The scientific community has previously dismissed repetitive regions as nonfunctional, “junk” DNA. However, recent evidence with the assistance of whole genome sequencing illuminates the significant role repeats might play in genomes. In the 1960s, scientists identified these repetitive elements as the explanation for the negative correlation between an organism’s phenotypic complexity and its genome size [1]. For instance, repeats constitute almost 46% of the entire human genome and prokaryotic genomes contain roughly 10% repetitive regions, a significant amount considering their small sizes [2].

Two categories of repetitive regions exist—interspersed repeats and tandem repeats (TRs). Interspersed repeats, the more predominant type of repeat, are remnants of transposons dispersed throughout the genome. Such elements are responsible for the diverse array of genome sizes amongst various species [3]. On the other hand, TRs are repetitive DNA, which exist directly adjacent, or in tandem, to one another (Figure 1). TRs are often referred to as satellite DNA because they were first identified as sequences constituting the second or “satellite” band after subjection through density-gradient centrifugation [4].

On the basis of unit length (unit = repeated sequence of DNA—see Figure 1), TRs are further divided into two subcategories—microsatellites and minisatellites. Microsatellites, or simple sequence repeats (SSRs), are short TRs with unit length between one to ten nucleotides. Minisatellites are TRs with unit length larger than ten nucleotides. For the purposes of this review, we limit our discussion to tandem repeats.

Tandem repeats are evolutionarily pertinent due to their instability; they mutate at rates between 10⁻³ and 10⁻⁶ per cellular generation (i.e., 1 to 10 orders of magnitude greater than point mutations) [5]. Repeat polymorphisms usually occur from the addition or deletion of repeat units, rather than nucleotide substitutions. For instance, in a CTGA tract, most mutations occur by the addition or deletion of an entire CTGA unit as opposed to rare cases in which only a part of the repeat unit is altered (e.g., deletion of two nucleotides GA) (Figure 1).

Two major models have been proposed to explain TR expansions and contraction: strand-slippage replication and recombination. Strand-slippage replication (slipped-strand mispairing or DNA slippage) is a DNA replication error by which mispairing occurs between the template and nascent strands. As such, the template strand can loop out, causing contraction; the nascent strand can also loop out, leading to repeat expansion. Recombination events, such as unequal crossing over and gene conversion may additionally lead to contractions and expansions of TR sequences [5,6].

Various studies suggest alternative explanations for mutation events. Some studies implicate that strand-slippage replication dominates micro- and minisatellite instability [7]; others indicate that strand-slippage replication generally associates with microsatellite instability whereas recombination effects dominate minisatellite instability [8]. However, the precise mechanism by which repeat mutations occur remains unclear.

The frequency of repeat mutation depends on repeat tract: the longer and purer the repeat, the higher the mutation frequency whereas the shorter and less pure the repeat, the lower the mutation frequency. Even a few impurities drastically reduce mutability of repeat regions [9], indicating that impure repeats demonstrate far greater stability than pure repeats. One study showcases that even a single variant repeat in an otherwise pure poly GT tract increases its stability fivefold [10]. According to Legendre et al. 2007, the number of repeat units is the most important determinant of TR stability, above purity and repeat unit length. Base composition also affects repeat stability: polyC and polyG tracts are more unstable than polyA and polyT tracts [11].

Cellular processes may additionally influence TR mutation rates. It has been shown that increased transcription rates can enhance repeat instability; in yeast, transcription of a poly GT tract destabilizes the repeat region four-to-ninefold with higher levels of transcription causing an additional destabilizing effect of two- to three-fold [12].

External factors may also significantly influence repeat stability. Classic examples include CT repeat contraction upon fungal infection [13] and repeats in bacteria that undergo frequent adaptive, environmentally stimulated mutations [14]. Likewise, inhibition of Hsp90 (a protein generally involved in responding to severe environmental changes) increases CAG repeat contraction by tenfold, while not affecting the rate of point mutations, illustrating how environmental stresses may trigger TR mutations [15].

Whole genome sequencing has enlightened researchers on the prevalence of repetitive regions in the genome. A comprehensive survey of the various software packages and algorithms for TR detection has been previously published [16]. Certain obstacles remain in our quest to understand more about TRs. One significant issue arises due to the tedious nature of TR identification. Despite the availability of numerous algorithms for identifying TRs (i.e., Tandem Repeat Finder, Sputnik, TROLL) which define certain requirements for TRs based on the number of repeated units, purity of repeats, as well as length of repeat region, no definite guideline exists and algorithms vary from one to another. Therefore, it proves to be quite difficult in assigning a proper cutoff score and an overestimation of TR regions may ensue without the enforcement of stringent guidelines for TR identification.

