Mitochondrial DNA
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74 Terms
What is mitochondrial DNA (mtDNA)?
DNA found inside mitochondria, separate from the nuclear DNA found in the cell nucleus.
Where is mitochondrial DNA located?
Inside the mitochondria.
What shape is the mitochondrial genome?
Circular.
How many base pairs does the human mitochondrial genome contain?
16,569 base pairs.
Who first sequenced the human mitochondrial genome?
Anderson et al. in 1981 using the Sanger sequencing method.
What was the original mitochondrial reference sequence called?
The Cambridge Reference Sequence (CRS).
What is the revised Cambridge Reference Sequence (rCRS)?
The corrected mitochondrial reference sequence published by Andrews et al. in 1999.
Why was the original CRS revised?
Andrews et al. identified and corrected 11 nucleotide errors while retaining seven rare polymorphisms.
What is the GenBank reference number for the rCRS?
NC_012920.
What is the function of the rCRS in forensic analysis?
It provides a reference sequence against which an individual's mitochondrial DNA sequence can be compared.
What is heteroplasmy?
The presence of two or more different mitochondrial DNA variants within the same cell or individual.
Why can heteroplasmy occur?
Mitochondrial DNA can accumulate mutations, resulting in different versions of mtDNA within an individual.
How quickly does the mitochondrial genome evolve compared with nuclear DNA?
Approximately 6–17 times faster.
Why can heteroplasmy complicate forensic mtDNA analysis?
Different mtDNA variants within the same individual may produce mixed or difficult-to-interpret sequencing results.
What does homoplasmy mean?
When the mitochondrial DNA copies being considered have the same nucleotide sequence at a particular position.
How is human mitochondrial DNA normally inherited?
Almost exclusively through the maternal line.
Why is mitochondrial DNA maternally inherited?
Paternal mitochondria are generally diluted or actively eliminated after fertilisation.
What are the proposed mechanisms explaining maternal mtDNA inheritance?
The dilution model, active elimination of paternal mitochondria and mechanisms involving TFAM.
What does TFAM stand for?
Mitochondrial transcription factor A.
What is the control region of mitochondrial DNA?
A non-coding region involved in regulating mitochondrial DNA replication and transcription.
What is the approximate mutation rate of the mtDNA control region stated in the lecture?
Approximately 2.5 mutations per site per million years.
How many genes are found in the human mitochondrial genome?
37 genes.
How many transfer RNA genes are found in mtDNA?
22 tRNA genes.
How many ribosomal RNA genes are found in mtDNA?
Two rRNA genes.
How many polypeptide-coding genes are found in mtDNA?
13 genes.
What is a mitochondrial nucleoid?
A structure formed by mitochondrial DNA associated with DNA-binding proteins.
What is the main structural protein associated with mitochondrial nucleoids?
TFAM (mitochondrial transcription factor A).
Approximately how many copies of the mitochondrial genome per cell are estimated in the lecture?
Approximately 2,000–2,700 copies.
Why is mtDNA useful in forensic science?
It is present in many copies per cell, making it useful when nuclear DNA is limited or degraded.
Which forensic samples are particularly suitable for mtDNA analysis?
Hair shafts, bones, teeth and other degraded biological samples.
Why is mtDNA useful for analysing hair shafts without roots?
Hair shafts may contain insufficient nuclear DNA, but mitochondrial DNA may still be recoverable.
What is a major disadvantage of mtDNA analysis?
It has lower individual discrimination than nuclear STR profiling because maternal relatives may share the same mitochondrial haplotype.
What is a mitochondrial haplotype?
A combination of mitochondrial DNA sequence variations that identifies a particular mitochondrial lineage.
What is the first stage of laboratory mtDNA analysis?
DNA extraction.
What are the main stages of mitochondrial DNA laboratory analysis?
DNA extraction, quantification, directed PCR, PCR clean-up, sequencing reaction, sequencing clean-up and sequence visualisation using capillary electrophoresis.
What is directed PCR in mtDNA analysis?
PCR amplification of a specific targeted region of the mitochondrial genome.
Why is mtDNA sequencing performed?
To determine the order of nucleotide bases in the mitochondrial DNA region being examined.
Why are separate forward and reverse sequencing reactions performed?
To sequence the DNA in both directions and improve the reliability of sequence interpretation.
What is sequencing clean-up?
