A hypervariable region (HVR) is a location within a sequence where polymorphisms frequently occur. It is used in two contexts: * In the case of nucleic acids, an HVR is where

base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

s frequently change. This can be due to a change in the number of repeats (which is seen in eukaryotic

nuclear DNA Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA contained within each cell nucleus of a eukaryotic organism. It encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. ...

) or simply low selective pressure allowing a great number of substitutions and indels (as in the case of

mitochondrial DNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondrion, mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the D ...

D-loop In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. An R-loop is similar to a D-loop, but in that cas ...

and 16S rRNA). * In the case of antibodies, an HVR is where most of the differences among antibodies occur. This region is also called the complementarity-determining region. Because there already is a separate article for the antibody region, this article will focus on the nucleic acid case.

Mitochondrial

There are two mitochondrial hypervariable regions used in human mitochondrial

genealogical DNA test A genealogical DNA test is a DNA-based Genetic testing, genetic test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to ...

ing. HVR1 is considered a "low resolution" region and HVR2 is considered a "high resolution" region. Getting HVR1 and HVR2 DNA tests can help determine one's

haplogroup A haplotype is a group of alleles in an organism that are inherited together from a single parent, and a haplogroup (haploid from the , ''haploûs'', "onefold, simple" and ) is a group of similar haplotypes that share a common ancestor with a sing ...

. In the revised Cambridge Reference Sequence of the human mitogenome, the most variable sites of HVR1 are numbered 16024-16383 (this subsequence is called HVR-I), and the most variable sites of HVR2 are numbered 57-372 (''i.e.,'' HVR-II) and 438-574 (''i.e.,'' HVR-III).''PhyloTree mt''
"Annotated mtDNA reference sequences: revised Cambridge Reference Sequence (rCRS)"
Retrieved on 4 February 2016. In some

bony fish Osteichthyes ( ; ), also known as osteichthyans or commonly referred to as the bony fish, is a Biodiversity, diverse clade of vertebrate animals that have endoskeletons primarily composed of bone tissue. They can be contrasted with the Chondricht ...

es, for example certain

Protacanthopterygii Protacanthopterygii is a superorder of ray-finned fish. They inhabit both Marine (ocean), marine and freshwater habitats. They appear to have evolved in the Cretaceous or perhaps late Jurassic, originating probably roughly 150 million years ago; ...

and

Gadidae The Gadidae are a family of marine fish, included in the order Gadiformes, known as the cods, codfishes, or true cods. It contains several commercially important fishes, including the cod, haddock, whiting, and pollock. Most gadid species ar ...

, the mitochondrial control region evolves remarkably slowly. Even functional mitochondrial

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s accumulate mutations faster and more freely. It is not known whether such hypovariable control regions are more widespread. In the Ayu (''Plecoglossus altivelis''), an

East Asia East Asia is a geocultural region of Asia. It includes China, Japan, Mongolia, North Korea, South Korea, and Taiwan, plus two special administrative regions of China, Hong Kong and Macau. The economies of Economy of China, China, Economy of Ja ...

n protacanthopterygian, control region

mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, ...

rate is not markedly lowered, but sequence differences between

subspecies In Taxonomy (biology), biological classification, subspecies (: subspecies) is a rank below species, used for populations that live in different areas and vary in size, shape, or other physical characteristics (Morphology (biology), morpholog ...

are far lower in the control region than elsewhere. This phenomenon completely defies explanation at present.

Ribosomal RNA

The 16S ribosomal RNA in prokaryotes have nine hypervariable regions where mutation rates are higher than neighboring parts, numbered V1 to V9. V4 one of the most conservative, while V3 is one of the fastest-evolving. These regions offer a way to quickly determine the identity of a prokaryote: because the surrounding regions are relatively conserved, a "universal primer" can be used to selectively amplify one or a stretch of several HV regions using PCR. The resultant amplicon is sequenced, and each unique sequence is termed an amplicon sequence variant (ASV). A database such as Greengenes2 can then be used to look up an ASV (often an exact match) in the taxonomic and phylogenetic trees.

Repeat sequences

Simple sequence repeats, specifically variable number tandem repeats and

microsatellite A microsatellite is a tract of repetitive DNA in which certain Sequence motif, DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organ ...

s, commonly occur in the human genome. Their repeated nature allows a unique form of mutation: the number of copies can increase or decrease when strand slippage occurs during DNA replication. (Regular point mutation still happens and could be more frequent than slippage.) Their copy number not only have use in forensics and ancestry testing, but are also linked to diseases.

References

External links

* {{MeshName, Hypervariable+region
DNA: Forensic and Legal Applications, Explanation of Hypervariable Regions
Genetic genealogy Genetic engineering Antibodies

Mitochondrial

Ribosomal RNA

Repeat sequences

See also

References

External links