Certain measures may be taken to prevent such scenarios (e.g., the shuffle method). Multiple, randomly shuffled sequences of similar size and composition as the sequence of interest are selected and subjected to a TR-finding program. These sequences are searched for TRs using various cutoff scores. The average number of TRs identified in these scrambled sequences then serves as a value of background noise produced by chance occurrence of TRs (for more details, see [17]. A sequence mining tool such as SERV identifies TRs in various DNA sequences and predicts a “variability score” of each repeat based on its purity, unit size, and number of repeat units [9]. These procedures allow for proper identification of significant, variable TRs rather than insignificant “background noise”.

Though repeats are overabundant in gene deserts, whole genome sequencing capabilities provide concrete evidence for the prevalence of repeats in coding regions as well. This is exemplified by the human genome; 17% of genes contain repeats in open reading frames and such values are comparable in other species as well [17,18] Microsatellites (<10 nt) are specifically enriched in regulatory genes that encode for transcription factors, DNA-RNA binding proteins, and chromatin modifiers [19]; minisatellites (>10) are prevalent in genes encoding extracellular or cell-surface genes [5].

Unlike repeats in noncoding regions, the high frequency of tri- and hexanucleotide repeats (units of 3 or 6 nucleotides) found in coding regions suggests a selective pressure against frameshift mutations [20]. For instance, of the 1 in 20 human genes that were found to contain TR polymorphisms, only approximately 1% of those genes exhibited frameshift mutations [21]. Exceptions apply to prokaryotes in which frameshift mutations act as a beneficial mechanism (to be further discussed later).

In coding regions, repeats exhibit biases for specific amino acids. Glutamine, arginine, glutamate, alanine, and serine residues largely dominate eukaryotic genomes [22] and [23] whereas serine, glycine, alanine, and proline residues dominate prokaryotic genomes [24]. Interestingly enough, hydrophobic residues such as isoleucine, methionine, and tryptophan residues are generally absent, indicating that preferences for certain residues are not random but stem from the functional role of repeats.

In many instances, repeat mutations, especially in gene deserts, have neutral effects and remain undetected. Cases like these may have contributed to the previous notion that repeats were nonfunctional junk or selfish DNA [25,26,27]. However, repeat instability in coding regions, promoters, and other regulatory regions may eventually proceed to alter gene function. In this review, we highlight the studies that implicate variable TRs with changes in gene function, starting by TRs located within regulatory regions (promoters and other regulatory sequences) and ending with studies on intragenic (i.e., coding) repeats.

Variable TRs in promoters can affect gene expression by altering the number of transcription factor binding sites. Frequent TR variability of repeat-containing transcription factor binding sites results in changes in the number of binding sites. An example of such a mechanism was first uncovered in pathogenic bacterial species. In Neisseria meningitidis, changes in the number of TAAA repeats located in the nadA promoter induces variable expression of the NadA adhesin protein. This highly frequent switching of phenotypic outcome, also referred to as phase variation, is mediated by the loss or gain of binding sites for the regulatory protein IHF [32]. A second, repeat-dependent, level of control on the same nadA promoter is discussed in the following paragraph. Rapid phenotypic switching mediated by intragenic (i.e., coding) repeats will be discussed in a later section of this review.

Changes in transcription factor binding sites as a result of unstable TRs have also been described in eukaryotes. A variable TCC repeat in the promoter region of the human epidermal growth factor receptor (a proto-oncogene) induces changes in gene expression by altering the number of binding sites for the transcriptional regulator Sp1 [33]. A change of one unit in a 61-bp repeat of the human reduced folate carrier gene promoter induces a significant change in gene expression. This repeat is polymorphic in the human population and binds the transcription factors Sp1 and AP2 in vitro [34]. Though these display a few examples of the role of TRs in transcription factor binding sites, a screen of polymorphic TRs located in a 10-kb region upstream of the transcription start sites in the human genome reveals that there are many more TRs that bind regulatory proteins and thus act as cis-regulatory elements [35].

