Tandem repeat

Tandem repeats are patterns of nucleotides, the basic building blocks of DNA, that are repeated adjacent to each other in the genome. These sequences can range in length from two nucleotides to several thousand and can be found in all genomic DNA, including both coding (genes) and non-coding regions. The number of repeats in a given location can vary among individuals within a population, making tandem repeats useful for genetic fingerprinting and as markers in genetic linkage studies.

Types of Tandem Repeats

Tandem repeats are categorized based on the length of the repeat unit:

• Microsatellites or Short Tandem Repeats (STRs): These consist of repeat units that are 2-6 base pairs long. They are highly polymorphic and are commonly used in DNA profiling in forensic science, paternity testing, and genetic linkage analysis.
• Minisatellites: Also known as Variable Number Tandem Repeats (VNTRs), these have longer repeat units of 10-60 base pairs. They were the first type of DNA polymorphism to be used for DNA fingerprinting.
• Satellite DNA: This includes larger arrays of tandem repeats, such as alpha satellite DNA, which is found in centromeric regions, and telomeric DNA, which is found at the ends of chromosomes and consists of tandemly repeated sequences that protect the chromosome ends.

Function

The function of tandem repeats can vary:

• Structural: Some tandem repeats play a role in chromosome structure and stability, such as those found in centromeres and telomeres.
• Regulatory: Certain tandem repeats located in gene promoters or introns can influence gene expression.
• Evolutionary: Tandem repeats can contribute to genetic diversity and evolution through mechanisms such as slippage replication, leading to variations in the number of repeats, which can affect gene function and phenotype.

Genetic Disorders

Alterations in the number of tandem repeats can be associated with various genetic disorders:

• Fragile X syndrome: Caused by an expansion of a CGG trinucleotide repeat in the FMR1 gene.
• Huntington's disease: Results from an expanded CAG trinucleotide repeat in the HTT gene.
• Myotonic dystrophy: Characterized by an expanded CTG trinucleotide repeat in the DMPK gene.

Research and Applications

Tandem repeats are of significant interest in genetic research and medicine. They are used in genetic linkage studies to map genes associated with diseases and traits. In forensic science, STR analysis is a powerful tool for identifying individuals and establishing biological relationships.

Challenges

The high variability and polymorphic nature of tandem repeats can make them challenging to study, particularly with short-read sequencing technologies, which may struggle to accurately sequence and align highly repetitive DNA sequences.