the human genome is laden with repetitive sequences in the form of transposable elements ( tes ) and tandem repeats , which comprise 45% and 3% of the human genome , respectively .
using new methods capable of annotating repetitive sequences that have substantially diverged from known te sequences , recent analyses indicate that up to 6669% of the human genome may be composed of repetitive sequences , predominately in the form of tes .
tes , as their name implies , are able to move about in the genome and create interspersed repeats .
tes include dna transposons , long - terminal repeat ( ltr ) retrotransposons and non - ltr retrotransposons . in this review
, we will focus on non - ltr retrotransposons , which are the only active tes in the human genome .
non - ltr retrotransposons include long interspersed elements ( lines ) and short interspersed elements ( sines ) .
both mobilize via a  copy and paste  mechanism , which requires the transcription of a donor element into an rna intermediate and the subsequent reverse transcription and incorporation of the rna intermediate into the genome as a new dna copy ( i.e. , the retrotransposition process ) . among them , line-1s ( l1s ) are autonomous ; full - length l1s encode two proteins , orf1 and orf2 , which are essential for their mobilization ( fig . 
in contrast , sines are non - autonomous and their mobilization relies on l1 proteins .
1b ) and mouse b1 , both of which are derived from 7sl rna ; the second class is typified by mouse b2 elements , which are derived from trnas .
the quantity and mobility of non - ltr retrotransposons have made them important drivers of genomic diversity and evolution .
( a ) the locations of mononucleotide microsatellite seed sequences ( i.e. , 57 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 36 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
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 ) .
in contrast to interspersed repeats , tandem repeats consist of sequences that are sequentially repeated .
tandem repeats are classified by the size of their repeating unit : those with a repeating unit length of 16 base pairs ( bp ) are commonly referred to as microsatellites ( fig . 
however , the boundary between microsatellites and minisatellites is often disputed , where the latter typically refer to tandem repeats of greater unit sizes .
as they are highly polymorphic , both microsatellites and minisatellites have been instrumental in genetic mapping , evolutionary and phylogenetic studies as well as dna forensics .
this review focuses on microsatellites , which encompass mono- , di- , tri- , tetra- , penta- and hexa - nucleotide repeats .
notably , mononucleotide a repeats ( i.e. , poly(a ) dna tracts ) represent the most abundant microsatellite class with an overall length of 12 bp in the human genome . due to the repeating nature of these dna tracts , they are prone to rapid and variable contraction and expansion of repeat length ( fig . 
( a ) microsatellite anatomy and terminology . a mononucleotide microsatellite and a trinucleotide microsatellite are depicted .
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 .
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 89 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 ) .
the interrupted microsatellites may recover and continue expanding ( not shown ) or may be further mutated and eventually die .
collectively , the dynamics of these two entities are a major source of genomic variation and serve as the architectural framework for protein - coding genes .
recent work has revealed an intimate relationship between non - ltr retrotransposons and microsatellites . on one hand , non - ltr retrotransposons are a major source of new microsatellites as they give birth to microsatellites both concurrent and subsequent to their integration into the genome . on the other hand ,
the inherent instability of microsatellite repeats has a direct impact on the fitness of their non - ltr retrotransposon parent .
this review will focus on the interactions and mutation dynamics between non - ltr retrotransposons and microsatellites as well as the variability and rates of mutation of microsatellite repeats that make them instigators of genomic evolution .
it is proposed that each microsatellite locus possesses a lifecycle that begins with its  birth  into the genome and ends with its  death 
phase , a period that is punctuated by contractions and expansions , which dynamically shorten and lengthen the overall microsatellite length .
the most commonly proposed mechanism for microsatellite contractions and expansions is replication slippage by dna polymerases .
two other mutation mechanisms , base substitution and indel slippage , are also thought to play an important role in microsatellite birth and death .
one is through de novo retrotransposition by non - ltr retrotransposons , while the other involves the birth of proto - microsatellites from random sequences .
