Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Abstract

BackgroundIn the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3′UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.ResultsHere we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3′UTR. Comparative structural analyses of a human L1 3′UTR stem-loop showed a similarity to 3′UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5–7 bp loop, 8–10 bp stem with a bulge at a distance of 4–6 bp from the loop. The results show that a stem loop with a bulge exists at the 3′-end of Alu. We also found conserved stem-loop positions at 5′UTR and at the end of ORF2 and discuss their possible role.ConclusionsHere we presented an evidence for the presence of a highly conserved 3′UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3′-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3344-4) contains supplementary material, which is available to authorized users.

LINE- andAlu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV

“…Blue box in the 3′ UTR refers to G‐rich sequence. The stem‐loop density along L1 is shown for L1PA3 and is similar to those for other L1PA1‐L1PA4s (Grechishnikova & Poptsova ). The cumulative GC skewness calculated for L1PA3 as the sum of (G–C)/(G+C) of the adjacent 5‐base windows sliding along L1 sequence, and its profile is similar to that calculated for the neighboring L1PA2.…”

“…We have found that breakpoints of four CNV deletions whose proximal breakpoint L1 element was complete (pts 60.4, 165.3, 177.3, and 179.3) map in 5′ portion of the L1, whereas breakpoints of deletions with proximal breakpoint mapping to incomplete L1 (pts 54.3, 57.3, 127.3, 153.3, and 155.3) or non‐L1 sequence (pts 111.3, 119.3, and 139.3) clustered within 3′ one‐third portion of the L1PA2 or L1PA3 (Figure a). To shed more light on structural features within L1PA2 and L1PA3 that might be causatively linked to the observed nonrandom distribution of DNA breakpoints along L1 sequence and L1's susceptibility to DNA breaks in general, locations of deletion breakpoints were analyzed in the context of GC content (https://www.biologicscorp.com/tools/GCContent), GC skewness (https://stothard.afns.ualberta.ca/cgview_server) (Grigoriev, ), potential to form palindromic structures (Grechishnikova & Poptsova ), and the presence of homologous recombination‐associated PRDM9‐binding 7‐mer 5′‐CCTCCCT‐3′ or degenerate 13‐mer 5′‐CCNCCNTNNCCNC‐3′motif (Billings et al., ; Myers, Freeman, Auton, Donnelly, & McVean, ). The average GC content around sequenced breakpoints (regions of microhomology or, in its absence, those flanking breakpoints by 20 bp on each side) is 39% ( SD ± 2%), thus similar to overall 42% GC content of each of these two L1PAs (Figure a).…”

“…Grechishnikova and Poptsova () bioinformatically predicted potential of the evolutionarily young L1HS and L1PA1‐L1PA8 elements and Alu repeats to adopt stem‐loop structure. For instance, three conserved stem‐loop clusters could form at L1's 5′UTR, two in the middle of the ORF2, two at the end of ORF2, one at the 3′UTR, and numerous less conserved palindromes along the entire L1 length.…”

“…We have next inquired whether distribution of the breakpoints along L1 sequences is random or it correlates with the presence of some DNA structural features. We have found that breakpoints of four CNV deletions whose proximal breakpoint L1 element was complete (pts 60.4, 165.3, 177.3 afns.ualberta.ca/cgview_server) (Grigoriev, 1998), potential to form palindromic structures (Grechishnikova & Poptsova 2016), and the presence of homologous recombination-associated PRDM9binding 7-mer 5 ′ -CCTCCCT-3 ′ or degenerate 13-mer 5 ′ -CCNCCNT NNCCNC-3 ′ motif (Billings et al, 2013;Myers, Freeman, Auton, Donnelly, & McVean, 2008). The average GC content around sequenced breakpoints (regions of microhomology or, in its absence, those flanking breakpoints by 20 bp on each side) is 39% (SD ± 2%), thus similar to overall 42% GC content of each of these two L1PAs (Figure 2a).…”

“…Breakpoints of CNVs with full-length L1 at their ends are located closer to the 5 ′ end of L1, whereas breakpoints of CNVs with L1 only at one of their two breakpoints are located closer to the 3 ′ end of L1. Grechishnikova and Poptsova (2016) bioinformatically predicted potential of the evolutionarily young L1HS and L1PA1-L1PA8 elements and Alu repeats to adopt stem-loop structure. For instance, three conserved stem-loop clusters could form at L1's 5 ′ UTR, two in the middle of the ORF2, two at the end of ORF2, one at the 3 ′ UTR, and numerous less conserved palindromes along the entire L1 length.…”