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: Another important factor that might contribute to editing variability is the structure of the Alu neighborhood. In this work, we have only referred to the nearest reversely oriented Alu repeat. However, the full picture is much more complex. A typical Alu repeat has many neighboring Alu's and the folding of the entire transcript should be considered (see Figure 9). In addition, editing itself might modify the RNA folds, so the relevant paired Alu element might change dynamically.
Affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.