it is the goal of this review to integrate these two pathways and highlight the role of non - ltr retrotransposons in microsatellite genesis .
non - ltr retrotransposons can give birth to microsatellites concurrently to their integration into the genome ( i.e. , the first pathway ; fig . 
the association between a - rich microsatellites and non - ltr retrotransposons has been repeatedly observed by many independent studies .
a recent analysis of microsatellites at orthologous loci in three primate genomes estimated that upon retrotransposition , alus and l1s contribute to 36% of mono- , di , tri- and tetranucleotide microsatellites in human , chimpanzee and orangutan genomes .
this pathway is best illustrated by the birth of poly(a ) microsatellites . to mobilize , non - ltr retrotransposons require a poly(a ) tail at the 3 end of their sequence ( discussed later ) .
thus , a common feature of alu and l1 insertions that have integrated into the genome is the presence of a 3 poly(a ) dna tail ( fig .  1 ) .
these a - rich sequences are born into the genome as mature microsatellites , far above the threshold size ( fig . 
3 ) . in humans , 90% of these poly(a ) repeats are derived from poly(a ) tails of l1 and alu sequences .
even this may be an underestimate because l1 can integrate a pure poly(a ) dna tract into the genome if the insertion is severely 5 truncated ; such events would typically be undetected .
the abundance of l1 and alu sequences in the primate genomes likely accounts for the overrepresentation of poly(a)/poly(t ) repeats compared with poly(c)/poly(g ) repeats .
in contrast , dinucleotide microsatellites are most abundant in rodents , and ac repeats are the most frequent dinucleotide repeat in all vertebrates . not surprisingly , 15% of ac repeats are derived from the ac - rich tails of b2 sine elements found in the mouse genome .
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 .
( 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 .
the second pathway posits that microsatellites initially arise from random sequences via mutation as proto - microsatellites , small tandem repeated sequences that are below the length threshold for mature microsatellites ( fig . 
theoretically , these initiating loci can be found everywhere in the genome . however , the overwhelming abundance of tes in the human genome made it the perfect hotbed for microsatellite births .
it has been suggested that the conversion of aaa to naa is a major mechanism for the generation of all a - rich trinucleotide repeats in the human genome as over 60% of gaa , caa and taa repeats with repeat number of 8 or higher are located within alu poly(a ) tails .
furthermore , poly(a ) tails have also been implicated in the birth of dinucleotide and tetranucleotide microsatellites . aside from their 3 tails ,
both alu and l1 have internal proto - microsatellite sequences that can birth new microsatellites subsequent to their integration ( fig .  1 ; fig .  3 ) .
an analysis of microsatellites at orthologous loci in three primate genomes indicates that 26% of microsatellite births and
it is noteworthy that microsatellites are found in distinct distributions over the length of l1 and alu elements , likely reflecting differences in their sequence compositions .
l1 sequences are at - rich and give rise to microsatellites during and after their insertion along their entire length ( fig . 
in contrast , alus are gc - rich and microsatellite births and deaths are enriched at the 3 poly(a ) tail and the middle a stretch that connects the left and the right monomers ( fig . 
the middle a - rich region of alu elements tends to expand and mature into poly(a ) microsatellites and can also give rise to gaa repeats .
approximately 2% of gaa repeats with a repeat number of 8 or longer are located in the alu middle a tract ; one of such gaa microsatellite is positioned in intron 1 of the frda gene and its expansion is responsible for the neuromuscular disorder friedreich s ataxia .
classic studies on microsatellite mutation rates utilize pedigree analysis , usually in cancer patients with microsatellite instability .
several model systems , including e. coli , yeast , human and mouse cells have also been described and used to obtain in vivo mutation rates .
in addition , computational and mathematical models have been utilized to describe the behavior of microsatellites by comparing genomic sequences from large scale sequencing efforts and from evolutionarily related species .
the majority of computational studies and in vivo studies focus exclusively on pure or perfect repeats , which contain only nucleotides pertaining to the repeating unit .
