Abstract
Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation, namely changes in tandem repeat number. Historically, tandem repeats have been designated as non functional “junk” DNA, mostly as a result of their highly unstable nature. With the exception of tandem repeats involved in human neurodegenerative diseases, repeat variation was often believed to be neutral with no phenotypic consequences. Recent studies, however, have shown that as many as 10% to 20% of coding and regulatory sequences in eukaryotes contain an unstable repeat tract. Contrary to initial suggestions, tandem repeat variation can have useful phenotypic consequences. Examples include rapid variation in microbial cell surface, tuning of internal molecular clocks in flies and the dynamic morphological plasticity in mammals. As such, tandem repeats can be useful functional elements that facilitate evolvability and rapid adaptation.
Highlights
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) are prevalent in genes encoding extracellular or cell-surface genes [5]
We focus on studies which reveal the mechanism through which repeats in non-coding regions affect downstream gene expression
Large scale genomic studies mainly focus on Single Nucleotide Polymorphisms (SNPs) and Copy
Summary
Recent evidence with the assistance of whole genome sequencing illuminates the significant role repeats might play in genomes. 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]. 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]. TRs are repetitive DNA, which exist directly adjacent, or in tandem, to one another (Figure 1). On the basis of unit length (unit = repeated sequence of DNA2see Figure 1), TRs are further divided into two subcategories2microsatellites and minisatellites. Microsatellites, or simple sequence repeats (SSRs), are short TRs with unit length between one to ten nucleotides. For the purposes of this review, we limit our discussion to tandem repeats
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