Indel
Encyclopedia
Indel is a molecular biology term that has different definitions in different fields:
In coding region
s of the genome, unless the length of an indel is a multiple of 3, they produce a frameshift mutation
. For example, a common microindel which results in a frameshift causes Bloom syndrome
in the Japanese population. Indels can be contrasted with a point mutation
; where an Indel inserts and deletes nucleotides from a sequence, a point mutation is a form of substitution that replaces one of the nucleotides. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed.
Indels, as defined as either an insertion or deletion, can be used as genetic markers in natural populations, especially in phylogenetic studies.
An indel change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) stop codon
in a different frame. Indels that are not multiples of 3 are particularly uncommon in coding regions but relatively common in non-coding regions. There are approximately 192-280 frameshifting indels in each person
. Note, however, the absolute rate of indels in most known genomes, including humans, tends to be markedly lower than base substitutions, except near highly repetitive regions, including homopolymers and microsatellites.
The term "indel" has been co-opted in recent years by genome scientists
for use in the sense described above. This is a change from its original use and meaning, which arose from systematics
. In systematics, researchers could find differences between sequences, such as from two different species. But it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 G
nucleotides at a locus and species B has 5 G's at the same locus. If the mode of selection is unknown, we can't tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When we cannot infer the phylogenetic direction of the sequence change, the sequence change event is referred to as an "indel".
- In evolutionary studies, indel is used to mean an insertion or a deletion and indels simply refers to the mutation class that includes both insertions, deletions, and the combination thereof, including insertion and deletion events that may be separated by many years.
- In germline and somatic mutation studies, however, indel describes a special mutation class, defined as a mutation resulting in a colocalized insertion and deletion and a net gain or loss in nucleotides, and microindel is defined as an indel that results in a net gain or loss of 1 to 50 nucleotides.
In coding region
Coding region
The coding region of a gene, also known as the coding sequence or CDS, is that portion of a gene's DNA or RNA, composed of exons, that codes for protein. The region is bounded nearer the 5' end by a start codon and nearer the 3' end with a stop codon...
s of the genome, unless the length of an indel is a multiple of 3, they produce a frameshift mutation
Frameshift mutation
A frameshift mutation is a genetic mutation caused by indels of a number of nucleotides that is not evenly divisible by three from a DNA sequence...
. For example, a common microindel which results in a frameshift causes Bloom syndrome
Bloom syndrome
Bloom's syndrome , also known as Bloom–Torre–Machacek syndrome, is a rare autosomal recessive chromosomal disorder characterized by a high frequency of breaks and rearrangements in an affected person's chromosomes. The condition was discovered and first described by dermatologist Dr...
in the Japanese population. Indels can be contrasted with a point mutation
Point mutation
A point mutation, or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA. Often the term point mutation also includes insertions or deletions of a single base pair...
; where an Indel inserts and deletes nucleotides from a sequence, a point mutation is a form of substitution that replaces one of the nucleotides. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed.
Indels, as defined as either an insertion or deletion, can be used as genetic markers in natural populations, especially in phylogenetic studies.
An indel change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) stop codon
Stop codon
In the genetic code, a stop codon is a nucleotide triplet within messenger RNA that signals a termination of translation. Proteins are based on polypeptides, which are unique sequences of amino acids. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide...
in a different frame. Indels that are not multiples of 3 are particularly uncommon in coding regions but relatively common in non-coding regions. There are approximately 192-280 frameshifting indels in each person
. Note, however, the absolute rate of indels in most known genomes, including humans, tends to be markedly lower than base substitutions, except near highly repetitive regions, including homopolymers and microsatellites.
The term "indel" has been co-opted in recent years by genome scientists
Science
Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe...
for use in the sense described above. This is a change from its original use and meaning, which arose from systematics
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...
. In systematics, researchers could find differences between sequences, such as from two different species. But it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 G
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
nucleotides at a locus and species B has 5 G's at the same locus. If the mode of selection is unknown, we can't tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When we cannot infer the phylogenetic direction of the sequence change, the sequence change event is referred to as an "indel".