Mitochondrial D-loop 3' (CA)n repeat polymorphism: optimization of analysis and population data

Assembly and analysis of the complete mitochondrial genome of Leonurus japonicus (Lamiaceae)

Leonurus japonicus Houtt. (L. japonicus), as an important plant resource with both ornamental and medicinal value, has now spread worldwide and is widely studied. Currently, its chromosomal genome and chloroplast genome (cpDNA) have been reported, but the mitochondrial genome (mtDNA) has not yet been explored. In this study, we extracted DNA from fresh leaves of L. japonicus and performed sequencing and assembly of its mtDNA using both second-generation and third-generation sequencing technologies. The complete mtDNA of L. japonicus is 382,905 bp in length, with a GC content of 45.13%. This genome includes 15 tRNA genes, 32 protein-coding genes (PCGs), and 4 rRNA genes. In this mtDNA genome, we predicted a total of 480 RNA editing sites among the 32 PCGs. Subsequently, we conducted analyses on repetitive sequences, organelle genome sequence migration, and Relative Synonymous Codon Usage (RSCU). There are 28 homologous sequence fragments between the mtDNA and cpDNA of L. japonicus, which are related to the migration of 10 mtDNA genes. The RSCU analysis predicted 28 high-frequency codons, most of which prefer to end with A/U. Selection pressure analysis indicated that the Ka/Ks ratio for the majority of PCGs is less than 1, suggesting they are highly conserved during evolutionary processes. Phylogenetic results from 24 species indicate that the genera Leonurus and Scutellaria within the Lamiaceae family have the closest relationships. In summary, we have successfully assembled the complete mtDNA of L. japonicus by integrating second-generation and third-generation sequencing data for the first time. Subsequent multi-faceted analyses have allowed us to gain deeper insights into the numerous features of this genome, providing important reference data for the molecular genetics, dynamic evolution, and species identification of this plant. This work promotes the conservation and development of this important resource of medicinal and edible plants.

The Analysis of Genetic Polymorphism on Mitochondrial Hypervariable Region III in Thai Population

Mitochondrial DNA (mtDNA) analysis is a genetic marker for human identification, especially matrilineal inheritance. Hypervariable regions (HVR) I and II of mtDNA have been currently performed for human identification worldwide. Further examination of HVRIII has been conducted with the aim of enhancing the power of discrimination. The aim of this research is to provide informative data on the polymorphisms of HVRIII in the Thai population in order to establish a national database for human identification. Thai people who were unrelated through the maternal lineage were recruited for blood collections. The mtDNA was extracted by Chelex extraction, amplified by polymerase chain reaction, and analyzed using Sequencing Analysis Software. The most common mutation in HVRIII was base substitution, followed by deletion and insertion. We discovered 40 unique haplotypes, with haplotype 489C being the most frequent. The haplotype diversity, power of discrimination, and random match probability were 0.8014, 0.7987, and 0.2013, respectively. Five-CA repeats were the most frequently observed in nucleotide positions 514-523. Our database can be employed as supplementary markers in addition to nuclear deoxyribonucleic acid (DNA) markers in forensic investigations. Moreover, the data could potentially enhance genetic identification and anthropological genetics research in Thailand.

Mitochondrial DNA (CA)n dinucleotide repeat variations in Sinhalese and Vedda populations in Sri Lanka

Sinhalese and Vedda people are respectively the major ethnic group and the descendants of the probably earliest inhabitants of Sri Lanka, both believed to have a long history of settlement on the island. However, very little information is available on the origin and possible migration patterns of the two populations. Some studies have focused on (CA) dinucleotide repeat variations located in the mitochondrial hypervariable region 3 (HVS3) (base pairs 514-524) as a useful biomarker to understand migration patterns of different populations. Hence, here we analyze these repeat variations in these two ethnic groups to understand their historical roots and possible patterns of gene flow. Blood samples were collected from healthy, maternally unrelated individuals (N = 109) and mitochondrial D-loop was amplified and sequenced. The (CA)₄ dinucleotide repeat in hypervariable region 3 was detected in the majority of Vedda samples while the remaining samples were defined by a (CA)₅ cluster. In contrast, the (CA)₅ repeat was the most frequent among Sinhalese followed by (CA)₄ and (CA)₇ repeats. Haplogroup diversity of (CA)₄ variation indicated that the majority of Sinhalese individuals grouped into the M30 haplogroup while Vedda clustered into the R5a2b and U7a2 haplogroups. No significant differences in diversity measures were observed among the two populations. However, Multidimensional Scaling indicated a separate clustering for aboriginal Vedda and contemporary Sinhalese populations. Results from this study can be used together with mitochondrial DNA information from hypervariable regions 1 and 2 to perform anthropological and forensic investigations in the two populations studied.

