Precise sequence assignment of replication origin in the control region of chick mitochondrial DNA relative to 5? and 3? D-loop ends, secondary structure, DNA synthesis, and protein binding

1995 ◽  
Vol 28 (5) ◽  
pp. 401-409 ◽  
Author(s):  
Margit M. K. Nass
Keyword(s):  
Mitochondrial Dna ◽  
Secondary Structure ◽  
Protein Binding ◽  
Dna Synthesis ◽  
Control Region ◽  
Replication Origin ◽  
D Loop ◽  
Sequence Assignment

scholarly journals Protein binding to a single termination-associated sequence in the mitochondrial DNA D-loop region.

1993 ◽  
Vol 13 (4) ◽  
pp. 2162-2171 ◽  
Author(s):  
C S Madsen ◽  
S C Ghivizzani ◽  
W W Hauswirth
Keyword(s):  
Mitochondrial Dna ◽  
Protein Binding ◽  
Loop Formation ◽  
Sequence Element ◽  
Conserved Sequence ◽  
Loop Region ◽  
In Organello ◽  
Close Proximity ◽  
D Loop

A methylation protection assay was used in a novel manner to demonstrate a specific bovine protein-mitochondrial DNA (mtDNA) interaction within the organelle (in organello). The protected domain, located near the D-loop 3' end, encompasses a conserved termination-associated sequence (TAS) element which is thought to be involved in the regulation of mtDNA synthesis. In vitro footprinting studies using a bovine mitochondrial extract and a series of deleted mtDNA templates identified a approximately 48-kDa protein which binds specifically to a single TAS element also protected within the mitochondrion. Because other TAS-like elements located in close proximity to the protected region did not footprint, protein binding appears to be highly sequence specific. The in organello and in vitro data, together, provide evidence that D-loop formation is likely to be mediated, at least in part, through a trans-acting factor binding to a conserved sequence element located 58 bp upstream of the D-loop 3' end.

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 Detection of somatic mutations in the mitochondrial DNA control region D‑loop in brain tumors: The first report in Malaysian patients

2017 ◽  
Author(s):  
Abdul Mohamed Yusoff ◽  
Khairol Mohd Nasir ◽  
Khalilah Haris ◽  
Siti Mohd Khair ◽  
Abdul Abdul Ghani ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Brain Tumors ◽  
Control Region ◽  
Somatic Mutations ◽  
Mitochondrial Dna Control Region ◽  
First Report ◽  
D Loop

scholarly journals Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

2016 ◽  
Vol 113 (30) ◽  
pp. E4276-E4285 ◽  
Author(s):  
Gokhan Akman ◽  
Radha Desai ◽  
Laura J. Bailey ◽  
Takehiro Yasukawa ◽  
Ilaria Dalla Rosa ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Mitochondrial Disease ◽  
Genetic Information ◽  
Disease Mechanism ◽  
Dna Segregation ◽  
D Loop ◽  
Mitochondrial Dna Replication ◽  
Pathological Variant ◽  
Potential Substrate

The genetic information in mammalian mitochondrial DNA is densely packed; there are no introns and only one sizeable noncoding, or control, region containing key cis-elements for its replication and expression. Many molecules of mitochondrial DNA bear a third strand of DNA, known as “7S DNA,” which forms a displacement (D-) loop in the control region. Here we show that many other molecules contain RNA as a third strand. The RNA of these R-loops maps to the control region of the mitochondrial DNA and is complementary to 7S DNA. Ribonuclease H1 is essential for mitochondrial DNA replication; it degrades RNA hybridized to DNA, so the R-loop is a potential substrate. In cells with a pathological variant of ribonuclease H1 associated with mitochondrial disease, R-loops are of low abundance, and there is mitochondrial DNA aggregation. These findings implicate ribonuclease H1 and RNA in the physical segregation of mitochondrial DNA, perturbation of which represents a previously unidentified disease mechanism.

scholarly journals Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region

1989 ◽  
Vol 17 (22) ◽  
pp. 8949-8965 ◽  
Author(s):  
Howard T. Jacobs ◽  
Elaine R. Herbert ◽  
James Rankine
Keyword(s):  
Mitochondrial Dna ◽  
Sea Urchin ◽  
Replication Origin ◽  
Sea Urchin Egg ◽  
D Loop ◽  
Origin Region

Protein binding to a single termination-associated sequence in the mitochondrial DNA D-loop region

1993 ◽  
Vol 13 (4) ◽  
pp. 2162-2171
Author(s):  
C S Madsen ◽  
S C Ghivizzani ◽  
W W Hauswirth
Keyword(s):  
Mitochondrial Dna ◽  
Protein Binding ◽  
Loop Formation ◽  
Sequence Element ◽  
Conserved Sequence ◽  
Loop Region ◽  
In Organello ◽  
Close Proximity ◽  
D Loop

A methylation protection assay was used in a novel manner to demonstrate a specific bovine protein-mitochondrial DNA (mtDNA) interaction within the organelle (in organello). The protected domain, located near the D-loop 3' end, encompasses a conserved termination-associated sequence (TAS) element which is thought to be involved in the regulation of mtDNA synthesis. In vitro footprinting studies using a bovine mitochondrial extract and a series of deleted mtDNA templates identified a approximately 48-kDa protein which binds specifically to a single TAS element also protected within the mitochondrion. Because other TAS-like elements located in close proximity to the protected region did not footprint, protein binding appears to be highly sequence specific. The in organello and in vitro data, together, provide evidence that D-loop formation is likely to be mediated, at least in part, through a trans-acting factor binding to a conserved sequence element located 58 bp upstream of the D-loop 3' end.

scholarly journals Analysis of mitochondrial dna control region d-loop in gliomas: result of 52 patients

2020 ◽  
Author(s):  
Sirin Kilicturgay Yuksel ◽  
Koray Ozduman ◽  
Engin Yilmaz ◽  
Necmettin Pamir ◽  
Cemaliye Boylu Akyerli
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Mitochondrial Dna Control Region ◽  
D Loop

scholarly journals Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

2011 ◽  
Vol 57 (6) ◽  
pp. 758-767 ◽  
Author(s):  
Xiaoli Wang ◽  
Jiangyong Qu ◽  
Naifa Liu ◽  
Xinkang Bao ◽  
Sen Song
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
Divergence Time ◽  
Population Expansion ◽  
Middle Pleistocene ◽  
Distribution Analysis ◽  
D Loop ◽  
Limited Gene Flow ◽  
Partial Isolation

Abstract Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 polymorphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. himalayansis based on the analysis on mtDNA D-loop sequences.

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