A-to-I editing of coding and non-coding RNAs by ADARs

Abstract

Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. This A-to-I editing occurs not only in protein-coding regions of mRNAs, but also frequently in non-coding regions that contain inverted Alu repeats. Editing of coding sequences can result in the expression of functionally altered proteins that are not encoded in the genome, whereas the significance of Alu editing remains largely unknown. Certain microRNA (miRNA) precursors are also edited, leading to reduced expression or altered function of mature miRNAs. Conversely, recent studies indicate that ADAR1 forms a complex with Dicer to promote miRNA processing, revealing a new function of ADAR1 in the regulation of RNA interference.

Figure 1. Deamination of adenosine to inosine by adenosine deaminases acting on RNA (ADAR) proteins

a | Three human ADAR family members (ADAR1, ADAR2 and ADAR3), two human ADAD (adenosine deaminase domain-containing) family members (TENR and TENRL), Drosophila melanogaster dAdar, and two Caenorhabditis elegans ADAR proteins (ADR-1 and ADR-2), share common functional domains. These include two or three repeats of the double-stranded RNA (dsRNA)-binding domain (dsRBD) and a catalytic deaminase domain. Certain structural features, such as Z-DNA-binding domains (Zα and Zβ) and the Arg-rich, single-stranded RNA (ssRNA)-binding R domain, are unique to particular ADAR members. b | ADARs catalyse a hydrolytic deamination reaction that converts adenosine to inosine (top). Whereas adenosine base-pairs with uridine, inosine behaves like a guanosine, as it base-pairs with cytidine in a Watson–Crick-bonding configuration (bottom). NES, nuclear export signal; NLS, nuclear localization signal. Part b reprinted with permission from REF. , Annual Reviews.

Figure 2. Cellular localization of adenosine deaminases acting on RNA 1 (ADAR1) and ADAR2

a | Exportin 1 (XPO1) binds to the nuclear export signal (NES) located within the Zα domain of ADAR1p150 and regulates its nuclear export together with RAN·GTP. Nuclear export of ADAR1p110 is mediated by XPO5–RAN·GTP and regulated by double-stranded RNA (dsRNA) binding to its dsRNA-binding domains (dsRBDs). The nuclear localization signal (NLS) located in dsRBD3 is responsible for localization of both ADAR1p150 and p110 in the nucleus and nucleolus. Nuclear import of ADAR1p110 is mediated by binding of transportin 1 (TRN1) to dsRBD3, which is inhibited by binding of dsRNA. b | The nuclear and nucleolar localization of ADAR2 is regulated by binding of karyopherin subunit α1 (KPNA1) and KPNA3 to an NLS located in the amino-terminal region. Phosphorylation of Thr32 by a currently unknown kinase enables interaction of ADAR2 with the prolyl-isomerase PIN1 in a dsRNA-binding-dependent manner, which isomerizes Pro33 and positively controls the nuclear localization and stability of ADAR2. The E3 ubiquitin ligase WWP2 promotes rapid degradation of ADAR2 in the cytoplasm, which is why ADAR2 is usually not detected in the cytoplasm. Ub, ubiquitin.

