitochondrial DNA epigenetics can be found in literature. Methods In this study, mitochondrial DNA from buccal swabs collected from a young Caucasian population (n = 69) have been used to examine potential correlation between mitochondrial DNA copy number and methylation with body composition (BMI, WHtR and bioimpedance measurements). Results A negative correlation between mitochondrial DNA copy number and BMI was measured in females (p = 0.028), but not in males. The mean percentage of D-loop methylation is significantly higher in overweight than in lean female subjects (p = 0.003), and a specific CpG located in the D-loop shows per se an association with impaired body composition (p = 0.004). Body composition impairment is predicted by a combined variable including mtDNA copy number and the D-loop methylation (AUC = 0.785; p = 0.009). Conclusions This study corroborates the hypothesis that mitochondrial DNA carries relevant information about body composition. However, wider investigations able to validate the usage of mtDNA methylation from buccal swabs as a biomarker are warranted.

Mitochondrial DNA copy number and D-loop region methylation in carriers of amyotrophic lateral sclerosis gene mutations

Epigenomics ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1431-1443 ◽  
Author(s):  
Andrea Stoccoro ◽  
Lorena Mosca ◽  
Vittoria Carnicelli ◽  
Ugo Cavallari ◽  
Christian Lunetta ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Mitochondrial Dna ◽  
Copy Number ◽  
Gene Mutations ◽  
Dna Copy Number ◽  
Loop Region ◽  
Mitochondrial Dna Copy Number ◽  
D Loop ◽  
Lateral Sclerosis

scholarly journals Decreased mitochondrial D-loop region methylation mediates an increase in mitochondrial DNA copy number in CADASIL

2022 ◽  
Vol 14 (1) ◽  
Author(s):  
Jiewen Zhang ◽  
Junkui Shang ◽  
Fengyu Wang ◽  
Xuejing Huo ◽  
Ruihua Sun ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Dysfunction ◽  
Copy Number ◽  
Control Group ◽  
Compensatory Mechanism ◽  
Dna Copy Number ◽  
Gender Stratification ◽  
Loop Region ◽  
Mitochondrial Dna Copy Number ◽  
D Loop

Abstract Background Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a typical neurodegenerative disease associated with mitochondrial dysfunction. Methylation of the D-loop region and mitochondrial DNA copy number (mtDNAcn) play a critical role in the maintenance of mitochondrial function. However, the association between D-loop region methylation, mtDNAcn and CADASIL remains unclear. Methods Overall, 162 individuals were recruited, including 66 CADASIL patients and 96 age- and sex-matched controls. After extracting genomic DNA from the peripheral white blood cells, levels of D-loop methylation and mtDNAcn were assessed using MethylTarget sequencing and real-time PCR, respectively. Results We observed increased mtDNAcn and decreased D-loop methylation levels in CADASIL patients compared to the control group, regardless of gender stratification. Besides, we found a negative correlation between D-loop methylation levels and mtDNAcn. Mediation effect analysis shows that the proportion of the association between mtDNAcn and CADASIL that is mediated by D-loop methylation is 11.6% (95% CI 5.6, 22.6). After gender stratification, the proportions of such associations that are mediated by D-loop methylation in males and females were 7.2% (95% CI 2.4, 19.8) and 22.0% (95% CI 7.4, 50.1), respectively. Conclusion Decreased methylation of the D-loop region mediates increased mtDNAcn in CADASIL, which may be caused by a compensatory mechanism of mitochondrial dysfunction in patients with CADASIL.

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