Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs

Abstract

Primary transcripts of certain microRNA (miRNA) genes are subject to RNA editing that converts adenosine to inosine. However, the importance of miRNA editing remains largely undetermined. Here we report that tissue-specific adenosine-to-inosine editing of miR-376 cluster transcripts leads to predominant expression of edited miR-376 isoform RNAs. One highly edited site is positioned in the middle of the 5′-proximal half "seed" region critical for the hybridization of miRNAs to targets. We provide evidence that the edited miR-376 RNA silences specifically a different set of genes. Repression of phosphoribosyl pyrophosphate synthetase 1, a target of the edited miR-376 RNA and an enzyme involved in the uric-acid synthesis pathway, contributes to tight and tissue-specific regulation of uric-acid levels, revealing a previously unknown role for RNA editing in miRNAmediated gene silencing.Many developmental and cellular processes are regulated by microRNA (miRNA)-mediated RNA interference (RNAi) (1-4). After incorporation into the RNA-induced silencing complex, miRNAs guide the RNAi machinery to their target genes by forming RNA duplexes, resulting in sequence-specific mRNA degradation or translational repression (1,2,4). The generation of mature miRNAs requires the processing of primary transcripts (pri-miRNAs) (5), and A → I RNA editing occurs to certain pri-miRNAs (6-8).Human chromosome 14 and syntenic regions of the distal end of mouse chromosome 12 harbor the miR-376 cluster of miRNA genes (9). The six human miR-376 RNAs (miR-376a2, -376b, -368, -B1, and -B2) (Fig. 1A) and three mouse miR-376a-c RNAs ( fig. S1A) have highly similar sequences ( fig. S2). Expression of miR-376 RNAs is detected in the placenta, developing embryos, and adult tissues (9,10).All of the miR-376 RNA cluster members are transcribed into a long primary transcript encompassing the entire region and (except human miR-B1) undergo extensive and * To whom correspondence should be addressed. ykawahara@wistar.org (Y.K.); kazuko@wistar.org (K.N.). † These authors contributed equally to this work. simultaneous A → I editing at one or both of two specific sites (+4 and +44) in select human and mouse tissues and specific subregions of the brain ( Fig. 2 and table S1) (11). The +4 site of some pri-miR-376 cluster genes (e.g., human -376b and -368) is genomically encoded as G and thus not subject to A → I editing (Fig. 1A). Certain miR-376 members, such as primiR-376a2, -376b, and -368, are nearly 100% edited at the +44 site in the human cortex and medulla (Figs. 1B and 2 and table S1), whereas no editing was detected in other tissues (e.g., the +4 site of human pri-miR-376a1 in liver and the +44 site of mouse pri-miR-376a in all tissues). In select members of the cluster, substantial editing (∼20 to 55%) occurs at the −1 site, and infrequent editing occurs at several additional sites (table S1). In contrast, no editing was detected in human pri-miR-654 and mouse pri-miR-300. Although these two pri-miRNAs are located within the miR-376 cluster, t...

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

“…In addition to editing in the miR-376 cluster described previously (Kawahara et al 2007b(Kawahara et al , 2008, we found another eight miRNAs that are edited within the seed of either the miRNA or the miRNA*. A-to-I editing could also affect miRNA loading, and thereby indirectly affect targeting.…”

Origins and evolution of ADAR‐mediated RNA editing

“…In addition to recoding, a few beneficial ADAR targets in noncoding RNA are fixed (Fig. 2C), such as miRNA (47). Third, these fixed ADAR targets will also be lost via mutation.…”

Proteome diversification by adenosine to inosine RNA-editing

“…Editing of microRNA precursors inhibits or alters processing and changes the sequence of both seed sequence in microRNAs and targeting sequences in mRNAs. [6][7][8]49 Transcribed primiRNAs are cleaved by Drosha, the resulting pre-miRNAs are exported from the nucleus to the cytoplasm and finally, the 21-23 bp miRNAs are generated by Dicer cleavage. One strand of the mature miRNA is incorporated into RISC (RNA-induced silencing complex) and binds to complementary sequences mainly in the 3' UTR of target mRNAs.…”

“…Editing can affect their processing by Drosha or Dicer but can also alter microRNA:mRNA interactions. [5][6][7][8][9] In coding regions of mRNA editing events are relatively rare. However, during the last years several evolutionary conserved adenosine to inosine editing events have been identified in coding regions.…”