Identification of widespread ultra-edited human RNAs

Adenosine-to-inosine modification of rna molecules (a-to-i rna editing) is an important mechanism that increases transciptome diversity. it occurs when a genomically encoded adenosine (a) is converted to an inosine (i) by adar proteins. sequencing reactions read inosine as guanosine (g); therefore,current methods to detect a-to-i editing sites align rna sequences to their corresponding dna regions and identify a-to-g mismatches. however,such methods perform poorly on rnas that underwent extensive editing (ultra-editing),as the large number of mismatches obscures the genomic origin of these rnas. therefore,only a few anecdotal ultra-edited rnas have been discovered so far. here we introduce and apply a novel computational method to identify ultra-edited rnas. we detected 760 ests containing 15,646 editing sites (more than 20 sites per est,on average),of which 13,668 are novel. ultra-edited rnas exhibit the known sequence motif of adars and tend to localize in sense strand alu elements. compared to sites of mild editing,ultra-editing occurs primarily in alu-rich regions,where potential base pairing with neighboring,inverted alus creates particularly long double-stranded rna structures. ultra-editing sites are underrepresented in old alu subfamilies,tend to be non-conserved,and avoid exons,suggesting that ultra-editing is usually deleterious. a possible biological function of ultra-editing could be mediated by non-canonical splicing and cleavage of the rna near the editing sites. © 2011 carmi et al.