imperfect repeats , in contrast , have additional nucleotides that do not belong to the repeating units .
overall , the rate of microsatellite mutation is highly variable , and it is influenced by several factors , including the number of repeating units , unit repeat length , sequence composition , genomic loation and the secondary structures of the repeat .
specifically , microsatellites become highly mutable when the number of repeating units exceeds a threshold value .
although there is disagreement on the exact threshold value , the consensus is that the threshold represents the size that allows the sequence to acquire slippage mutations at a higher rate than the genomic average .
the threshold values for mono- , di- , tri- and tetranucleotide repeats are estimated to be 89 , 45 , 3.44 and 4 respectively .
in fact , the distinct mutational behaviors manifested by microsatellite before and after they reach the threshold have prompted some researchers to consider microsatellites only as those that exceed their respective threshold .
once a tandem repeat has reached its threshold , experimental studies with human and mouse models have shown that the mutation rate increases exponentially as the number of repeating units increases ( table 1 ) .
however , due to the differences in the experimental systems used , it is difficult to compare across these studies .
the exponential increase in mutation rates is not seen in mismatch repair deficient cells , indicating that mismatch repair proteins are implicated in the expansion process ( table 1 ) .  
contraction rate ; number in parenthesis is the contraction rate for the same repeat ; trinucleotide studies focus primarily on mismatch repair deficient cells .
trinucleotide repeats that cause disease tend to be more unstable in the germline than in somatic cell lines .
sequence composition also affects mutability . for similar sized repeats , ga repeats are more mutable than ca repeats and sequences with higher gc content have lower rates of mutation ( table 1 ) .
stability increases with the complexity of the repeating pattern , as demonstrated in tetranucleotide repeat studies . despite a doubling of repeat unit length , di- and tetranucleotide repeats have similar stabilities ( table 1;tc vs. ttcc ) .
in contrast , mononucleotide microsatellites , such as those associated with retrotransposons , are highly unstable and hypermutable in the germline .
for example , the human bat-40 locus is an intronic poly(a ) tract of 40 a s in the 3--hydroxysteroid dehydrogenase gene ( hsd3b1 ) .
. five - fold more mutant alleles are found in sperm than in leukocytes of the same individual .
the bat-40 poly(a ) microsatellite has not been identified to be associated with non - ltr retrotransposons ; here , we report that it is in fact the poly(a ) tail of an alujb element . despite experimental focus on the expansion dynamics of microsatellites ,
the mutation dynamics for very long ( > 50 bp ) mononucleotide repeats had been frequently overlooked because of their rarity in the genome . using a transgenic l1 mouse model
, we characterized the contraction dynamics of long poly(a ) tracts associated with nascent l1 insertions .
these poly(a ) microsatellites show rapid and variable contraction to lengths below 50 bp in both somatic and germ cells at frequencies of 14.8% and 13.3% , respectively . of note , these values represent the highest mutation frequencies hitherto reported for all microsatellite repeats , highlighting the extraordinary mutability of long poly(a ) tracts ( table 1 ) .
long poly(a ) microsatellites birthed into the genome via retrotransposition are predicted to shorten in length rapidly within the first few generations .
this prediction is consistent with observations from surveys of genomic resident alu and l1 sequences , which demonstrated an inverse correlation of poly(a ) tract length with the evolutionary age of the elements .
one prominent form of microsatellite death is interruption by a non - repeat base , which can arise from base substitutions or short indel mutations . in particular
, a comparison of human , chimpanzee and orangutan genomes suggests that substitutions are the primary cause of deaths for microsatellites of all lengths .
although not widely recognized , non - ltr retrotransposons may also act as a mechanism for microsatellite interruption .
such interruption can occur when new copies of non - ltr retrotransposons insert into pre - existing microsatellites .
