Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes

Moldovan, J. B.; Kopera, H. C.; Liu, Y.; Garcia-Canadas, M.; Catalina, P.; Leone, P. E.; Kitzman, J. O.; Kidd, J. M.; Garcia-Perez, J. L.; Moran, J.

doi:10.1101/2024.05.03.592410

bioRxiv · 10.1101/2024.05.03.592410

Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes

Moldovan, J. B.·Kopera, H. C.·Liu, Y.·Garcia-Canadas, M.·Catalina, P.·Leone, P. E.·Kitzman, J. O.·Kidd, J. M.·Garcia-Perez, J. L.·Moran, J.

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Abstract

Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1 or L1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing messenger RNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINE RNAs use strategies to hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.

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Moldovan, J. B., Kopera, H. C., Liu, Y., Garcia-Canadas, M., Catalina, P., Leone, P. E., Kitzman, J. O., Kidd, J. M., Garcia-Perez, J. L., Moran, J.. 2024-05-03. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. https://doi.org/10.1101/2024.05.03.592410

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