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.
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel. scarmi@shoshi.ph.biu.ac.il
Shai
S
Carmi
Itamar
I
Borukhov
Erez Y
EY
Levanon
D000241:Adenosine / Q000737:chemistry / Q000235:genetics; D000243:Adenosine Deaminase / Q000737:chemistry / Q000235:genetics*; D020087:Alu Elements / Q000235:genetics*; D020137:Base Pair Mismatch / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D005091:Exons; D020224:Expressed Sequence Tags / Q000737:chemistry; D016678:Genome; D023281:Genomics; D006151:Guanosine / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007288:Inosine / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D017393:RNA Editing / Q000235:genetics*; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins
D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; D006151:Guanosine; D007288:Inosine; D012313:RNA; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase; D000241:Adenosine