mammalian l1s are members of a diverse and widely distributed group of autonomous non - ltr retrotransposons that encode an endonuclease with homology to apurinic / apyrimidinic endonucleases ( ape ) . a small subset of these ape - type elements insert in a sequence - specific manner into microsatellites : ( 1 ) acay microsatellites are targeted by three waldo elements ( waldoag1,waldoag2 in the african malaria mosquito a. gambiae and walsofs1 in the earwig f. scudderi ) ;
( 2 ) ac microsatellites are targeted by a mino element in a. gambiae ( minoag1 ) ; ( 3 ) tc microsatellites are targeted by four kibi elements ( kibidr1 and kibidr2 in zebrafish d. rerio , kibifr1 in the torafugu f. rubripes , and kibitn1 in the green spotted pufferfish t. nigroviridis ) ; ( 4 ) ttc microsatellites are targeted by two koshi elements ( koshifr1 in f. rubripes and koshitn1 in t. nigroviridis ) ; ( 5 ) taa microsatellites are targeted by three dong elements ( dong in the silkworm b. mori , dongag in a. gambiae and dongbg in the freshwater snail b. glabrata ) .
the molecular mechanisms underlying microsatellite targeting by these ape - type non - ltr retrotransposons are not well understood .
it is believed that the sequence - specific cleavage by the endonuclease plays a major role in active targeting .
in addition , two ape - type elements ( waldo - a and waldo - b in the fruitfly d. melanogaster ) are frequently found within or close to ca microsatellites , most likely as a result of passive accumulation in these low recombination regions . microsatellites may also be targeted by dna transposons ; examples include mine-1 helitrons and micron mites .
the former insert at gaaa microsatellites in the genomes of the european corn borer o. nubilalis , the silkworm b. mori and the pink bollworm p. gossypiella , while the latter insert into ta microsatellites in the rice genome .
in contrast , mammalian l1s have a weak target site preference with a consensus sequence 5-ttaaaa-3. although they may fortuitously land in or near certain microsatellite sites , they are unlikely to serve as a major factor in disrupting microsatellites .
the relationship between microsatellites and non - ltr retrotransposons is not unidirectional . while both l1s and alus give birth to microsatellites , especially poly(a ) mononucleotide microsatellites
, these microsatellite sequences can also affect the fitness of their  parent  due to their unusually high mutation rates .
the impact of microsatellite instability on non - ltr retrotransposons depends on the location of the microsatellite , i.e. , whether it is internal or at the 3 terminal of the element .
the effect of variation in microsatellites internal to non - ltr retrotransposons is less understood .
newly inserted l1 and alu copies carry many mononucleotide proto - microsatellites ( fig .  1 ) .
as microsatellites are predicted to mutate faster than the genomic average , expansion and contraction of microsatellite loci internal to l1s may introduce frameshift mutations , abolishing l1 coding capacity ( fig . 
( 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 .
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 .
the 3 poly(a ) tail of an l1 or alu element is a crucial component of the retrotransposition process and therefore , its length directly affects their retrotransposition potential .
distinct cellular processes are responsible for the poly(a ) tail formation in l1 and alu elements .
l1 elements are transcribed by rna polymerase ii and poly(a ) polymerases produce a poly(a ) rna tail as the 3 end of an l1 mrna . in contrast , alu elements are transcribed by rna polymerase iii and the resulting transcripts are not polyadenylated .
however , active alu elements have a poly(a ) dna tract , which is transcribed as part of the alu rna .
the 3 poly(a ) rna tail is predicted to serve two important roles during retrotransposition .
first , the initial base pairing of these a s with the t - rich dna sequence at the target site may be required for efficient first - strand cdna synthesis during target - primed reverse transcription ( tprt ) .
the l1 orf1 protein is an rna - binding protein with nucleic acid chaperone activity and it may facilitate this strand transfer and annealing process .
second , increasing evidence indicates that these poly(a ) rna tails are bound by poly(a ) binding proteins ( pabps ) and that this interaction is critical for the formation of the ribonucleoprotein complex between l1 proteins and l1/alu rnas .
