scholarly journals Length heteroplasmy in the predominate mitochondrial DNA haplogroups in the Croatian population

2019 ◽  
Vol 2 (1) ◽  
pp. 19-23
Author(s):  
Lucija Barbaric ◽  
Korana Lipovac ◽  
Viktorija Sukser ◽  
Sara Rozic ◽  
Marina Korolija
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Mitochondrial Control Region ◽  
Length Heteroplasmy ◽  
Data Support ◽  
Variable Segment

Mitochondrial control region represents the most variable segment of the mitochondrial genome. The frequency and pattern of heteroplasmy has been described in several studies; however, none of the reports documented the Croatian population. In the present study, we screened the control region (1122 bp) of 95 individuals belonging to two predominant mitochondrial phylogenetic branches in the Croatian population, haplogroups H and U. Length heteroplasmy occurred in polycytosine (poly-C) tracts within three hypervariable segments of the control region with the following frequencies: HVSI - 26.3%, HVSII - 52.6% and HVSIII - 7.4%. Furthermore, the association between certain polymorphisms in HVSI and length heteroplasmy was investigated. Our results indicate that only polymorphisms located in the poly-C tract are associated with HVSI length heteroplasmy. The T to C transition at np 16189 is significantly associated with the occurrence of length heteroplasmy (p<0.0001). This effect was even stronger if the C insertion was present in the position 16193. The data support the hypothesis that an uninterrupted poly-C tract of more than eight cytosines leads to length heteroplasmy. Length heteroplasmy associated with the T to C substitution in np 16189 was predominantly found in haplogroup U.

Different methods to determine length heteroplasmy within the mitochondrial control region

2004 ◽  
Vol 118 (5) ◽  
pp. 274-281 ◽  
Author(s):  
Sabine Lutz-Bonengel ◽  
Timo S�nger ◽  
Stefan Pollak ◽  
Reinhard Szibor
Keyword(s):  
Control Region ◽  
Mitochondrial Control Region ◽  
Length Heteroplasmy

scholarly journals Unusual mtDNA Control Region Length Heteroplasmy in the COS-7 Cell Line

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 607
Author(s):  
Nataliya Kozhukhar ◽  
Sunil Mitta ◽  
Mikhail F. Alexeyev
Keyword(s):  
Mitochondrial Genome ◽  
Cell Line ◽  
Control Region ◽  
Tandem Repeats ◽  
Variable Number ◽  
Length Heteroplasmy ◽  
Repeat Units ◽  
Chlorocebus Aethiops ◽  
Region Length ◽  
Transcription And Replication

The COS-7 cell line is a workhorse of virology research. To expand this cell line’s utility and to enable studies on mitochondrial DNA (mtDNA) transcription and replication, we determined the complete nucleotide sequence of its mitochondrial genome by Sanger sequencing. In contrast to other available mtDNA sequences from Chlorocebus aethiops, the mtDNA of the COS-7 cell line was found to contain a variable number of perfect copies of a 108 bp unit tandemly repeated in the control region. We established that COS-7 cells are heteroplasmic with at least two variants being present: with four and five repeat units. The analysis of the mitochondrial genome sequences from other primates revealed that tandem repeats are absent from examined mtDNA control regions of humans and great apes, but appear in lower primates, where they are present in a homoplasmic state. To our knowledge, this is the first report of mtDNA length heteroplasmy in primates.

Biological Significance and Profile of Length Heteroplasmy in the Hypervariable Segments of the Human Mitochondrial DNA Control Regions from Blood Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3815-3815
Author(s):  
Myung-Geun Shin ◽  
Hyeoung-Joon Kim ◽  
Hye-Ran Kim ◽  
Hee-Nam Kim ◽  
Il-Kwon Lee ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Blood Cells ◽  
Biological Significance ◽  
Length Heteroplasmy ◽  
Conserved Sequence ◽  
Healthy Donors ◽  
Mtdna Sequence ◽  
Mtdna Replication ◽  
Two Peaks

