Non-LTR retrotransposons and microsatellites: Partners in genomic variation

Abstract

The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsatellites, which are born both concurrently and subsequently to L1 and Alu integration into the genome. Likewise, the mutation dynamics of microsatellite repeats have a direct impact on the fitness of their non-LTR retrotransposon parent owing to microsatellite expansion and contraction. This review explores the interactions and dynamics between non-LTR retrotransposons and microsatellites in the context of genomic variation and evolution.

Keywords: Alu; LINE-1; genomic instability; genomic variation; microsatellite; mononucleotide repeat; mutation rate; poly(A); retrotransposition; retrotransposon.

Figure 1. Non-LTR retrotransposons are hotbeds for new microsatellites. (A) The locations of mononucleotide microsatellite seed sequences (i.e., 5–7 bp proto-microsatellites) are diagramed along the length of the consensus human L1 sequence. Five proto-microsatellites within the sequence are 7 units long, only one nucleotide below the threshold for mononucleotide microsatellites. A long poly(A) tail is highlighted at the 3′ end of the L1 element (in bold font; only 7 A’s shown due to space limitation). (B) The locations of 3–6 bp mononucleotide proto-microsatellites are diagramed along the length of the consensus Alu sequence. Unlike L1, Alu is G/C rich and only two poly(A) proto-microsatellites are found in the middle linker region between left and right monomers. Over time, the short proto-microsatellites may expand beyond the microsatellite threshold. A long poly(A) tail is highlighted at the 3′ end of the Alu element (in bold font; only 7 A’s shown due to space limitation). Note the 10-fold difference in scale between L1 and Alu elements.

Figure 2. The anatomy and lifecycle of a microsatellite. (A) Microsatellite anatomy and terminology. A mononucleotide microsatellite and a trinucleotide microsatellite are depicted. Each repeating unit is depicted as a box. The repeat unit length, the number of repeating units, and the overall length are noted for each microsatellite. Both microsatellites have the same number of repeating units, but the unit length and the overall length vary among them. (B) The birth and death lifecycle for microsatellites. Two pathways lead to microsatellite birth. The first involves LINE/SINE retrotransposition; a microsatellite, typically a mature poly(A) repeat, is born into the genome concurrently upon LINE/SINE integration. The second pathway involves birth from random sequences (not shown) and/or proto-microsatellites via base substitution, indel and replication slippage. When a poly(A) tract reaches 8–9 A’s, it is considered a mature microsatellite. As the length increases, length contractions outweigh expansions, or vice versa, forming an indefinite loop (thus, bypassing the path to death). Microsatellite sequences can also be interrupted by mutations. The interrupted microsatellites may recover and continue expanding (not shown) or may be further mutated and eventually die.

Figure 3. Non-LTR retrotransposons can give birth to microsatellites both concurrently and subsequently to their integration in the genome. (A) Concurrent birth occurs via the integration of a long poly(A) tract, which is part of the Alu or L1 element. Additionally, the integrated element carries proto-microsatellites, depicted by the middle A stretch. Here, the waved line represents genomic DNA target, and the gray box represents the body of an Alu or L1 element. (B) Subsequent to integration, both the poly(A) tail microsatellite and the internal proto-microsatellites may expand or contract due to DNA polymerase slippage. This process creates a variety of microsatellite length polymorphisms in somatic and germ cells. (C) Subsequent to integration, the poly(A) tail microsatellite may also be mutated via base substitution or indel to form a new repeating unit, here depicted as TA at the end of the poly(A) tract. The combination of mutational forces may eventually lead to the formation a new dinucleotide microsatellite at the 3′ end of the retrotransposon.

Figure 4. Microsatellite instability alters the retrotransposition potential of non-LTR retrotransposons. (A) Effect of internal microsatellite loci. Expansions or contractions of proto-microsatellite loci inside an L1 element can cause frameshift mutations, leading to loss of ORF1 and/or OFR2 function. The mutagenized L1 element would be unable to mobilize itself and to support Alu retrotransposition. (B) Effect of the 3′ poly(A) microsatellite on Alu elements. The contraction or expansion of an Alu’s poly(A) tail diminishes or stimulates its retrotransposition, respectively, presumably because the length of its poly(A) RNA tail is positively correlated with the efficiency of target-primed reverse transcription (TPRT). (C) Effect of the 3′ poly(A) microsatellite on L1 elements. Due to the random nature of integration, an L1 sequence may not have a GT rich region downstream to its polyadenylation signal. However, there is evidence that the L1 poly(A) tail exerts a crucial role in ensuring proper polyadenylation of L1 mRNA in the absence of a strong GT-rich downstream sequence. The relative efficiency in mobilization is depicted by a difference in size of L1 mRNA and protein products.

Figure 5. Polymorphism and population dynamics of poly(A) microsatellites. The schematic illustrates the mutation dynamics of poly(A) microsatellites across generations, beginning with an individual who has a newly acquired long poly(A) microsatellite from L1 or Alu retrotransposition. Color is used to distinguish the size and mutability of the microsatellite, where darker color indicates longer poly(A) tails that are more mutable. A long poly(A) microsatellite can expand or contract between generations and give rise to variations in the offspring. However, when a poly(A) microsatellite mutates below the threshold repeat number, the rate of mutation decreases to the average genomic mutation rate.