Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposition poses a mutagenic threat to human genomes. Human cells have therefore evolved strategies to regulate L1 retrotransposition. The APOBEC3 (A3) gene family consists of seven enzymes that catalyze deamination of cytidine nucleotides to uridine nucleotides (C-to-U) in single-strand DNA substrates. Among these enzymes, APOBEC3A (A3A) is the most potent inhibitor of L1 retrotransposition in cultured cell assays. However, previous characterization of L1 retrotransposition events generated in the presence of A3A did not yield evidence of deamination. Thus, the molecular mechanism by which A3A inhibits L1 retrotransposition has remained enigmatic. Here, we have used in vitro and in vivo assays to demonstrate that A3A can inhibit L1 retrotransposition by deaminating transiently exposed single-strand DNA that arises during the process of L1 integration. These data provide a mechanistic explanation of how the A3A cytidine deaminase protein can inhibit L1 retrotransposition.DOI: http://dx.doi.org/10.7554/eLife.02008.001.
Highlights
Long INterspersed Element-1 (LINE-1 or L1) derived sequences comprise roughly 17% of human genomic DNA (Lander et al, 2001)
These events would be repaired by combined actions of uracil DNA glycosylase (UNG) and apyrimidinic endonuclease (APE), which we speculate could lead to the integration of a 5′ truncated L1 cDNA that lacks evidence of deamination
We further propose that A3A can act on transiently exposed single-strand genomic DNA flanking L1 integration sites (Figure 4B,C)
Summary
Long INterspersed Element-1 (LINE-1 or L1) derived sequences comprise roughly 17% of human genomic DNA (Lander et al, 2001). It is estimated that the average human genome contains 80–100 retrotransposition-competent (i.e., active) L1s (Sassaman et al, 1997; Brouha et al, 2003). ORF1 encodes an ∼40 kDa protein (ORF1p) that binds L1 RNA as a trimer (Holmes et al, 1992; Hohjoh and Singer, 1996; Martin et al, 2003; Khazina and Weichenrieder, 2009). ORF2 encodes an ∼150 kDa protein (ORF2p) (Ergun et al, 2004; Doucet et al, 2010; Taylor et al, 2013b) with DNA endonuclease (Feng et al, 1996) and reverse transcriptase (Mathias et al, 1991) activities.
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