Mitochondrial DNA variability to explore the relationship complexity of Schizothoracine (Teleostei: Cyprinidae)

Despite numerous studies on the taxonomy of a highly complex group of schizothoracine (snow trouts), with over five recognized species from Kashmir, India (Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus) based on traditional morphological data, the relationships between these species is poorly understood and the taxonomic validity is still under debate. To resolve the evolutionary relationships among these species, we sequenced mitochondrial fragments, including 16Sr RNA, Cytb and the D-loop. Separate analyses of 16S and Cytb showed intermixing of the species and 16S was found more conserved than Cytb. The D-loop was found highly variable and showed length variation between and within species. Length variation was observed in di-nucleotide (TA)n microsatellite repeats with a variable number of repeat units (n = 7-14) that did not show heteroplasmy. Central conserved sequence blocks (CSBs) in D-loop sequences were found comparable to other vertebrate species. All phylogenetic reconstructions recovered the focal taxa as a monophyletic clade within the schizothoracines. Analyses with combined mitochondrial data sets showed close genetic relationships of all the five species. In addition to a close relationship between S. niger and S. curvifrons, two distinct groupings of S. ecoscinus and S. plagiostomus were supported by all the analyses. This study gives an insight into molecular phylogeny of the species and improves our understanding of historical and taxonomic relationships derived from morphological and ecological studies.

Development of a multiplex PCR system of 59 mitochondrial SNPs and genetic analysis in Chinese population

The analysis of SNPs located on the mitochondrial DNA can provide information on maternal genetics. In the present study, a set of 59 SNPs were detected simultaneously using three multiplex allele-specific PCR and subsequent CE. Allele-specific primers were designed with different sizes to allow for specifically amplified paired alleles in the same reaction. An allelic ladder based on reference alleles was also created to maintain high-quality analysis standard. Samples from 400 unrelated individuals (200 of Han population and 200 of Uyghur population, China) were successfully analyzed and assigned into 106 relevant haplotypes, resulting in a discrimination power of 98.5%. The haplotype diversity was 0.978 for Han and 0.972 for Uyghur, respectively. Pairwise comparison of haplotype frequency distributions showed significant difference across ethnicities. These results suggest that the 59-SNP PCR system is a reliable, rapid, and economical method for large-scale screening of mitochondrial DNA variation, adding a new aspect for forensic individual identification.

Genetic diversities of cytochrome B in Xinjiang Uyghur unveiled its origin and migration history

Background

Uyghurs are one of the many populations of Central Eurasia that is considered to be genetically related to Eastern and Western Eurasian populations. However, there are some different opinions on the relative importance of the degree of Eastern and Western Eurasian genetic influence. In addition, the genetic diversity of the Uyghur in different geographic locations has not been clearly studied.

Results

In this study, we are the first to report on the DNA polymorphism of cytochrome B in the Uyghur population located in Xinjiang in northwest China. We observed a total of 102 mutant sites in the 240 samples that were studied. The average number of mutated nucleotides in the samples was 5.126. A total of 93 different haplotypes were observed. The gene diversity and discrimination power were 0.9480 and 0.9440, respectively. There were founder and bottleneck haplotypes observed in Xinjiang Uyghurs. Xinjiang Uyghurs are more genetically related to Chinese population in genetics than to Caucasians. Moreover, there was genetic diversity between Uyghurs from the southern and northern regions. There was significance in genetic distance between the southern Xinjiang Uyghurs and Chinese population, but not between the northern Xinjiang Uyghurs and Chinese. The European vs. East Asian contribution to the ten regional Uyghur groups varies among the groups and the European contribution to the Uyghur increases from north to south geographically.

Conclusion

This study is the first report on DNA polymorphisms of cytochrome B in the Uyghur population. The study also further confirms that there are significant genetic differences among the Uyghurs in different geographical locations.

Helicobacter pylori induces mitochondrial DNA mutation and reactive oxygen species level in AGS cells

To investigate the role of ROS in the helicobacter pylori (Hp) induced mtDNA mutations, AGS cells were treated by extracts of Hp11638 or Hp11638M. The ROS levels, cytochrome C reductions, and intracellular ATP levels were measured. The coding region and the D-Loop region were amplified and sequenced. Results showed the ROS levels, cytochrome C reduction and mtDNA mutations were markedly increased and cell viability decreased after treatment with both Hp extracts, and 616 mutations were detected in D-Loop region and 3 heteroplasmic point mutations in the Cytb gene. No mutations were found in the coding region. The mutation rates of mtDNA D-Loop region were positively correlated with the ROS levels and negatively to the ATP levels.

