Inside the mitochondrion is a certain type of DNA. That's different in a way from the DNA that's in the nucleus. This DNA is small and circular. It has only 16, or so base pairs in it. This organelle is the mitochondrion, the powerhouse of eukaryotic cells. In contrast to the human nuclear genome, which consists of 3.
Despite its small size, the mitochondrial genome can be used to establish maternal family ties, thanks to its maternal pattern of inheritance. Mutations in the mitochondrial genome have also been associated with diverse forms of human disease and aging. Figure 2 Similar to the nuclear genome, the mitochondrial genome is built of double-stranded DNA, and it encodes genes Figure 2.
Many interesting features distinguish human mitochondrial DNA from its nuclear counterpart, including the following:. Why do mitochondria have such a high mutation rate? The POLG protein consists of two domains: a catalytic domain that exhibits polymerase activity, and an exonuclease domain that is involved in the recognition and removal of DNA base-pair mismatches that occur during DNA replication.
A recent study suggests that mitochondria may have a nucleotide imbalance that leads to decreased POLG fidelity and higher mitochondrial DNA mutation rates Song et al.
In the aforementioned study, Song and colleagues measured the mitochondrial levels of free deoxynucleotide triphosphates dNTPs , the building blocks of new DNA strands made during DNA replication , in tissues from young and old rats.
As shown in Table 1, the researchers did not detect differences in the nucleotide levels in tissues taken from young versus old rats. However, they found that mitochondrial dNTP levels were highly divergent, and that dGTP was by far the most abundant nucleotide in the mitochondria of most tissues.
The data show that the frequency of mutation is higher for dNTP pools like those in mitochondria than in dNTP pools with equal ratios.
All rights reserved. Relative frequencies were normalized to 1 micromolar dNTP pools for each enzyme. When a dNTP pool from skeletal muscle mitochondria was incubated with wild-type POLG, the mutant frequency x 10 -4 was 13 and the relative frequency was 1. When the filled-in lacZ gene was introduced into bacterial host cells, the resulting color of the bacterial cell colony was used to report whether a mutation had occurred: blue colonies represented the wild-type lacZ gene, whereas light blue or white colonies represented clones that had acquired a mutation in the filled-in lacZ gene.
The DNA sequence of individual lacZ clones was also determined, so that the nature of the mutation could be deduced Song et al. Song et al. Due to the maternal pattern of mitochondrial inheritance, males with a mitochondrial disease are not considered to be at risk for transmitting the disorder to their offspring.
It's important to remember that there are many mitochondria within a cell, each with its own mtDNA and potential mutations. Thus, when discussing mitochondrial mutations, it is necessary to think of mutations present across the entire mitochondrial population rather than in a single mitochondrion. Although mitochondrial populations are considered heteroplasmic, with variations among the many mtDNA genomes, mothers can have mitochondrial populations that are homoplasmic for a given mitochondrial mutation; in this case, the majority of their mitochondrial genome would harbor the mutation.
Homoplasmic mitochondrial mutations will be transmitted to all maternal offspring; however, due to the complex interplay between the mitochondrial and nuclear genomes, it is often difficult to predict disease outcomes, even with homoplasmic mitochondrial populations. A list of clinical disorders associated with mitochondrial mutations is provided in Table 3. One of these mitochondria-associated disorders is Leber hereditary optic neuropathy LHON , which leads to a loss of vision in both eyes and is most commonly associated with a homoplasmic mitochondrial DNA mutation, although heteroplasmic transmission also occurs Man et al.
These findings point to the likely involvement of other genes and environmental factors. Similarly, a homoplasmic mutation in a mitochondrial genome-encoded ribosomal RNA , called RNR1, causes postlingual deafness deafness that occurs after three years of age, when a child has already learned to speak.
The clinical symptoms of this disease are associated with the administration of a particular type of antibiotic Prezant et al. Therefore, environmental factors also contribute to the phenotypes associated with this mitochondrial mutation. What are some clues that may suggest a mitochondrial link to disease?
Some clinical features include a maternal family history and the involvement of several different tissues. Furthermore, because mitochondria function as the powerhouses of our cells, mitochondrial mutations often lead to more pronounced phenotypes in tissues that have high energy demands, such as brain, retinal, skeletal muscle, and cardiac muscle tissues.
