Low copy repeats (LCRs), also known as segmental duplications (SDs), are highly
homologous sequence elements within the
eukaryotic genome.
Repeats
The repeats, or duplications, are typically 10–300
kb in length, and bear greater than 95%
sequence identity
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Ali ...
. Though rare in most mammals, LCRs comprise a large portion of the
human genome
The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the n ...
owing to a significant expansion during
primate evolution. In humans,
chromosomes Y and
22 have the greatest proportion of SDs: 50.4% and 11.9% respectively.
Misalignment of LCRs during
non-allelic homologous recombination Non-allelic homologous recombination (NAHR) is a form of homologous recombination that occurs between two lengths of DNA that have high sequence similarity, but are not alleles.
It usually occurs between sequences of DNA that have been previously ...
(NAHR)
is an important mechanism underlying the
chromosomal microdeletion disorders as well as their reciprocal duplication partners. Many LCRs are concentrated in "hotspots", such as the 17p11-12 region, 27% of which is composed of LCR sequence. NAHR and
non-homologous end joining
Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology direct ...
(NHEJ) within this region are responsible for a wide range of disorders, including
Charcot–Marie–Tooth syndrome type 1A,
hereditary neuropathy with liability to pressure palsies
Hereditary neuropathy with liability to pressure palsy (HNPP) is a peripheral neuropathy, a condition that affects the nerves.update 2014 Pressure on the nerves can cause tingling sensations, numbness, pain, weakness, muscle atrophy and even para ...
,
Smith–Magenis syndrome
Smith–Magenis Syndrome (SMS), also known as 17p- syndrome, is a microdeletion syndrome characterized by an abnormality in the short (p) arm of chromosome 17. It has features including intellectual disability, facial abnormalities, difficulty sl ...
,
and
Potocki–Lupski syndrome
Potocki–Lupski syndrome (PTLS), also known as dup(17)p11.2p11.2 syndrome, trisomy 17p11.2 or duplication 17p11.2 syndrome, is a contiguous gene syndrome involving the microduplication of band 11.2 on the short arm of human chromosome 17 (17p1 ...
.
Detection
The two widely accepted methods for SD detection
Genome-wide detection of segmental duplications
/ref> are:
*1. Whole-genome assembly comparison (WGAC), and
*2. Whole-genome shotgun sequence detection (WSSD).
See also
* Pseudogenes
Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are ...
* Molecular evolution
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics ...
* Comparative genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...
* Inparanoid
* Tandem exon duplication Tandem exon duplication is defined as duplication of exons within the same gene to give rise to the subsequent exon. A complete exon analysis of all genes in ''Homo sapiens'', ''Drosophila melanogaster'', and '' Caenorhabditis elegans'' has shown 1 ...
* 1q21.1 copy number variations
* Segmental duplication on the human Y chromosome
Segmental duplication are blocks of DNA ranging from 1 to 400 kb in length which recur at multiple sites within the genome, sharing greater than 90% similarity. Multiple studies have found a correlation between the location of segmental dupl ...
References
{{Repeated sequence
Molecular genetics
Mutation