Heteroplasmy in hair: study of mitochondrial DNA third hypervariable region in hair and blood samples

Mitochondrial DNA (mtDNA) analysis has proved useful for forensic identification especially in cases where nuclear DNA is not available, such as with hair evidence. Heteroplasmy, the presence of more than one type of mtDNA in one individual, is a common situation often reported in the first and second mtDNA hypervariable regions (HV1/HV2), particularly in hair samples. However, there is no data about heteroplasmy frequency in the third mtDNA hypervariable region (HV3). To investigate possible heteroplasmy hotspots, HV3 from hair and blood samples of 100 individuals were sequenced and compared. No point heteroplasmy was observed, but length heteroplasmy was, both in C-stretch and CA repeat. To observe which CA "alleles" were present in each tissue, PCR products were cloned and re-sequenced. However, no variation among CA alleles was observed. Regarding forensic practice, we conclude that point heteroplasmy in HV3 is not as frequent as in the HV1/HV2.

Analysis association between mitochondrial genome instability and xenobiotic metabolizing genes in human breast cancer

The aim of this study was to determine the existence of association between the genetic polymorphisms of metabolizing genes GSTM-1, GSTT-1, and NAT-2, and the presence of mitochondrial genome instability (mtGI) in breast cancer cases. Ninety-four pairs of tumoral/nontumoral breast cancer samples were analyzed. Our samples showed 40.42% of mtGI by analysis of two D-loop region markers, a (CA)n mtMS starting at the 514-bp position, and four informative MnlI sites between the 16,108-16,420-bp. GSTM-1 null genotype has shown a significant association with mtGI presence (chi(2) = 7.62; P = 0.006) in breast cancer cases; moreover, these genotypes also are related to an increased risk for mtDNA damage (odds ratio [OR] = 3.71 [1.41-9.88]; 95% Cornfield confidence interval [CI]). These results suggest that the absence of GSTM-1 enzymatic activity favors chemical actions in damaging the mtDNA. Analysis of GSTT-1 and NAT-2 polymorphisms showed no association with mtGI (chi(2) = 0.03; P = 0.87 and chi(2) = 2.76; P = 0.09, respectively). The analysis of invasive breast cancer cases showed mtGI in 74.36% of ILC cases (29 of 39 samples), and in only 18.75% (9 out of 48) IDC cases; this result suggests a possible relation between mtDNA mutations and variations in molecular pathways of tumor development.

Association of mitochondrial DNA displacement loop (CA)n dinucleotide repeat polymorphism with breast cancer risk and survival among Chinese women

Mitochondrial genome alternations may be involved in carcinogenesis. The noncoding region of the mitochondrial DNA (mtDNA) displacement loop (D-loop) has emerged as a mutational hotspot. Using data from a population-based case-control study conducted among Chinese women in Shanghai, we evaluated associations of breast cancer risk and survival with the mtDNA D-loop (CA)(n) dinucleotide repeat polymorphism. Included in the study were 1,058 cases and 1,129 age frequency-matched community controls that participated in the Shanghai Breast Cancer Study between 1996 and 1998. Breast cancer patients were followed to determine intervals of overall survival and disease-free survival. Overall, there was no association between the mtDNA D-loop (CA)(n) repeat polymorphism and breast cancer risk. Patients with multiple alleles of the mtDNA D-loop (CA)(n) polymorphism (heteroplasmy) had significantly poorer disease-free survival than those with one allele of the mtDNA D-loop (CA)(n) polymorphism (hazard ratio 1.62; 95% confidence interval, 1.16-2.26). These results suggest that the mtDNA D-loop (CA)(n) repeat polymorphism may be associated with breast cancer survival. Additional studies with a larger sample size are warranted.

Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groups

Allele frequencies of mitochondrial D-loop (CA)(n) repeat was carried out in six Chinese ethnic groups: Han ethnic group in Beijing, Uygur ethnic group in Kashi of Xinjiang province, Li ethnic group in Hainan province, Yao ethnic group in Junan of Guangxi province, Tibet ethnic group in Lasa of Xizang province and Yi ethnic group in Honghe of Yunnan province. A total of 542 individuals were typed. Comparative analyses between our population data and other populations gathered from the literature were performed.

