Mechanism of nuclear retention of promiscuously A-to-I edited RNA in higher eukaryotic cells

Double-stranded RNA triggers various profound cellular reactions, which depend not only on different intracellular dsRNA locations, but also on the intrinsic structure and length of the duplex. One of the major cellular responses to nuclear dsRNA is the covalent base modification of the target dsRNA by a ubiquitously expressed enzyme, ADAR. ADAR works on dsRNA and alters adenosines to inosines in the RNA duplex. Two types of ADAR editing of dsRNA have been found, selective editing and the promiscuous hyperediting. Hyperedited RNA has been suggested to undergo a novel regulatory pathway. How do cells discriminate between selectively edited mRNAs that encode new protein isoforms, and dsRNA-induced, promiscuously edited RNAs that encode nonfunctional, mutant proteins? We have developed a Xenopus oocyte model system which shows that a variety of hyperedited, inosine-containing RNAs are specifically retained in the nucleus. To uncover the mechanism of inosine-induced retention, HeLa cell nuclear extracts were used to isolate a multiprotein complex that binds specifically and cooperatively to inosine-containing RNAs. This complex contains the inosine-specific RNA binding protein p54nrb, the splicing factor PSF, and the inner nuclear matrix structural protein matrin 3. We provide evidence that one function of the complex identified here is to anchor hyperedited RNAs to the nuclear matrix, while allowing selectively edited mRNAs to be exported. Our results also suggest an important mechanism about how nuclear antisense RNA, that forms the duplex with its target, plays a role in the regulation of gene expression. This information might help in the design and implementation of effective antisense RNA approaches to inhibit specific gene expression.