scholarly journals Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua.

Genetics ◽  
1992 ◽  
Vol 132 (1) ◽  
pp. 211-220 ◽  
Author(s):  
E Arnason ◽  
D M Rand
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Gadus Morhua ◽  
Tandem Repeats ◽  
Atlantic Cod ◽  
Length Variation ◽  
The North ◽  
Loop Region ◽  
D Loop ◽  
Displacement Model

Abstract The mitochondrial DNA of the Atlantic cod (Gadus morhua) contains a tandem array of 40-bp repeats in the D-loop region of the molecule. Variation among molecules in the copy number of these repeats results in mtDNA length variation and heteroplasmy (the presence of more than one form of mtDNA in an individual). In a sample of fish collected from different localities around Iceland and off George's Bank, each individual was heteroplasmic for two or more mtDNAs ranging in repeat copy number from two (common) to six (rare). An earlier report on mtDNA heteroplasmy in sturgeon (Acipenser transmontanus) presented a competitive displacement model for length mutations in mtDNAs containing tandem arrays and the cod data deviate from this model. Depending on the nature of putative secondary structures and the location of D-loop strand termination, additional mechanisms of length mutation may be needed to explain the range of mtDNA length variants maintained in these populations. The balance between genetic drift and mutation in maintaining this length polymorphism is estimated through a hierarchical analysis of diversity of mtDNA length variation in the Iceland samples. Eighty percent of the diversity lies within individuals, 8% among individuals and 12% among localities. An estimate of theta = 2N(eo) mu greater than 1 indicates that this system is characterized by a high mutation rate and is governed primarily by deterministic dynamics. The sequences of repeat arrays from fish collected in Norway, Iceland and George's Bank show no nucleotide variation suggesting that there is very little substructuring to the North Atlantic cod population.

scholarly journals Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle.

1990 ◽  
Vol 10 (11) ◽  
pp. 5671-5678 ◽  
Author(s):  
B H Annex ◽  
R S Williams
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Striated Muscle ◽  
Dna Structure ◽  
Triplex Dna ◽  
Mtdna Copy Number ◽  
Loop Region ◽  
D Loop ◽  
Heavy Strand ◽  
Light Strand

Mitochondrial DNA (mt DNA) in cells of vertebrate organisms can assume an unusual triplex DNA structure known as the displacement loop (D loop). This triplex DNA structure forms when a partially replicated heavy strand of mtDNA (7S mtDNA) remains annealed to the light strand, displacing the native heavy strand in this region. The D-loop region contains the promoters for both heavy- and light-strand transcription as well as the origin of heavy-strand replication. However, the distribution of triplex and duplex forms of mtDNA in relation to respiratory activity of mammalian tissues has not been systematically characterized, and the functional significance of the D-loop structure is unknown. In comparisons of specialized muscle subtypes within the same species and of the same muscle subtype in different species, the relative proportion of D-loop versus duplex forms of mtDNA in striated muscle tissues of several mammalian species demonstrated marked variation, ranging from 1% in glycolytic fast skeletal fibers of the rabbit to 65% in the mouse heart. There was a consistent and direct correlation between the ratio of triplex to duplex forms of mtDNA and the capacity of these tissues for oxidative metabolism. The proportion of D-loop forms likewise correlated directly with mtDNA copy number, mtRNA abundance, and the specific activity of the mtDNA (gamma) polymerase. The D-loop form of mtDNA does not appear to be transcribed at greater efficiency than the duplex form, since the ratio of mtDNA copy number to mtRNA was unrelated to the proportion of triplex mtDNA genomes. However, tissues with a preponderance of D-loop forms tended to express greater levels of cytochrome b mRNA relative to mitochondrial rRNA transcripts, suggesting that the triplex structure may be associated with variations in partial versus full-length transcription of the heavy strand.

scholarly journals Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1035-1048 ◽  
Author(s):  
Gerald S Wilkinson ◽  
Frieder Mayer ◽  
Gerald Kerth ◽  
Barbara Petri
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Tandem Repeats ◽  
Repeated Sequence ◽  
Repeat Number ◽  
Repeat Units ◽  
Loop Region ◽  
Control Region Sequences ◽  
Number Comparison ◽  
D Loop

Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.

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

Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle

1990 ◽  
Vol 10 (11) ◽  
pp. 5671-5678
Author(s):  
B H Annex ◽  
R S Williams
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Striated Muscle ◽  
Dna Structure ◽  
Triplex Dna ◽  
Mtdna Copy Number ◽  
Loop Region ◽  
D Loop ◽  
Heavy Strand ◽  
Light Strand

Mitochondrial DNA (mt DNA) in cells of vertebrate organisms can assume an unusual triplex DNA structure known as the displacement loop (D loop). This triplex DNA structure forms when a partially replicated heavy strand of mtDNA (7S mtDNA) remains annealed to the light strand, displacing the native heavy strand in this region. The D-loop region contains the promoters for both heavy- and light-strand transcription as well as the origin of heavy-strand replication. However, the distribution of triplex and duplex forms of mtDNA in relation to respiratory activity of mammalian tissues has not been systematically characterized, and the functional significance of the D-loop structure is unknown. In comparisons of specialized muscle subtypes within the same species and of the same muscle subtype in different species, the relative proportion of D-loop versus duplex forms of mtDNA in striated muscle tissues of several mammalian species demonstrated marked variation, ranging from 1% in glycolytic fast skeletal fibers of the rabbit to 65% in the mouse heart. There was a consistent and direct correlation between the ratio of triplex to duplex forms of mtDNA and the capacity of these tissues for oxidative metabolism. The proportion of D-loop forms likewise correlated directly with mtDNA copy number, mtRNA abundance, and the specific activity of the mtDNA (gamma) polymerase. The D-loop form of mtDNA does not appear to be transcribed at greater efficiency than the duplex form, since the ratio of mtDNA copy number to mtRNA was unrelated to the proportion of triplex mtDNA genomes. However, tissues with a preponderance of D-loop forms tended to express greater levels of cytochrome b mRNA relative to mitochondrial rRNA transcripts, suggesting that the triplex structure may be associated with variations in partial versus full-length transcription of the heavy strand.

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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