Abstract A high incidence of mitochondrial DNA (mtDNA) variations was observed in both hypervariable region (HV) 1 and HV2; most mtDNA sequence variations were localized at poly C tract at nucleotides (nt) 303-315 (CCCCCCCTCCCCC, 7CT5C) in the HV2. Another poly C tract variant in HV1 at nt 16184-6193 have been suggested to be related with diabetes, dilated cardiomyopathy and some cancers. Poly C tract in HV2 is part of the conserved sequence block II located in 92-bp from the heavy strand replication origin. It is not yet clear whether poly C variants at nt 303–315 would lead to alterations in mtDNA replication. We hypothesized that some severe alterations in poly C tracts may lead to impairment of mtDNA replication. Here we present the profile of length heteroplasmy in HV from blood cells and its biological significance. A total of 57 maternally unrelated healthy donors were included and heparinized bloods were obtained from five age groups including 12 cord bloods. We amplified and sequenced the 1,121-bp control region including HV1 and HV2. In an attempt to investigate mtDNA length heteroplasmy, we carried out a qualitative and quantitative profiling length heteroplasmy using size-based PCR product separation by capillary electrophoresis (ABI 3100 Genetic Analyzer and ABI Prism Genotyper version 3.1). Length heteroplasmy was further confirmed by cloning and sequencing. Quantitative analysis of mtDNA molecules was performed using the QuantiTect SYBR Green PCR kit (Qiagen) and Rotor-Gene 3000 (Corbett Research) and standard plot was obtained from cloned cytochrome b gene. The mtDNA control region sequences showed 57 different haplotypes resulting from 77 polymorphic positions. Common polymorphisms were 73A>G (98%), 263A>G (91%), 16223C>T (47%), 16189T>C (35%), 150C>T (25%) and 152T>C (18%). The patterns of length heteroplasmy in the HV2 region were classified into 6 types. In the HV1 region, length heteroplasmy showed 8 variant peak patterns. The distribution of length heteroplasmy in poly C tracts at nt 303 – 315 was mtDNA mixture of 7CT6C+8CT6C (53%), 8CT6C+9CT6C (26%), 8CT6C+9CT6C+10CT6C (11%), 9CT6C+10CT6C +11CT6C (5%), 9CT6C+10CT6C (3%) and 7CT6C+6CT6C (2%). The distribution of length heteroplasmy pattern in poly C tract at nt 16184 – 16193 was 5CT4C+5CT3C (60%), 9C+10C+11C+12C (21%), 9C+10C+11C (5%), 3CT6C+3CT5C (3%), 9C+10C+11C+12C+13C (3%), 3CT4C+3CT3C (3%), 10C+11C+12C (2%), and 8C+9C+10C+11C+12C (2%). Interestingly, this study revealed that all healthy subjects showed length heteroplasmy in the HV1 and HV2 regions in contrast to previous studies. Length heteroplasmy in poly C 303–315 showed two groups of two peaks (n = 48) and more than three peaks (n = 9). MtDNA content from group with three peaks in poly C 303–315 (61,983,373 molecules/ul ± 33,219,871, mean±SD) was markedly lower than those with two peaks (133,777,955 molecules/ul ± 87,209,377). In conclusion, significantly higher rate of length heteroplasmy was observed in HV1 and HV2 from healthy donors and the presence of more than three mtDNA types in poly C at nt 303 – 315 might be associated with impairment of mtDNA replication.

Profound Length Heteroplasmic Alterations in Mitochondrial DNA Control Region From Primary AML Cells: Implication of Impaired Mitochondrial Replication and Demonstration of ‘vicious cycle’ Hypothesis.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3116-3116
Author(s):  
Myung-Geun Shin ◽  
Hye Ran Kim ◽  
Hyeoung-Joon Kim ◽  
Hoon Kook ◽  
Tai Ju Hwang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Copy Number ◽  
Regulatory Region ◽  
Mtdna Control Region ◽  
Vicious Cycle ◽  
Mtdna Copy Number ◽  
Length Heteroplasmy ◽  
Region Length ◽  
D Loop

