Genome-wide analysis of Alu editability.
Bottom Line: We use large RNA-seq data sets to analyze the editing levels in 203 798 Alu repeats residing within human genes.This effect alone accounts for 28% of the total variance in editability.In addition, the number of Alu repeats of the same and reverse strand in the genomic vicinity, the expressed strand of the Alu, Alu's length and subfamily and the occurrence of reversely oriented neighbor in the same intron\exon all contribute, to a lesser extent, to the Alu editability.
Affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.Show MeSH
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Mentions: It is important to stress that we define editability as the fraction of adenosines being converted. Thus, having less adenosines and less putative editing sites should not affect editability naively. However, we do see that shorter Alus are less editable (Figure 4). This is probably due to the weaker dsRNA structure created by these shorter elements. In addition, very long Alu elements, longer than the typical value of ∼300 bp, are also less well edited, as the dsRNA structure that forms upon binding to their neighboring Alu is unlikely to cover them fully. Similarly, having a short Alu as a reversely oriented neighboring Alu also reduces editability for the same reason. Altogether, these effects explain only ∼4% of the remaining variance.
Affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.