indeed , retrotransposition assays demonstrate that the poly(a ) tail is strictly required for alu mobilization and that its retrotransposition activity is positively correlated with the length of poly(a ) tails . in parallel , poly(a ) tail shortening in expressed l1 mrnas impairs rnp formation and retrotransposition .
therefore , the high mutability of poly(a ) tails has direct impact on l1 and alu retrotransposition .
once captured in genomic dna , the initial long 3 poly(a ) tract undergoes rapid shortening in the first few generations .
in fact , genome - wide , the length of the poly(a ) tract is inversely correlated with the evolutionary age of alu and l1 subfamilies .
as the length of the poly(a ) tail is a key determinant of alu activity , a - tail expansion due to microsatellite instability is predicted to promote its retrotransposition and , conversely , its contraction would predict the extinction of an alu s ability to mobilize ( fig . 
indeed , newly generated alu copies typically have longer poly(a ) tails than the original donor elements .
additionally , a nascent retrotransposition - competent alu element is able to propagate its newfound mobility to progeny copies through poly(a ) tail expansion during reverse transcription .
it is generally accepted that the l1 poly(a ) tail is regenerated during each round of retrotransposition via reverse transcription of the polyadenylated l1 mrna .
thus , the length of the poly(a ) tail in the donor l1 element may affect l1 retrotransposition only if it alters transcription and polyadenylation .
a canonical polyadenylation signal contains a conserved aataaa hexamer and a downstream gt - rich region .
the l1 polyadenylation signal is atypical in that a poly(a ) tail separates the aataaa hexamer from any downstream sequence ; the sequence composition of the latter is determined by chance depending on where the donor element is inserted during the previous round of retrotransposition .
such a configuration may predispose an l1 element to bypass its own polyadenylation signal and instead to use a stronger polyadenylation signal fortuitously situated further downstream .
nevertheless , the poly(a ) tail appears to exert a critical role in proper polyadenylation of l1 mrna in the absence of a strong gt - rich downstream sequence ( fig . 
although full length transcription is possible in the context of a weak polyadenylation context , the presence of a string of 17 a s brings about significant increases in the transcriptional efficiency . although its presence and length is not as critical for l1 mobility as for alu mobility , the poly(a ) tail s dynamics still subtly influence the efficiency of its parent in a disadvantageous genomic neighborhood .
the availability of complete genome sequences for many organisms has enabled genome - wide analyses of repeat distribution . microsatellites with overall repeat length of 12 bp or longer make up 1.3% of the reference human genome ( i.e. , 13.3 kb per mb genome , excluding hexameric repeats at telomeres ) .
although the overall density of microsatellites is relatively uniform in all human chromosomes , the distribution of each repeat class ( mono- , di- , tri- etc . ) varies : ( 1 ) mononucleotide microsatellites show a uniform distribution among exonic , intronic and intergenic regions ( note  exonic regions  herein include not only protein - coding sequences but also 5 and 3 untranslated regions ) ; ( 2 ) di- , tetra- and pentanucleotide microsatellites are relatively depleted in exonic regions ( 74% , 75% and 87% of the genome average , respectively ) ; ( 3 ) tri- and hexanucleotide microsatellites are enriched in exonic regions ( 191% and 146% of the genome average , respectively ) . the vast majority of human microsatellites that are conserved during vertebrate evolution are found in intergenic and intronic regions , consistent with the prediction that microsatellites in exonic regions are more disruptive to gene function . in comparison , the two major types of non - ltr retrotransposons , l1s and alus , display contrasting distribution patterns relative to genes .
alus typically are overrepresented inside genes ( i.e. , residing anywhere in a transcription unit ) as well as within 30 kb from annotated genes . in addition , alus display no orientation bias relative to genes .
in contrast , l1s show prominent orientation bias within genes : while antisense l1s are close to the predicted density , sense l1s are strongly depleted within genes .