Abstract Abstract 3116 Poster Board III-53 Mitochondrial DNA (mtDNA) control region (displacement (D)-loop including HV1 and HV2) is a non-coding region of 1124 bp (nucleotide positions, np 16 024–576), which acts as a promoter for both the heavy and light strands of mtDNA, and contains essential transcription and replication elements (Blood 2004;103:4466-77). Importantly, mutations in the D-loop regulatory region might change mtDNA replication rate by modifying the binding affinity of significant trans-activating factors (Eur J Cancer 2004;40:2519-24). Thus, length heteroplasmic alterations of mtDNA control region may be related with mitochondrial dysfunction resulting in ‘vicious cycle’ (Mol Med Today 2000;6:425-32). In an attempt to investigate profiling of mtDNA length heteroplasmic alterations in primary AML cells, we carried out a quantitative size-based PCR product separation by capillary electrophoresis (ABI 3130XL Genetic Analyzer and ABI Prism Genotyper version 3.1) using six targets (np 303-315 poly C, np 16184-16193 poly C, np 514-511 CA repeats, np 3566-3572 poly C, np 12385-12391 poly C and np 12418-12426 poly A). Length heteroplasmy was further confirmed by cloning and sequencing. Quantitative analysis of mtDNA molecules was performed using the QuantiTect SYBR Green PCR kit (Qiagen) and Rotor-Gene 3000 (Corbett Research). Forty-eight AML bone marrow samples were collected after receiving Institutional Review Board approval and informed consent. There were profound alterations of mtGI in 303 poly C, 16184 poly C and 514 CA repeats. The length heteroplasmy pattern of 303 poly C tract in the HV2 region disclosed mixture of 7C, 8C, 9C and 10C mtDNA types. In the HV2 region, length heteroplasmy in poly-C tract at np 303 - 309 exhibited 5 variant peak patterns: 7CT6C+8CT6C (50.0%), 8CT6C+9CT6C (14.0%), 8CT6C+ 9CT6C+ 10CT6C (10.4%), 9CT6C+10CT6C+11CT6C (8.3%) 9CT6C + 10CT6C + 11CT6C+12CT6C (2.1%). The length heteroplasmy pattern of 514-523 CA repeats in the HV2 region exhibited 2 variant peak patterns: CACACACACA (56.3%) and CACACACA (43.7%). In the HV1 region, length heteroplasmy in the poly-C tract at np 16184 - 16193 exhibited 9 variant peak patterns: 5CT4C+5CT3C (31.0%), 6CT4C+6CT3C (2.1%), 9C+10C+11C+12C (16.7%), 9C+10C+11C (2.1%), T4CT4C+5CT3C (4.2%), 9C+10C+11C+12C+13C (2.1%), 3CTC4C+5CT3C (2.1%), 10C+11C+12C+13C (4.2%), 8C+9C+10+11C (2.1%). Primary AML cells revealed decreased enzyme activity in respiratory chain complex I, II and III. AML cells had about a two-fold decrease in mtDNA copy number compared with normal blood mononuclear cells. Current study demonstrates that profound length heteroplasmic alterations in mtDNA control region of primary AML cells may lead to impairment of mitochondrial biogenesis (reduction of mtDNA copy number) and derangement of mitochondrial ATP synthesis. During this perturbation, mitochondria in primary AML cells might produce a large amount of reactive oxygen species, which causes the vicious cycle observed in chronic inflammatory diseases and cancers as well. Disclosures No relevant conflicts of interest to declare.

scholarly journals Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii

2006 ◽  
Vol 273 (1605) ◽  
pp. 3101-3123 ◽  
Author(s):  
Pierre Berthier ◽  
Laurent Excoffier ◽  
Manuel Ruedi
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Mitochondrial Control Region ◽  
Gene Pools ◽  
Single Class ◽  
Myotis Myotis ◽  
Variable Segment ◽  
The Alps ◽  
Well Differentiated