A number of clinical syndromes are currently believed to be associated with mitochondrial disease. Possible examples include Pearson syndrome, Leigh syndrome, progressive external ophthalmoplegia, exercise-induced muscle pain , fatigue, and rhabdomyolysis. As previously mentioned, mitochondrial DNA in humans is always inherited from a person's mother Figure 4.
As a result, we share our mitochondrial DNA sequence with our mothers, brothers, sisters, maternal grandmothers, maternal aunts and uncles, and other maternal relatives. Due to the high mutation rates associated with mitochondrial DNA, significant variability exists in mitochondrial DNA sequences among unrelated individuals. However, the mitochondrial DNA sequences of maternally related individuals, such as a grandmother and her grandson or granddaughter, are very similar and can be easily matched.
Mitochondrial DNA sequence data has proved extremely useful in human rights cases, as it is a great a tool for establishing the identity of individuals who have been separated from their families. This approach has been very successful for the following reasons Owens et al. One of the most prominent researchers to use mitochondrial DNA sequence data to tackle human rights issues is Dr.
A particularly interesting example of Dr. King's work occurred in Argentina. As a result of a military dictatorship that overthrew the existing Argentinean government in , thousands of citizens disappeared between and , including infants and children who were abducted along with their parents. In addition, some children were born to women who were pregnant at the time of their kidnappings.
After the military dictatorship was defeated, a new government commission predicted that at least 8, and possibly as many as 30, people had been kidnapped, including documented infants and children. In , the grandmothers of these orphans formed the Associacion de Abuelas de Plaza de Mayo in an effort to identify their missing grandchildren, many of whom were illegally adopted by military families.
In , King used mitochondrial DNA sequence data to reunite some of these Argentinean orphans with their grandmothers. King collected blood samples from orphaned children and from women who had lost their children and grandchildren. Using mitochondrial DNA sequence data, she then matched more than 60 orphans with their biological families. In fact, as recently as , a young Argentinean man named Guillermo was finally reunited with his grandmother and sister.
Guillermo's parents were kidnapped by security forces in October ; Guillermo's mother, Patricia, was pregnant at the time of her kidnapping, and Guillermo was born one month later. Papers nonrelated with human or animal mitochondrial DNA were excluded. Our search was not refined by publishing date, journal or impact factor of the journal, authors or authors affiliations. Mitochondria are cellular organelles that contain an extrachromosomal genome, which is both different and separate from the nuclear genome.
Essentially, the mtDNA is a five mm histone-free circular double-stranded DNA molecule, with around 16 base-pairs and weighting 10 7 Daltons Taanman, All the 13 protein products are part of the enzyme complexes that constitute the oxidative phosphorylation system. Other characteristic features of the mtDNA are the intronless genes and the limited, or even absent, intergenic sequences, except in one regulatory region.
The origin of replication is located at the non-coding or D-loop region, a 1 base pairs segment that is located between positions 16 and , according to the CRS numeration Anderson et al.
The D-loop region, also comprehends two transcription promotors, one for each strand. Nucleotide positions in the mtDNA genome are numbered according to the convention presented by Anderson et al.
More precisely, the numerical designation of each base pair is initiated at an arbitrary position on the H strand, which continues thereafter and around the molecule for approximately 16 base pairs. The apparent lack of mtDNA repair mechanisms and the low fidelity of the mtDNA polymerase lead to a significant higher mutation rate in the mitochondrial genome, when compared to the nuclear genome.
The small size and relatively high inter-person variability of the HV regions are very useful features for forensic testing purposes. The collection of similar haplotypes defined by the combination of single nucleotide polymorphisms SNPs in mtDNA inherited from a common ancestor defines an haplogroup which was formed as a result of the sequential accumulation of mutations through maternal lineage Mitchell et al.
A mitochondrion contains 2 to 10 copies of mtDNA and each somatic cell can have up to 1, mitochondria Elson et al. This specific characteristic can be very helpful in forensic cases, such as in the analysis of the remains of a missing person, where the known maternal relatives can provide some reference samples for a direct comparison to the mtDNA type.
The haploid and monoclonal nature of the mtDNA in most individuals simplifies the process of interpretation of the DNA sequencing results. There are two classes of heteroplasmy, related to length polymorphisms and to point substitutions.