Variable TRs in promoters not only affect the number of transcription factor binding sites, but can also induce changes in spacing between critical promoter elements (Figure 2). In the nadA promoter of N. meningitidis (see above), changes in the number of TAAA repeats also induce changes in spacing between distal and proximal binding sites (flanking the TAAA repeat) for the NadR repressor protein [36]. Additionally, the transcript level of the N. meningitidis membrane protein PorA correlates with the number of guanidine residues within the -10 and -35 spacer region in the upstream promoter. A mere loss or gain of one nucleotide in this polyGuanidine TR leads to significant changes in PorA transcription [37]. Similarly, in Haemophilus influenzae, promoter TRs modulate the expression of genes involved in the formation of adhesive appendages or fimbriae. Variation in a TA dinucleotide repeat in the bidirectional promoter of two genes hifA and hifB alters the critical spacing between the -10 and -35 consensus sequence, thus affecting the bidirectional transcription initiation of both genes [38]. Several phase variable outer membrane proteins, whose expression is attributed to similar promoter TRs, have also been described in Bordetella pertussis [39], and Mycoplasma hyorhinis [40].

Genome-wide sequencing suggests there are many more pathogenic bacteria, than the ones mentioned above, in which tandem repeat-mediated phase variation is operable. In fact, more than 30 N. meningitidis genes are expected to be phase variable as a result of unstable TRs [41].

It seems that this form of gene expression regulation (changes in spacing between functional promoter elements) is common among several pathogenic bacterial species. This rapid phenotypic switching, results in a heterogeneous bacterial population in which some individuals are better suited to environmental changes (e.g., attack by the immune system) and consequently have better chances of survival.

DNA is intricately organized in the nucleus and packaged into structures called nucleosomes, in which DNA is wrapped around an octamer of four core histones, to form chromatin. Chromatin structure is highly dynamic and has large implications in the regulation of gene expression, especially since histone complexes affect accessibility of transcription factors to DNA.

Several studies indicate a possible role for repetitive amino acid tracts in mediating effects on chromatin structure. A number of authors demonstrate the importance of polyA and polyT tracts as constituents of promoter regions that inhibit nucleosome formation [42,43,44]. Additionally, Vinces et al. illustrates TR enrichment in nucleosome-free regions of yeast promoter regions and supports this finding with preliminary observations in human promoters (Figure 3). Mutants were made in repeat-containing promoters of several yeast genes and found to affect gene expression and nucleosome positioning. This study unveils that TRs behave as nucleosome-inhibiting sequences that allow for an open chromatin structure [31]. The authors also find that approximately 25% of yeast genes contain TRs, which has strong implications for the importance of TRs as crucial components in genomes of higher-order eukaryotes that regulate DNA structure and facilitate DNA melting. The following section further explores the role of TRs in the regulation of DNA structure.

Though DNA is normally found as B-DNA (right-handed helical conformation), in rare cases, it may exist as Z-DNA (left-handed helical conformation). This conformation is drastically different from the normal B-DNA, that it might block access of transcription factors to DNA. Several studies suggest a role for TRs as elements that assist in Z-DNA formation. Alternating purines and pyrimidines, which favor the Z conformation, are found as TR sequences in the genome. Authors Naylor and Clark find evidence for a CA repeat lying upstream of the rat prolactin gene that enables Z-DNA formation. Additionally, this repeat inhibits gene transcription by potentially deterring transcriptional efficacy of RNA polymerase II [45]. Specific Z-DNA-binding proteins also influence Z-DNA gene expression as exemplified by the effect of double stranded RNA adenosine deaminase (ADAR1) proteins that bind promoter Z-DNA to activate gene expression [46].The structure of DNA greatly influences gene expression and these studies allude to the possible importance of TRs for DNA structure.

Tandem repeats in introns and untranslated regions can influence gene expression by modulating the activity of RNA-binding proteins. The mechanistic role of TRs in recruiting RNA-binding proteins has been proposed to explain the overlapping clinical features of two genetically unrelated neurological diseases. Expansion of a CTG repeat in the 3' UTR of the DMPK gene causes myotonic dystrophy type 1 (DM1) and the expansion of a CCTG repeat in intron 1 of the ZNF9 gene causes myotonic dystrophy type 2 (DM2). The expanded RNAs adopting a stable hairpin structure, bind to and alter the activity of RNA processing proteins CUG-BP1 and MNBL [47]. This leads to aberrant splicing of numerous transcripts (i.e., downstream targets) involved in different cellular processes.