in addition , both sense and antisense l1s are significantly underrepresented within 5 kb from annotated genes .
the differential distribution of alus and l1s relative to genes is not a result of target preference because both are retrotransposed by l1 proteins .
rather it is consistent with the predicted impact of sense - oriented l1s on premature polyadenylation , cryptic splicing and/or inhibition of transcriptional elongation .
this idea is further supported by the random chromosomal distribution of recent endogenous l1 and alu copies in the human genome and de novo insertions from l1 transgenes in mice .
furthermore , the large catalog of polymorphic alu and l1 insertions clearly shows that exons can be targeted in proportion to their abundance in the genome . due to their dynamic nature
, microsatellite loci are highly polymorphic among individuals . by comparing the reference human genome to a second genome ,
overall , 2.7% of the microsatellite loci are polymorphic , a frequency that is 45-fold higher than single nucleotide polymorphism ( 0.06% ) .
exonic , especially the coding exonic sequences , show the least amount of microsatellite variation as compared with intergenic and intronic sequences , reflecting increased selective constraints on exonic sequences .
polymorphism incidence increases with repeat number , an observation that is reproduced by surveying polymorphic microsatellite loci among individual genomes from the 1000-genome project .
there is remarkable heterogeneity in the levels of variation at specific microsatellite loci . for example , the trinucleotide repeat in the 5utr of the fragile x mental retardation 1 ( fmr1 ) gene is one of the most studied microsatellite loci with respect to polymorphism in ethnically diverse , healthy individuals .
the range of repeat number varies from population to population ; the overall range is 6 to 87 in surveyed populations . a repeat number of > 200 is considered a full mutation , which is typically associated with intellectual and developmental disabilities .
whole - genome as well as targeted sequencing has also started to reveal the extent of genetic variations caused by non - ltr retrotransposons .
polymorphisms in non - ltr retrotransposons are manifested as indels ( i.e. , insertions in one genome and deletions in another genome ) , a common form of structural variations ( other forms include tandem duplications , inversions and translocations ) .
recent whole - genome sequencing efforts have cataloged a large number of structural variations among diverse human populations .
detailed analyses of mutational mechanisms indicate 2030% of svs are caused by non - ltr retrotransposons .
on average , each human genome contains 10002000 polymorphic non - ltr retrotransposons , with 7985% alu , 1217% l1s and 3% svas .
based on the number of polymorphic insertions and the estimated genetic distance between individual genomes , the frequency of retrotransposition has been calculated as one alu insertion in 21 births and one l1 insertion in 108 to 212 births .
most intriguingly , an analysis of the 1000 genomes project pilot data set suggests a recent increase in retrotransposition rates in humans .
these insertions continuously generate new germline polymorphisms that can be passed across generations ( fig .  5 ) .
as compared with humans , tes play an even bigger role in generating structural variations in the mouse genome .
this discrepancy can be largely explained by the presence of a large number of active ltr retrotransposons in the mouse genome besides non - ltr retrotransposons .
together , retrotransposon insertions contribute to  of structural variations between two inbred mouse lines , with 52% , 43% and 5% contribution from ltr retrotransposons , l1s and sines , respectively .
in addition to retrotransposition in the germline , non - ltr retrotransposons are active in somatic tissues , including normal brain tissues and most epithelial cancers ( further discussed in the next section ) . despite the significant progress made thus far , it should be noted that the discovery of structural variations mediated by tes remains a challenge because of the technical difficulty in de novo assembling repetitive sequences from short sequence reads as well as the high sequence depth that is required for detecting low - frequency alleles .