Mitochondrial D-loop (CA)n repeat length heteroplasmy: frequency in a German population sample and inheritance studies in two pedigrees

Sequence analysis of the human mitochondrial genome (mtDNA) has proven to be a valuable tool in forensic identity testing and the analysis of crime scene stains. In contrast to the very expensive sequencing technique, typing of different length variants can greatly facilitate screening of a large number of traces for their relevance during casework. Within the mitochondrial control region, a dinucleotide (CA)( n ) repeat locus is present. To assess the discrimination power of this marker, we have determined (CA)( n ) allele distribution and the frequency of heteroplasmy in a population sample of 2,458 Germans. The inclination to develop heteroplasmic mixtures (CA)( n )/(CA)( n-1) was positively correlated with the number of CA repeats in the mtDNA. In addition, we have studied the inheritance patterns of (CA)( n ) repeat sequence heteroplasmy in two pedigrees. In one pedigree, we also found a length heteroplasmy in the homopolymeric C-tract (nt 303-309). Our data show stable inheritance of heteroplasmy within the homopolymeric C-stretch, but rather unstable inheritance regarding the (CA)( n ) repeat locus.

Forensic mass screening using mtDNA

At the forensic autopsy of a sexual murder victim, some trace hairs, possibly belonging to the perpetrator, were saved. Initially, the analysis of a pubic hair shaft only revealed the presence of the mitochondrial (mt) DNA haplotype profile consisting of the (CA)(6) allele and the complete hypervariable region 1 (HV1) and 2 (HV2) sequence. Later, typing of some further telogene trace hairs, which had been stored for several years, yielded a nuclear short tandem repeat (STR) profile. We used both the mtDNA haplotype and the STR profile to start a DNA mass screening project involving 2,335 male citizens of the relevant communities. MtDNA screening was carried out by using the CA repeat amplification in combination with an SNP typing procedure based on the restriction site analysis of amplified d-loop sequences. The aim of our paper is to put mass screening with mtDNA up for discussion.

Phantom mutation hotspots in human mitochondrial DNA

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

Different methods to determine length heteroplasmy within the mitochondrial control region

The first and second hypervariable regions of the human mitochondrial DNA control region contain two homopolymeric stretches of cytosine (nt 16184-16193 and nt303-315, respectively). According to the Cambridge reference sequence these homopolymeric stretches are interrupted by thymine (T), at positions 16189 and 310, respectively. Monotonous runs of the same base have been suggested to be hot spots for mutations, probably caused by replication slippage, resulting in length heteroplasmy. This paper describes a rapid method based on restriction cleavage of labelled PCR products encompassing the homopolymeric tract in HVII to quantify the relative proportions of different length variants present in an individual. To compare the accuracy of this method, cloned PCR products from several heteroplasmic individuals have been additionally sequenced.

Mitochondrial DNA CA dinucleotide repeats in Koreans: the presence of length heteroplasmy

The mitochondrial DNA HV3 region contains CA dinucleotide repeats which display length polymorphism. To analyze this for forensic purposes, we designed a fluorescence-labelled PCR primer set for short amplification products and carried out genotyping by using capillary electrophoresis. A total of 4 alleles with 4-7 repeat units were observed and the genetic diversity was estimated to be 0.5120 in 500 unrelated Koreans. Interestingly, three individuals showed two or three length variants, i.e. length heteroplasmy.

Nuclear and mitochondrial DNA microsatellite instability in Chinese hepatocellular carcinoma

AIM: To study the nuclear microsatellite instability (nMSI) at BAT26 and mitochondral microsalellite instability (mtMSI) in the occurrence and development of hepatocellular carcinoma and the relationship between nMSI and mtMSI.

METHODS: nMSI was observed with PCR and mtMSI with PCR-SSCP in 52 cases of hepatocellular carcinoma.

RESULTS: mtMSI was detected in 11 out of the 52 cases of hepatocellular carcinoma (21.2%). Among the 11 cases of hepatocellular carcinoma with mtMSI, 7 occured in one locus and 4 in 2 loci. The frequency of mtMSI in the 52 cases of hepatocellular carcinoma showed no correlation to sex, age, infection of hepatitis B, liver cirrhosis as well as positive AFP of the patients (P > 0.05). In addition, nMSI was detected in 3 out of 52 cases of hepatocellular carcinoma (5.8%) and there was no correlation of the incidence of mtMSI to that of nMSI (P > 0.05).

