Discovery and characterization of Alu repeat sequences via precise local read assembly.
Bottom Line: In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of AluYa5 and AluYb8 insertions.The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations.Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.
Affiliation: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.Show MeSH
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Mentions: To assess the length distribution of non-reference Alu variants from our call set, we focused on insertions assembled from the AluYa5 and AluYb8 subfamilies. We reasoned that analysis of these particular subfamilies should provide the most informative resource for comparison given their representation as the majority of identified variants. We further limited analysis to those Alu that were suitable for genotyping, as insertions that do not meet our criteria for genotyping may erroneously appear to be truncated due to an incomplete breakpoint assembly. This resulted in an analysis set of 351 AluYa5 and 215 AluYb8 insertions. Based on nucleotide alignments of the assembled insertions against their respective consensus, we examined the collective coverage of assembled elements, per subfamily, in comparison to the nucleotide positions relative to their respective consensus (also refer to the plots in Figure 3A and B).
Affiliation: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.