Human transposon tectonics

Abstract

Mobile DNAs have had a central role in shaping our genome. More than half of our DNA is comprised of interspersed repeats resulting from replicative copy and paste events of retrotransposons. Although most are fixed, incapable of templating new copies, there are important exceptions to retrotransposon quiescence. De novo insertions cause genetic diseases and cancers, though reliably detecting these occurrences has been difficult. New technologies aimed at uncovering polymorphic insertions reveal that mobile DNAs provide a substantial and dynamic source of structural variation. Key questions going forward include how and how much new transposition events affect human health and disease.

Figure 1

Human retrotransposons. A. Composition of the human genome with respect to high copy number repeats. Data are from the RepeatMasker analysis of the hg19 human genome assembly (Genome Reference Consortium GRCh37). The illustration shows fractions of the genome derived from the major orders (Wicker et al., 2007) of retrotransposons. The remaining 55% of the genome bears low homology to TEs, although substantial portions may be derived from mobile DNA. B. Transposon types illustrated as fractions of total ongoing activity. AluY are the most prolific source of new insertions at one de novo germ line insertion per 20 births; L1 and SVA are thought to be comparable in current activity, responsible for one insertion per 100–200 births. C. Schematic showing an accumulation of interspersed repeat insertions over time. New integrations are stochastic events in individuals (star), such that co-existence with the antedating ‘empty’ allele occurs in the population initially. In the schematic, two alleles are present currently, reflecting presence and absence of the most recent insertion [a retrotransposon insertion polymorphism (RIP)]. As persisting insertions age, they become ‘fixed’ or invariant in the population and decrease in sequence likeness to similar elements (black to gray). D. Structure of the most active retroelements in human genomes. L1 LINEs have a CpG rich 5′UTR with an internal RNA polII promoter (5′ rightward arrow), two open reading frames encoding ORF1p and ORF2p (pink segments), and a 3′ UTR with a polyadenylation (pA) sequence. The ORF2 reading frame encodes endonuclease (EN) and reverse transcriptase (RT) domains. Alu elements are derived from 7SL ribosomal RNAs; they have two internal ‘monomer’ sequences with a centrally located A-rich sequence and an RNApolIII promoter (A and B, gray). The sequence ends in multiple adenosines (A_n). SVAs are composites of other repeats, from left to right, a CCCTCTn repeat, two tandem Alu-like sequences in antisense (leftward arrows), a VNTR (variable number tandem repeat) region, and a SINE-R region with HERV homology. Sequence suggests RNApolII driven transcription (5′ rightward arrow), and there is a 3′ AAUAAA sequence (pA).

Figure 2

L1 LINE propagation. L1 retrotranspositition requires RNA and two proteins encoded by L1; they assemble into ribonucleic acid particles during translation. Reverse transcription of the RNA is coupled to insertion as it initiates from the 3′-OH of the broken strand (target primed reverse transcription, TPRT). Resolution of the structure results in target site duplication (TSD).

Figure 3

A. Families of L1 LINEs have expanded over evolutionary time in primate genomes in a singular succession of retrotransposition “waves”; that is, elements have accumulated in a specific order, with L1PA5 insertions preceding L1PA4 preceding L1PA3, L1PA2 and L1PA1 (Boissinot and Furano, 2001). For the last two million years, continued L1 activity is largely owed to the L1(Ta) subset (L1PA1). A 3 nucleotide sequence in the 3′UTR of L1(Ta) can be used to physically distinguish its members from sequences of older L1 LINEs in the human genome; this can lend specificity to L1(Ta) mapping PCRs. B. Similarly, insertion of a 8 base pair sequence near the 3′ end of AluYb8/9 subfamilies are characteristic sequences which can be used to specifically recover insertion sites of these elements.

Figure 4

A schematic of retrotransposon dynamics. (A.) An L1 insertion (1) of moderate activity (blue) and allelic frequency (circle size) is shown (1). It templates new insertions, many of which are 5′ truncated or mutated at the time of insertion (gray denotes inactivity). The new insertions segregate mostly as neutral alleles; some accumulate to a higher allele frequency over time (larger gray circles in subsequent panels). (B.) A new insertion is generated that is highly competent or ‘hot’ for retrotransposition (2, blue) because of features intrinsic to its sequence or by its location in an expression-permissive target site. (C.) This ‘hot’ L1 templates others; there may be a tendency to template other full-length, ‘hot’ progeny insertions. ‘Hot’ elements are continually lost through negative selection (3, interrupted diagonal), or (D.) mutation (2, interrupted arrow from C). However, some remain to potentiate other retrotransposition events (4). It is envisioned that these ‘hot’ elements are relatively transient in genomes due to purifying selection against them, do not achieve high allele frequency, but are responsible for the bulk of transposition in modern humans.