A process that removes excess fluorescently labelled ddNTPs and unwanted components after the sequencing reaction.
Why is sequencing clean-up important?
It reduces competition during capillary injection and decreases background fluorescence.
What does EPG stand for?
Electropherogram.
What is an electropherogram used for in mtDNA analysis?
It provides a visual representation of the sequencing results.
How are mitochondrial haplotypes generated?
By sequencing a targeted region or the entire mitochondrial genome and recording differences from the rCRS.
What happens after the target mitochondrial DNA region is sequenced?
The sequence is compared with the revised Cambridge Reference Sequence.
What are deviations from the rCRS?
Nucleotide differences between the sample sequence and the reference sequence.
How are mtDNA differences recorded?
Using nucleotide position numbers followed by the base present in the sample.
What does a mitochondrial haplotype represent?
The recorded nucleotide differences between an individual's mtDNA sequence and the rCRS.
What are the three possible outcomes of forensic mtDNA comparison?
Inclusion, exclusion or inconclusive.
What does an inclusion result mean in mtDNA analysis?
The questioned sample and reference sample have compatible mitochondrial DNA sequences.
What does an exclusion result mean in mtDNA analysis?
The mitochondrial DNA sequences contain differences that are inconsistent with the samples originating from the same mitochondrial lineage.
What does an inconclusive mtDNA result mean?
The available sequence information is insufficient to make a reliable inclusion or exclusion decision.
What does ISFG stand for?
International Society for Forensic Genetics.
What did the ISFG DNA Commission recommend in 2014?
Sequencing the entire mitochondrial control region, covering nucleotide positions 16024–576, as a minimum for forensic analysis.
Why is sequencing the entire control region recommended?
It increases the ability to distinguish mitochondrial haplotypes and assign haplogroups.
How can sequencing the entire mitochondrial genome improve forensic discrimination?
It provides additional genetic information and can distinguish more individuals than sequencing only a limited region.
What percentage of randomly sampled individuals could have distinct haplotypes when the complete mtGenome is sequenced, according to the lecture?
Over 90%.
What is EMPOP?
The EMPOP database is a searchable international database of mitochondrial DNA haplotypes.
What is the purpose of the EMPOP database?
To provide high-quality mitochondrial DNA population data for forensic comparisons and frequency estimation.
Why is EMPOP useful in forensic investigations?
It allows forensic scientists to compare mitochondrial haplotypes with population data.
What is a haplogroup?
A group of related mitochondrial DNA haplotypes that share common ancestral genetic markers.
How are mitochondrial haplogroups identified?
By examining sequence differences and assigning the mitochondrial sequence to a group based on shared genetic variations.
What can mitochondrial haplogroups reveal?
Information about maternal ancestry and historical population origins.
How far back can mitochondrial haplogroup ancestry potentially be traced according to the lecture?
Approximately 30 generations or more.
What are ancestral biogeographic origins?
The geographical origins and historical migration patterns of ancestral populations.
Why is ancestral information useful in forensic investigations?
It may provide investigative intelligence about the possible maternal ancestry of an unknown individual.
Can mitochondrial haplogroups identify a specific individual?
No, they provide information about maternal lineage rather than unique individual identity.
What is the difference between mtDNA and nuclear DNA inheritance?
mtDNA is normally inherited maternally, whereas nuclear DNA is inherited from both biological parents.
What is one major advantage of mtDNA compared with nuclear STR analysis?
There are many copies of mtDNA per cell, increasing the likelihood of obtaining results from degraded or limited samples.
What is one major disadvantage of mtDNA compared with nuclear STR analysis?
It has lower discriminatory power because individuals from the same maternal lineage may share a haplotype.
Why might maternal relatives have matching mitochondrial DNA profiles?
They inherit mitochondrial DNA through the same maternal lineage.
Can mtDNA distinguish between siblings who share the same mother?
Usually not, because they generally inherit the same maternal mitochondrial lineage.
Why is mtDNA particularly useful in unidentified human remains investigations?
It can be recovered from bones, teeth and hair shafts when nuclear DNA is too degraded or limited.
What is the main purpose of comparing mtDNA with the rCRS?
To identify and record sequence variations that form the individual's mitochondrial haplotype.
What is the main limitation of using mtDNA for individual identification?
A matching haplotype cannot necessarily distinguish between individuals belonging to the same maternal lineage.