The two sibling bat species Myotis myotis and Myotis blythii occur in sympatry over wide areas of Southern and Central Europe. Morphological, ecological and previous genetic evidences supported the view that the two species constitute two well-differentiated groups, but recent phylogenetic analyses have shown that the two species shared some mtDNA haplotypes when they occurred in sympatry. In order to see whether some genetic exchange occurred between the two species, we sequenced a highly variable segment of the mitochondrial control region in both species living in sympatry and in allopatry. We also analysed the nuclear diversity of 160 individuals of both species found in two mixed nursery colonies located north and south of the Alps. MtDNA analysis confirmed that European M. blythii share multiple, identical or very similar haplotypes with M. myotis . Since allopatric Asian M. blythii presents mtDNA sequences that are very divergent from those of the two species found in Europe, we postulate that the mitochondrial genome of the European M. blythii has been replaced by that of M. myotis . The analysis of nuclear diversity shows a strikingly different pattern, as both species are well differentiated within mixed nursery colonies ( F ST =0.18). However, a Bayesian analysis of admixture reveals that the hybrids can be frequently observed, as about 25% of sampled M. blythii show introgressed genes of M. myotis origin. Contrastingly, less than 4% of the M. myotis analysed were classified as non-parental genotypes, revealing an asymmetry in the pattern of hybridization between the two species. These results show that the two species can interbreed and that the hybridization is still ongoing in the areas of sympatry. The persistence of well-differentiated nuclear gene pools, in spite of an apparent replacement of mitochondrial genome in European M. blythii by that of M. myotis , is best explained by a series of introgression events having occurred repeatedly during the recent colonization of Europe by M. blythii from Asia. The sharp contrast obtained from the analysis of mitochondrial and nuclear markers further points to the need to cautiously interpret results based on a single class of genetic markers.

Evaluating length heteroplasmy in the human mitochondrial DNA control region

2009 ◽  
Vol 124 (2) ◽  
pp. 133-142 ◽  
Author(s):  
Lucy Forster ◽  
Peter Forster ◽  
Susan M. R. Gurney ◽  
Matthew Spencer ◽  
Christopher Huang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Length Heteroplasmy ◽  
Mitochondrial Dna Control Region ◽  
Human Mitochondrial Dna

scholarly journals Erratum to: Evaluating length heteroplasmy in the human mitochondrial DNA control region

2010 ◽  
Vol 124 (4) ◽  
pp. 319-319
Author(s):  
Lucy Forster ◽  
Peter Forster ◽  
Susan M. R. Gurney ◽  
Matthew Spencer ◽  
Christopher Huang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Length Heteroplasmy ◽  
Mitochondrial Dna Control Region ◽  
Human Mitochondrial Dna

scholarly journals Mitochondrial DNA and Morphological Variation of White-Winged Doves in Texas

The Condor ◽  
2000 ◽  
Vol 102 (4) ◽  
pp. 871-880
Author(s):  
Christin L. Pruett ◽  
Scott E. Henke ◽  
Susan M. Tanksley ◽  
Michael F. Small ◽  
Kelly M. Hogan ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Mexico ◽  
Control Region ◽  
Morphological Variation ◽  
Range Expansion ◽  
Phylogenetic Signal ◽  
Mitochondrial Control Region ◽  
Morphological Characters ◽  
Zenaida Asiatica ◽  
Haplotype Frequencies

Abstract White-winged Doves (Zenaida asiatica) in Texas are separated into four subspecies primarily based on morphological variation. However, problems differentiating the subspecies by morphological measurements alone and a recent range expansion have led to questions about their systematic status and population structure. We evaluated both morphological characters and a 289 base-pair segment of the mitochondrial control region from 183 White-winged Doves taken from 31 locations in Texas, New Mexico, and Arizona. Twenty-seven variable base changes were observed, which resulted in 44 haplotypes. An analysis of haplotypes yielded little phylogenetic signal; however, analyses of haplotype frequencies indicated geographic heterogeneity between doves collected in the four historic subspecies ranges. Doves from the range expansion areas were intermediate in size and genetically homogenous. Morphological analyses suggested congruency between control region variation and body size. Our data support the recognition of two subspecies of White-winged Doves with a zone of intergradation in the range expansion areas. The dispersal of White-winged Doves into the expansion areas appears to be a congruent process by both subspecies.

scholarly journals A molecular characteristic of the Anatidae mitochondrial control region – a review

2018 ◽  
Vol 18 (1) ◽  
pp. 3-15 ◽  
Author(s):  
Joanna Warzecha ◽  
Agnieszka Fornal ◽  
Maria Oczkowicz ◽  
Monika Bugno-Poniewierska
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Close Relationships ◽  
Genetic Research ◽  
Mitochondrial Control Region ◽  
Coding Region ◽  
Conserved Domain ◽  
Control Region Sequences ◽  
D Loop

Abstract Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.

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