CONCLUSION: mtMSI may be involved in the coccurrence and development of hepatocellular carcinoma and it is independent of nMSI.

Frequent somatic mutations of mitochondrial DNA in esophageal squamous cell carcinoma

Recent studies of various cancers, such as those of the breast, head and neck, bladder and lung, reported that 46-64% of somatic mutations in the D-loop region of mitochondrial DNA (mtDNA) are observed. However, in esophageal cancer, only a low rate (5%) of somatic mutations has so far been reported in one article (Hibi, K. et al., Int J Cancer 2001;92:319-321). Thus, to confirm this we analyzed the somatic mutations for hypervariable regions (HVR-I and HVR-II) in the D-loop of mtDNA to reevaluate the possibility of mitochondrial genetic instability in this cancer. We amplified both HVRs by PCR and DNA samples obtained from 38 esophageal tumors and matched normal tissues, and then sequenced them. Comparing the sequences of tumors to those of normal tissues, we found 14 somatic mutations in 13 patients (34.2%). Eleven mutations were at the C consecutive stretch from position 303 to 309 of MITOMAP in the mitochondria databank (http://www.mitomap.org/), 1 at position 215 in HVR-II and 2 at positions 16,304 and 16,324 in HVR-I. There were 41 types of germ line variations in HVR-I including 2 not so far recorded in the mtDNA databank and 17 in HVR-II including 1 not yet recorded. We also determined nuclear genome instability of these 38 specimens by analyzing 3 independent microsatellite sequences. While 4 specimens showed a single microsatellite change, which is tumor specific, we did not find any co-relation between a somatic mtDNA mutation and microsatellite instability of nuclear genome DNA. These results suggest that mtDNA mutations might show a genetic instability in esophageal cancer independently from a nuclear genome instability.

Mitochondrial genome instability in human cancers

Malfunction of mismatch repair (MMR) genes produces nuclear genome instability (NGI) and plays an important role in the origin of some hereditary and sporadic human cancers. The appearance of non-inherited microsatellite alleles in tumor cells (microsatellite instability, MSI) is one of the expressions of NGI. We present here data showing mitochondrial genome instability (mtGI) in most of the human cancers analyzed so far. The mtDNA markers used were point mutations, length-tract instability of mono- or dinucleotide repeats, mono- or dinucleotide insertions or deletions, and long deletions. Comparison of normal and tumoral tissues from the same individual reveals that mt-mutations may show as homoplasmic (all tumor cells have the same variant haplotype) or as heteroplasmic (tumor cells are a mosaic of inherited and acquired variant haplotypes). Breast, colorectal, gastric and kidney cancers exhibit mtGI with a pattern of mt-mutations specific for each tumor. No correlation between NGI and mtGI was found in breast, colorectal or kidney cancers, while a positive correlation was found in gastric cancer. Conversely, germ cell testicular cancers lack mtGI. Damage by reactive oxygen species (ROS), slipped-strand mispairing (SSM) and deficient repair are the causes explaining the appearance of mtGI. The replication and repair of mtDNA are controlled by nuclear genes. So far, there is no clear evidence linking MMR gene malfunction with mtGI. Polymerase gamma (POLgamma) carries out the mtDNA synthesis. Since this process is error-prone due to a deficiency in the proofreading activity of POLgamma, this enzyme has been assumed to be involved in the origin of mt-mutations. Somatic cells have hundreds to thousands of mtDNA molecules with a very high rate of spontaneous mutations. Accordingly, most somatic cells probably have a low frequency of randomly mutated mtDNA molecules. Most cancers are of monoclonal origin. Hence, to explain the appearance of mtGI in tumors we have to explain why a given variant mt-haplotype expands and replaces part of (heteroplasmy) or all (homoplasmy) wild mt-haplotypes in cancer cells. Selective and/or replicative advantage of some mutations combined with a severe bottleneck during the mitochondrial segregation accompanying mitosis are the mechanisms probably involved in the origin of mtGI.

Efficiency of forensic mtDNA analysis. Case examples demonstrating the identification of traces

The paper presents results of forensic mitochondrial DNA analyses which were aimed at typing the traces caused by touching or abrasion of skin cells. Five cases of strangulation tool investigation are summarised. Two cases of homicide could be cleared up by identifying the mtDNA of both the victim and the suspect on cables which had obviously been used as strangulation tools. In eight of 10 cases, weapons could be reliably assigned to their users. The mtDNA of the users could be even detected on cartridges after firing. In one case, evidence of a suicide could be provided by means of mtDNA sequencing of the wiping traces on a suicide note.