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 .
the impact of a microsatellite or a transposable element and its associated variability is dependent on its genomic location .
the most direct phenotypic impact of microsatellites and retrotransposons is manifested as disease causing mutations .
microsatellite instability has been implicated in a variety of human diseases with over 40 neurological , neurodegenerative and neuromuscular disorders associated with trinucleotide repeat instability .
well known examples include huntington s disease , fragile x syndrome and friedreich s ataxia .
unlike static mutations , which can be stably passed from one generation to the other , alleles with expanded microsatellites may continue to expand over the course of the individual s life or through germline transmission . depending on the genomic neighborhood , variation in microsatellite length
these mechanisms have been best characterized in trinucleotide repeat expansion disorders and typically consist of one ( or the combination ) of three following three pathways : the loss of function at the protein level , the gain of function at the protein level , or the gain of function at the rna level .
the latter is gaining increased attention due to the recognized role of non - coding rna in epigenetic pathways .
a noticeable absence among these molecular mechanisms is a loss of function at the rna level , a potential mechanism that should be investigated in future studies .
likewise , de novo retrotransposition has been implicated in a variety of sporadic human diseases , including hemophilia , apert syndrome , neurofibromatosis type 1 and congenital muscular dystrophy .
a multitude of molecular mechanisms have been proposed to account for the mutagenesis effect for intronic or exonic insertions .
a less emphasized impact is post - insertional genome instability mediated by non - ltr retrotransposons , which likely poses even greater hazard to the human genome .
for example , nonallelic homologous recombination ( nahr ) between two separate copies of alu repeats may generate structural variations , such as indel , inversion and translocation mutations .
in addition , a hallmark of non - ltr retrotransposition is the formation of a pair of target site duplications ( tsds ) that flank the new insertion .
these tsds represent pre - insertion l1 endonuclease cleavage sites and may be targeted for subsequent cleavage by other l1 endonucleases .
it is proposed that new double strand breaks in tsds may trigger rearrangement events due to their adjacency to non - ltr retrotransposons with abundant homologous copies .
these mechanisms highlight the dynamic nature of l1 and alu sequences in the human genome . furthermore , as has been discussed earlier , non - ltr retrotransposons are not static entities after insertion ; they are a significant source for microsatellite genesis .
high - frequency microsatellite instability ( msi - h ) is a molecular feature of tumors associated with hereditary nonpolyposis colorectal cancers ( hnpcc ; lynch syndrome ) and has been seen in other sporadic cancers , usually of the gastrointestinal system .
these tumors generally arise from defects in the mismatch repair system , leaving dna vulnerable to a high degree of mutation within microsatellites .
detection of msi - h tumors is often achieved with a reference panel of five microsatellites , including two mononucleotide and three dinucleotide markers .
the two mononucleotide markers , bat26 and bat25 , contain ( a)26 and ( a)25 repeats , respectively ; their length changes can be easily discerned even in the absence of normal tissue .
it is thought that msi - h contributes to tumorigenesis mainly through mutating genes with coding microsatellites .
a recent genome - wide survey yields the initial glimpse of microsatellite mutational landscapes in msi - h gastric cancers .
there are four to 6-fold higher microsatellite mutations in genes in msi - h gastric cancers than microsatellite stable ( mss ) cancers .
only a very small fraction of microsatellite mutations ( 0.1% ) are located in protein - coding exonic regions ; the remaining are found in 5utr , 3utr , intronic and intergenic regions of the genome .
importantly , genes with significant changes in mrna expression between msi - h and mss samples are enriched for microsatellite mutations in their utrs , indicating a role of non - coding microsatellite instability in regulating gene expression . a role of non - ltr retrotransposons in tumorigenesis
several studies have used nextgen sequencing approaches to detect genome - wide structural variations or specifically new retrotransposon insertions in tumor samples .
the first study identified 9 tumor - specific ( i.e. , somatic ) l1 insertions in 6 of the 20 lung tumors but none in 10 brain tumors by targeted sequencing . a subsequent study characterized retrotransposon insertions in 43 human tumors of different origins by whole - genome sequencing .
tumor - specific somatic insertions were found in all tumors of epithelial origin ( colorectal , prostate and ovarian ) , but not in blood or brain cancers . among epithelial cancers , colorectal cancers had the highest incidence of l1 insertions at an average of 9 insertions per tumor among 4 colorectal samples ; the fifth colorectal tumor sample alone had an astonishingly high number of 102 l1 insertions .
