A tandem repeat is a segment of deoxyribonucleic acid (DNA) where a specific pattern of one or more nucleotides is duplicated and arranged immediately next to itself in a continuous, head-to-tail fashion. These repetitive stretches are common features across the genomes of all life forms, constituting about 8% of the human genome. Their presence creates regions of high variability that are fundamental to both cellular operation and various scientific applications.
The Unique Structure of Tandem Repeats
The physical organization of a tandem repeat is defined by its core repeat unit, which is the specific sequence of DNA bases that is copied. This unit, also known as a motif, can be as short as a single base pair or extend to many thousands. For instance, a simple repeat might involve the two bases “AT” repeated four times, resulting in the sequence “ATATATAT.”
The number of these repeating units, referred to as the copy number, varies significantly between individuals and even between the two chromosomes within a single person. This high level of copy number variability, known as polymorphism, makes tandem repeats a unique source of genetic diversity.
Unlike non-repetitive DNA sequences, tandem repeats are prone to changes in length during DNA replication. This instability is largely driven by a mechanism called replication slippage, where the repetitive nature of the sequence causes the DNA polymerase enzyme to temporarily lose its place. The enzyme can then either skip a unit, leading to a contraction, or copy a unit twice, causing an expansion, which results in a high mutation rate compared to other genomic regions.
How Scientists Classify Tandem Repeats
Scientists categorize tandem repeats primarily based on the length of their core repeating unit, which helps standardize terminology across different fields of study.
The shortest of these are known as microsatellites, or Short Tandem Repeats (STRs). Microsatellites have a repeat unit size that ranges from just one to six base pairs.
The next category is minisatellites, often referred to as Variable Number Tandem Repeats (VNTRs). These repeats feature a longer core unit, typically ranging from 10 to 100 base pairs in length.
The term satellite DNA encompasses the longest and most abundant arrays of tandem repeats. These sequences often contain unit lengths that can reach up to a few thousand base pairs and are primarily located in specific, structural regions of the chromosome.
The Natural Role in Genome Function
Tandem repeats perform several important functions that contribute to the stability and regulation of the genome.
One of their most recognized roles is in maintaining chromosome structure. Telomeres, the specialized structures at the ends of chromosomes that protect them from damage, are composed of thousands of copies of a short, six-base-pair tandem repeat. Additionally, large arrays of satellite DNA are concentrated at the centromeres, the constricted regions where the two chromatids of a chromosome are joined. These sequences are necessary for the proper alignment and separation of chromosomes during cell division.
Repeats situated near or within genes also play a role in controlling genetic activity. When tandem repeats are located in gene promoters or untranslated regions, they can modulate the rate at which a gene is transcribed into RNA. This mechanism can effectively turn genes on or off, providing a mechanism for fast, reversible changes in gene expression.
The inherent instability of these repetitive sequences also serves as a source of rapid evolutionary change. Their high mutation rate allows organisms to quickly generate new alleles, potentially leading to rapid adaptation to environmental shifts. However, this same instability is the cause of more than 60 known human disorders, collectively called repeat expansion diseases, such as Huntington’s disease.
Applications in Forensics and Health
The hyper-variable nature of tandem repeats makes them indispensable tools in practical genetic applications.
Short Tandem Repeats (STRs) are the primary markers used worldwide in forensic DNA profiling, a process commonly known as DNA fingerprinting. A set of specific STR locations across the genome is analyzed to create a unique genetic profile. This is possible because the probability of two unrelated individuals sharing the exact same set of repeat lengths is astronomically low.
This same principle of individual-specific variation is applied in determining biological relationships, such as paternity testing. By comparing the repeat lengths at multiple loci between a child and a potential father, scientists can confirm or exclude biological parentage with high certainty.
Beyond identification, tandem repeats are valuable as genetic markers for mapping traits and diseases. The repeat patterns can be tracked through generations to observe the inheritance of a particular gene. Researchers also use tandem repeat analysis to screen for certain genetic conditions, such as trisomies (like Down syndrome).