Figure 3. Editing of Alu double-stranded RNAs (dsRNAs) and its consequences

a | Genome-wide inverted Alu repeats in introns and in 3′ untranslated regions (UTRs) form intramolecular RNA duplexes (Alu dsRNAs), which are edited by adenosine deaminases acting on RNA (ADARs). Inosines at intronic Alu dsRNAs are recognized by the splicing machinery as guanosines, thus effectively creating new splice sites, which results in the inclusion of intronic Alu sequences in the mature mRNAs (Alu exonization). b | Extensively edited Alu dsRNAs are retained in nuclear paraspeckles by a mechanism involving p54^nrb and the long non-coding RNA nuclear paraspeckle assembly transcript 1(NEAT1).The formation of paraspeckles is absolutely dependent on NEAT1.p54^nrb, and perhaps also NEAT1, bind specifically to inosine-containing RNAs such as extensively edited Alu dsRNA. Under certain conditions, such as stress, the paraspeckle-trapped RNA may be released into the cytoplasm for translation, as seen with the mouse Ctn RNA. Editing of short interspersed nuclear element (SINE) dsRNA within the 3′ UTR of the Ctn RNA leads to its nuclear retention. When cells are placed under stress, Ctn RNA is cleaved and polyadenylated at an alternative site, resulting in the loss of the edited SINE sequences and release of the mRNA from the nucleus as the protein-coding mCat2 (cationic amino acid transporter 2) mRNA. c | Extensively edited Alu dsRNAs may be degraded by endonuclease V (EndoV) together with Tudor-SN (TSN), thereby controlling the expression levels of genes harbouring Alu repeats. d | Extensively edited Alu dsRNA containing multiple and consecutive I·U mismatched wobble pairs (I·U-dsRNA) may suppress the interferon (IFN) signalling pathway, which would otherwise be activated by unedited Alu dsRNAs. Unedited long dsRNAs (viral and cellular) are potent inducers of IFN signalling. I·U-dsRNA may competitively inhibit the binding of dsRNA to retinoic acid-inducible gene 1(RIG1)or melanoma differentiation-associated protein 5 (MDA5), both of which are cytosolic sensors for dsRNA and upstream regulators of the mitochondrial antiviral signalling adaptor protein (MAVS)-mediated IFN activation pathway. e | Extensively edited Alu dsRNAs containing multiple inosines may contribute to heterochromatin formation and gene silencing. Vigilin binds to RNA containing multiple inosines, such as extensively edited Alu dsRNAs. Vigilin has been shown to form a complex with ADAR1, RNA helicase A (RHA), and 86 kDa subunit of Ku antigen (KU86)–KU70, which recruits the histone methyltransferase SUV39H1. SUV39H1 catalyses the methylation of H3 Lys9 (H3K9me), an epigenetic mark that is recognized by heterochromatin protein 1 (HP1), leading to the formation of heterochromatin and to gene silencing. AP1, activator protein-1; IRF3, interferon regulatory factor 3; NF-κB, nuclear factor-κB; pre-mRNA, precursor mRNA. Part a adapted from REF. , Nature Publishing Group.

Figure 4. Regulation of microRNA (miRNA) processing, expression and selectivity by RNA editing

a | Primary miRNAs (pre-miRNAs) are processed by the Drosha–DGCR8 complex into precursor miRNAs (pri-miRNAs) in the nucleus, exported to the cytoplasm by exportin 5 (XPO5)–RAN·GTP and processed by the Dicer–TAR RNA-binding protein (TRBP) complex into mature miRNA duplexes. One strand of this duplex is then loaded onto the RNA-induced silencing complex (RISC), which results in the degradation or the inhibition of translation of target mRNAs. Editing can affect any of the miRNA biogenesis steps, including Drosha cleavage, Dicer cleavage and RISC loading, as well as miRNA target selection. Known examples of miRNA editing and their consequences are shown. b | Silencing of phosphoribosyl pyrophosphate synthetase 1 (PRPS1) by miR-376a-5p edited at the +4 site by ADAR2 (adenosine deaminases acting on RNA2) and the consequent suppression of uric acid synthesis. A single A-to-I nucleotide change in the seed sequence of miR-376a-5p results in redirection of target gene selection. One of those genes, specifically targeted by the edited miR-376a-5p, is PRPS1, which encodes an essential enzyme involved in purine metabolism and the uric acid synthesis pathway. Repression of PRPS1 by the edited miR-376a-5p results in reduced expression of uric acid in certain tissues, such as brain, in which uric acid levels need to be tightly regulated. The 3′ untranslated region (UTR) of PRPS1 mRNA has two target sites for the edited miR-376a-5p (inset). AGO2, Argonaute 2; EBV, Epstein–Barr virus; KSHV, Kaposi sarcoma-associated herpes virus.

Figure 5. Regulation of RNA interference (RNAi) by adenosine deaminases acting on RNA (ADARs)

Two different types of interaction between RNA-editing and RNAi pathways are known, one antagonistic and the other stimulative. a | In antagonistic interactions, ADAR–ADAR homodimers edit long double-stranded RNA (dsRNA) and certain microRNA (miRNA) precursors. Editing changes the dsRNA structure and makes it less accessible to Drosha and/or Dicer, which consequently decreases the efficacy of RNAi by reducing the production of short interfering RNAs (siRNAs) and miRNAs. b | In the case of stimulative interactions, ADAR1, as part of a Dicer–ADAR1 heterodimer, promotes RNAi by increasing the Dicer cleavage reaction rate, thereby generating more siRNAs and miRNAs and enhancing RISC (RNA-induced silencing complex) loading and target mRNA silencing. AGO2, Argonaute 2. Figure adapted with permission from REF. , Elsevier.