interestingly , this tumor was the only colorectal sample that manifested msi - h with altered dna repair pathways , suggesting a common origin to both sources of genomic instability .
an independent study mapped tumor - specific l1 insertions in 16 colorectal tumors by targeted l1 sequencing .
intriguingly , although two samples with the highest number of somatic insertions showed microsatellite instability , no correlation was found between the number of insertions and the microsatellite instability status .
future studies with higher coverage and/or larger sample size may be needed to establish a connection between microsatellite instability and retrotransposon mutagenesis .
it should be emphasized that , in addition to somatic insertions , germline insertions may also be an important etiological factor in predisposing the carriers to cancers , as has been recently shown for hepatocellular carcinoma patients
. the precise role of retrotransposon insertions in cancer remains to be determined but they can have a significant impact on gene function .
consistent with sense - oriented l1 insertions being more disruptive to gene expression , genes targeted by sense insertions , but not those targeted by antisense insertions , showed statistically significant decrease in transcription . although usually highlighted for their negative roles , microsatellites and retrotransposons have evolutionary importance due to their ability to provide genetic novelties in human populations .
a salient example is sequence shuffling through 3 transduction . due to the weak nature of the l1 poly(a ) signal
, it is possible for l1 to bypass the signal during transcription and use an alternative poly(a ) signal downstream .
the latter involves a 3 transduction event that is severely 5 truncated , which leaves behind no l1 sequence to be associated with the mobilized sequence .
thus , 3 transduction has the potential to generate new genes and bring new regulatory features to the vicinity of other genes .
although no cases have been reported , it is conceivable that l1s could also mobilize microsatellites by the same mechanism .
another way of introducing evolutionary novelties is through trans - mobilization of cellular rnas , which form processed pseudogenes .
lastly , since the exciting discovery of somatic retrotransposition in the brain , it has been postulated that l1-induced neuronal diversity may be an important source for behavioral phenotypes and confer evolutionary advantage . beyond genome sequence changes ,
the importance of other epigenetic mechanism , including dna methylation , histone modification and nucleosome occupancy , is coming to light .
therefore , the insertion of an l1 into a genomic region may alter the previously existing epigenetic state ( and our unpublished data ) . due to their unique sequence composition , microsatellites can change the physical forms of dna where they occur , which can have implications for gene expression and genome stability .
though not all microsatellites meet the criteria to do so , many repeats form non - b dna structures .
these non - b forms of dna are often associated with locations of chromosomal breakage .
an inverse correlation exists between a repeat s ability to form non - b form dna and its abundance in the genome , suggesting that these unstable structures are selected against due to reduced evolutionary fitness .
the presence of poly(a ) tracts within promoter sequences also has implications for nucleosome organization .
poly(a ) repeats form shorter and more rigid helix structures and have a narrower minor groove , altering nucleosome positioning in manners which increase the binding ability of transcription factors . thus ,
the mobilization of retroelements and their associated poly(a ) tails present a direct manner for l1 , alu and sva elements to affect the genome compaction and expression dynamics of the local regions where they land . in summary ,
microsatellites and non - ltr retrotransposons are dynamic dna sequences that rapidly change from generation to generation .
expansion and mutation of microsatellites within l1 and alu sequences may change the size and sequence identity of these non - ltr retrotransposons , perhaps modulating their mobility .
future studies to compare the sequence of full length l1s may reveal how the dynamics of microsatellites affect the retrotransposons from which they are born .
 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 . 
Introduction: Non-LTR Retrotransposons and Microsatellites
Non-LTR Retrotransposons Give Birth to Microsatellites
Microsatellite Mutation Dynamics
Microsatellite Instability Affects Non-LTR Retrotransposon Mobility
Genomic Distribution and Polymorphisms
Functional Impacts on Genomes and Epigenomes