A study investigating the link between expression of the Bromodomain-Containing Gene (BRD2) and epilepsy in humans uncovered the role of variable intronic repeats in regulating gene expression through alternative mRNA splicing pattern. In intron 2 of the BRD2 gene, a polymorphic GT repeat is strongly associated with epilepsy. Gradual shortening from 13 GT repeats to 1 GT repeat results in a higher proportion of (non-productive) alternatively spliced BRD2 transcripts over normal transcripts. These alternative mRNAs produce non-functional BRD2 proteins [48]. Similarly, a change from 11 CA repeats to 13 repeats in an intron of the cystic fibrosis transmembrane regulator results in higher levels of a non-functional transcript (missing exon 9) [49]. These examples illustrate how intronic dinucleotide repeats alter splicing patterns, ultimately affecting translation and protein synthesis (Figure 4).

The studies described in this section indicate that variable TRs in regulatory regions can strongly impact gene expression and/or function through various mechanisms. The high prevalence of these repeats in diverse genomes suggest that this type of gene expression regulation (i.e., through variation in TR number) might be a common and conserved regulatory mechanism. The central question that remains is how can TR variability promote evolvability? And what are the effects on an organismal level?

The studies on bacterial phase variation clearly demonstrate how repeat variation (in promoters and coding regions—see further) enable phenotypic evolution, ultimately impacting the population; rapid changes in TRs create phenotypic variants within a population, leading to fast adaptation (e.g., to the immune system) and increased survival.

In eukaryotes, a recent study provides experimental evidence on the role of TRs as drivers of rapid evolution. Vinces et al. reports that yeast promoters containing TRs have evolved faster since their expression patterns are more divergent between and within yeast strains compared to promoters without repeats [31]. Promoter-containing repeats fused to a fluorescent marker to facilitate selection for higher gene expression provide experimental evidence for repeat-driven rapid evolution after a few rounds of selection: repeat-containing promoters yield variants with higher expression that are specifically linked to changes in promoter repeat number; repeat-less promoters do not show any changes in gene expression during the selection process [31]. This study firmly establishes that several promoter repeats generate expression variability at high rates, allowing for rapid evolution of gene expression.

In complex organisms, such studies are difficult to undertake, though some reports indicate that this might be the case for particular genes. The promoter of the MMP3 gene contains a variable polyT tract that is rapidly evolving in the primate lineage. In humans, variation in this repeat results in variable expression of the MMP3 gene, associated with risk of heart disease: the 5T allele results in higher MMP3 expression and is associated with myocardial infarction and aneurysm, whereas the 6T allele drives a lower MMP3 expression and is associated with coronary artery disease [50]. In European populations, the 5T allele seems to be under positive selection in comparison to other parts of the world. This highly variable repeat seems to drive the rapid evolution of the MMP3 gene expression and based on its associated phenotype in humans, it clearly exhibits a functional value.

Minisatellites are enriched in cell surface genes and conserved through evolution from yeast to humans [9]. Various studies indicate that polymorphisms in these minisatellites in fact confer functional variability.

The S. cerevisiae FLO1 gene encodes a cell-surface adhesin that mediates cell-cell and cell-surface adhesion. The gene contains a repeat tract consisting of tandemly repeated units of approximately 100 nt, which are variable across different yeast strains [5]. Phenotypic tests with isogenic strains differing only in their FLO1 repeat length illustrate that the intensity of the adhesion directly correlates with the length of the repeat (i.e., cells with longer FLO1 repeats adhere better to each other) [5] (Figure 5).

Flor yeast strains form buoyant biofilms on the air/liquid interface, allowing them to evade oxygen-deprived environments. Fidalgo et al. report that the extension of a minisatellite in FLO11, another adhesin-coding gene, contributes to biofilm formation. The repeat tract consists of serine/threonine-rich units (~100 nt), prone to O-glycosylation. The addition of covalently linked sugar groups renders the adhesins, and subsequently the cell wall, hydrophobic. Thus, an increased number of repeats enhances buoyancy of yeast strains. Additionally, transformation of S. cerevisiae strains, that generally sediment, with flor FLO11 repeat tract and promoter enable yeast cells to form buoyant biofilms [51].