Only the latter is important for forensic human identification. Most forensic laboratories worldwide do not report length polymorphisms and the guidelines on human identification with mtDNA do not point them as mandatory information Parson et al. Heteroplasmy manifests itself in diverse ways Stewart et al. An individual may show more than one mtDNA type in a single tissue. An individual may be heteroplasmic in one tissue sample and homoplasmic in another one.
Finally, an individual may exhibit one mtDNA type in one tissue and a different type in another tissue. Of the three possible scenarios, the last one is the least likely to occur. Wilson et al. The existence of heteroplasmic individuals and the limited knowledge about both the mechanism and the rate of heteroplasmy can be issues raised in an attempt to exclude mtDNA evidence from forensic investigations.
Hence, if an evidentiary hair sample contains one of the two heteroplasmic lineages that are observed in a reference sample, or vice versa, then the interpretation of exclusion may be incorrect. In this case, typing additional hairs may be required to solve the problem Budowle et al. As it was previously pointed out, it is accepted that the mitochondrial genome is maternally inherited.
Even though the sperm contains a few mitochondria in the neck and in the tail region, the male mitochondrial genome is destroyed either during or shortly after the fertilization. Nonethless, in the last years some cases of biparental mtDNA inheritance have been reported. In the most recent case, Luo and collaborators describe biparental mtDNA inheritance, either directly or indirectly, in 17 members of three multigenerational families, with results confirmed by two independent laboratories Luo et al.
Besides this report in humans, there are also a few examples of paternal inheritance of the mitochondrial genome in animals Gyllensten et al. Considering that listing more than bases in order to describe the results from a new HV1 and HV2 sequence would be unpractical, an alternative approach was developed which essentially identifies and reports the differences relative to the reference sequence rCRS Anderson et al.
Even though the process of naming mtDNA sequences seems simple and obvious, it is crucial to properly consider the nomenclatures, since complications might arise. To avoid ambiguities, facilitate haplotype identification and their assignment to existent haplogroups or to new haplogroups, phylogenetic-based nomenclature guidelines have been proposed. The phylogenetic approach provides an evolutionary based view of global mtDNA diversity that is scientifically sound because all mtDNA lineages derive from a common maternal ancestor.
Variants flanking long C tracts are subject to sequence-specific conventions. Length variation of the short A tract preceding 16 should be notated preferring transversions unless the phylogeny suggests otherwise. Regarding deletions, these are recorded by the number of the base s that is missing, with respect to the rCRS, followed by DEL or del or - for example DEL or del or When any of the four bases are observed, N notation should be used. For example, if the bases beyond the position were out of the register by one base due to the insertion of a C the mutation is designated as Two C insertions are designated as Overall, the large majority of individuals from African populations, and specially from sub-Saharan African populations, are categorized into one of the main haplogroup lineages that diverged from macro-haplogroup L: L0, L1, L2, L3, L4, L5 and L6 Allard et al.
The main haplogroups found in individuals from Asian populations are haplogroups M and N Allard et al. These guidelines referred to good laboratory practices, targeted region, amplification and sequencing ranges, reference sequence, alignment and notation, heteroplasmy, haplogrouping of mtDNA sequences, and databases and database searches. The incorporation of ddNTPs in newly synthesized DNA strands results in termination of the elongation process and correspondent knowledge about the specific nucleotide present at the sequence at each position.
Sanger sequencing method can produce reads from 25 up to nucleotides, allowing the read of a maximum of 96 kb nucleotides in 2 h. When this happens protons are released generating an electric signal that is proportional to the amount of protons released.
Data collection is carried out by a complementary metal-oxide semiconductor CMOS sensor array chip with the sensor surface present at the bottom of the well plate, and these chips can measure millions to billions of simultaneous sequencing reactions Liu et al. Finally, MinION Oxford Nanopore Technologies , a portable real-time sequencing device, allows ultra-long read lengths hundreds of kb albeit with lower accuracy Oikonomopoulos et al. Although PGM proved to be sensitive and accurate at detecting and quantifying mixture and heteroplasmy, there were some problems in the coverage of the mtDNA genome with some regions presenting extreme strand bias, and presenting false positives mostly generated by alignment problems in the analysis algorithms.
Both sequencing systems provided consistent estimation of mtDNA haplotypes. In the meantime, and according to current international guidelines Parson et al. Some forensic laboratories perform Sanger sequencing for HVI and HVII fragments, while others have already extended the study to the HVIII fragment and, in recent years, most of the forensic laboratories are introducing the amplification of the entire control region as routine methodology Chaitanya et al.
Attempting to improve the power of mtDNA in human identification, over the past decade some studies have been focused in the extension of the analyses to the whole mtDNA genome Duan et al. Nevertheless, it should be stressed that while the information from the entire mtDNA genome can contribute to refine the haplogroup obtained with the study of HVI, HVII and HVII fragments or the entire control region, it is not supposed to change the previous results to a different haplogroup of a completely different geographic ancestry.
When two mtDNA sequences, one from an evidence sample and another from a reference sample, cannot be excluded as being originated from the exact same source, it is necessary to convey some information concerning the rarity of the mtDNA profile.
The current practice is to count how many times a specific sequence is observed within a population database s Budowle et al. Overall, the population databases that are used in forensics comprehend several convenience samples, representing the major population groups of the potential contributors in terms of evidence. In its early stages, EMPOP was designed and envisioned to serve as a reference population database, specifically to be used in the evaluation of the mtDNA evidence around the world, aiming to provide the highest quality mtDNA data.
The architecture of this online database and its analysis tools have evolved over the last few years, even though the main emphasis of the EMPOP database remains to be mtDNA data quality. Therefore, and as a direct consequence, EMPOP not only serves as a reference population database, but also as a quality-control tool for scientists in forensic genetics, as well as in other disciplines.
Finally, and even though there is a significant number of high-quality reference population databases for forensic comparisons, EMPOP is the most comprehensive resource, especially from the standpoint of the populations that are represented in such database Parson et al.
EMPOP uses SAM, a string-based search algorithm that converts query and database sequences into alignment-free nucleotide strings and thus guarantees that a haplotype is found in a database query regardless of its alignment. For multiple possible haplogroups, most recent common ancestor MRCA haplogroups are provided. At EMPOP the geographical haplogroup patterns are provided via maps to visualize and better understand their geographical distribution Fig.
Currently, Mitomap is manually curated, frequently updated and a functionally rich resource, presenting high-quality human mtDNA data for clinicians, investigators and geneticists Ruiz-Pesini et al. Mitomap has three main categories for usage. It contains some background information regarding the human mitochondrial DNA, such as the general representation of mtDNA, haplogroups and their frequencies and illustrations of mtDNA, among others.
Furthermore, users can also find information about other mtDNA-specific databases, tools and useful resources. Mitomap stores the annotated listing of the mtDNA variants from both healthy individuals and patients. The frequencies of the variants are calculated from human mitogenomes retrieved from the GenBank. Therefore, users can retrieve information about the loci, the nucleotide change, the codon position and the number, among others, and download the most important data in different file formats.
Mitomap contains the Mitomaster analysis tool, currently providing the Application Programming Interface for it. The main function of this tool is to allow the identification of polymorphic positions, the calculation of variant statistics and the assignment of haplogroups to complete or partial mitogenomes. Such query might be performed by recurring to mtDNA sequences, to GenBank identifiers or to single nucleotide variants Brandon et al. From another perspective, ethical and legal problems may arise in the implementation of mtDNA databases.
The informative potential which the analysis of mtDNA entails can generate privacy questions Guillen et al. Mitochondrial diseases affect between 1 in 4, and 1 in 5, people.
In most people, primary mitochondrial disease is a genetic condition that can be inherited. Information about the mitochondrial genome composition may therefore enable the identification of the current or future state of health of an individual.
For this reason, the analysis of mtDNA must be carried out only on non-coding regions, which have not been associated with any kind of disease or phenotypical information. In the context of forensic analysis, both mtDNA sequences of a reference sample and an evidence sample s are compared.
When the sequences are unequivocally different, the conclusion is that they can be excluded as being originated from the same source. Although not stated in any research paper or guideline text, forensic routine laboratories tend to accept as an exclusion scenario when more nucleotide differences exist between the two sequences.