Similar observations have also been made in the human pathogen Candida albicans. The ALS gene family encodes adhesins similar in structure to the baker’s yeast flocculins that mediate biofilm formation. The length of the central repeat domain correlates with adhesion propensity (i.e., longer repeats generate more adhesive cells) [52]. Recombination events between the different ALS genes can generate cell-surface variability required to evade the host’s immune response [53].

Trinucleotide repeats, in particular polyglutamine (polyQ) repeats, are involved in a number of human neurodegenerative diseases (e.g., Huntington’s disease, fragile X syndrome, spinocerebellar ataxia), with numerous studies illustrating the conferral of such diseases upon repeat expansions exceeding a particular threshold. Though TRs involved in human diseases will not be discussed extensively here, it is important to note that severity and time of onset of these neurodegenerative diseases depend on the repeat expansion: longer repeats correlate with earlier disease onset and more severe symptoms (for a review on the role of repeats in human diseases, refer to [47]).

Considering the little we know, such devastating effects of TR mutations have often overshadowed our knowledge of TRs. However, the predominance of repetitive DNA sequences in functional parts of the genomes, despite such a high propensity for mutations and apparent low information content, hint at a greater role for TRs. In fact, though the genetic code is degenerate, amino acid repeats tend to be coded by pure DNA repeats, illustrating the conservation of repetitive regions on the DNA level as well as the protein level. These unstable repeats, might be tolerated in some coding sequences because they hold the potential for the acquisition of a beneficial novel/improved function (e.g., novel protein-protein interactions,). TRs may not merely be “junk DNA” as was previously assumed. We will highlight key studies that provide experimental evidence for this hypothesis in the following section.

Intragenic TRs can also mediate phase variation (see also section on repeats in non-coding regions). In the bacterium, Neisseria gonorrhoeae, repeat variations in the P. II family of cell surface genes allow for evasion of the host immune system [54]. Changes in the CTCTT pentameric microsatellite repeat in the coding region of the membrane signal peptide of cell surface genes, can either lead to correct or incorrect translation of proteins [55]. This switching between an ON and OFF state of the gene generates phenotypic variability in the population, providing individuals able to evade the host’s immune response (Figure 2).

Similar occurrences are seen in the lic1 gene of Haemophilus influenzae (enables the addition of phosphorylcholine moieties to cell membrane lipopolysaccharides (LPS)), which contains a variable intragenic CAAT repeat. Formation of a complete, functioning Lic1 protein or a truncated mutant depends on variation of an intragenic CAAT repeat. Differences in LPA structures promote different bacterial variants enabling survival of the bacterium in the host [56].

Phase variable genes are not merely limited to cell-surface genes; recent evidence suggests that regulatory genes, such as those encoding DNA-methyltransferases (mod genes), are also phase variable. The modA gene, in Neisseria and Haemophilus species, contains either an AGTC or AGCC repeat whose mutations directly alter the rate of phase variation [57]. The modA gene contains two potential start codons depending on repeat number but only the one that yields the longest transcript gives rise to a functional protein. Variation in ModA repeat number thus has consequences on the expression of its downstream targets that include outer membrane proteins, iron transporters and heat-shock proteins [57]. For instance, the OFF state of the modA gene leads to biofilm thickness and better survival rates of N. gonorrhoeae cells in human cervical epithelial cells [58]. The ability to engage in phase variation may provide a means to increase population fitness and facilitate rapid adaptation to a hostile environment.

Sequencing reveals the substantial presence of TRs in prokaryotic genomes, which suggests that rather than such an incidence being happenstance, some TRs are positively selected for rather than against [59]. Particularly in pathogenic bacteria, repeats in coding sequences are more favored at the N-terminus and depleted in the middle of the coding sequence [60]. This might increase the probability of frameshift mutations that facilitate phase variation. Thus, TRs may be useful elements that mediate phenotypic change enabling organisms to rapidly adapt to a changing environment. Ultimately, understanding phase variations in these prominent human pathogens may unveil new insights in combating significant health problems.

In humans, polyglutamine (polyQ) repeats have strong implications for neurodegenerative diseases [61]. In Drosophila melanogaster, polyQ repeats constitute one of the three most frequently found amino acid runs; the same can be said for the yeast genome [62]. Overall, polyQ tracts are abundant in the eukaryotic genome [24,62] and repeats encoding these residues are largely variable.

Here we showcase several studies regarding the possible functional role of polyQ repeats, ranging from its involvement in morphological variation to protein regulation.