If the mtDNA sequences are identical, the samples cannot be excluded since they must have the same origin or derive from the same maternal lineage. Several authors have suggested that samples with mtDNA with one-base difference should be further evaluated, mainly regarding their rate of mutation Alonso et al. In this section, we present some selected published cases of human identification with mtDNA.
Table 2 summarizes the selected published cases. Stoneking et al. Using hybridization with 23 sequence-specific oligonucleotide probes SSO targeting nine regions of HV1 and HV2 on the control region, they found that the skeletal sample and the mother shared the same mtDNA types, corroborating that those skeletal remains were of the missing child. Moreover, they anticipated that the mtDNA typing would be valuable not only in linking biological remains to missing individuals, but also in the analysis of material in sexual assault cases.
In July of , the body of a female, in a quite advanced state of decomposition, was discovered in an open field. Some fragments of the heel bone and fibula, plus samples of the hair and skin, were provided for the DNA analysis, as well as a blood sample from a putative sister of the deceased.
No statistical value was given to the evidence, since no database of the British population sequences were available at that time. Still, no differences were found between both sequences, the blood of the putative sister and the bone of the corpse, indicating they were sisters.
Gill et al. It was found that the sequences were very similar, corroborating the hypothesis that the bone remains were of Tsar Nicholas II. Most of the body's cells contain thousands of mitochondria, each with one or more copies of mitochondrial DNA.
These cells can have a mix of mitochondria containing mutated and unmutated DNA heteroplasmy. The severity of many mitochondrial disorders is thought to be associated with the percentage of mitochondria with a particular genetic change.
A buildup of somatic mutations in mitochondrial DNA has been associated with an increased risk of certain age-related disorders such as heart disease, Alzheimer disease, and Parkinson disease. Additionally, research suggests that the progressive accumulation of these mutations over a person's lifetime may play a role in the normal aging process. Genetics Home Reference has merged with MedlinePlus.
Learn more. The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health. Mitochondrial DNA. From Genetics Home Reference. Description Mitochondria are structures within cells that convert the energy from food into a form that cells can use. Health Conditions Related to Chromosomal Changes The following chromosomal conditions are associated with changes in the structure or number of copies of mitochondrial dna.
Age-related hearing loss Changes in mitochondrial DNA are among the best-studied genetic factors associated with age-related hearing loss. More About This Health Condition. Cyclic vomiting syndrome Some cases of cyclic vomiting syndrome, particularly those that begin in childhood, may be related to changes in mitochondrial DNA. Cytochrome c oxidase deficiency Mutations in at least three mitochondrial genes can cause cytochrome c oxidase deficiency, which is a condition that can affect several parts of the body, including the muscles used for movement skeletal muscles , the heart, the brain, or the liver.
Leigh syndrome Mutations in one of several different mitochondrial genes can cause Leigh syndrome, which is a progressive brain disorder that usually appears in infancy or early childhood. Nonsyndromic hearing loss Mutations in mitochondrial DNA are associated with nonsyndromic hearing loss, which is loss of hearing that is not associated with other signs and symptoms. Progressive external ophthalmoplegia Mitochondrial DNA deletion or mutation can be involved in an eye condition called progressive external ophthalmoplegia.
Cancers Mitochondrial DNA is prone to somatic mutations, which are a type of noninherited mutation. Other disorders Inherited changes in mitochondrial DNA can cause problems with growth, development, and function of the body's systems. Maternal inheritance in cyclic vomiting syndrome. Am J Med Genet A. The mitochondrion: a perpetrator of acquired hearing loss. Hear Res. Epub Jan Primary Mitochondrial Disorders Overview. Arch Neurol. Mitochondrial DNA and disease.
Ann Med. EFNS guidelines on the molecular diagnosis of mitochondrial disorders. Eur J Neurol. Mitochondrial dysfunction in hearing loss. Epub Nov 6. Impact of the mitochondrial genetic background in complex III deficiency. PLoS One. Molecular pathogenetic mechanism of maternally inherited deafness. Ann N Y Acad Sci. Alterations of mitochondrial DNA in common diseases and disease states: aging, neurodegeneration, heart failure, diabetes, and cancer.
Curr Med Chem. Arch Dis Child. The neurology of mitochondrial DNA disease. Lancet Neurol. Mitochondrial disease: mutations and mechanisms. Neurochem Res.
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