Review
ADAR editing in double-stranded UTRs and other noncoding RNA sequences

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ADARs are a family of enzymes, present in all animals, that convert adenosine to inosine within double-stranded RNA (dsRNA). Inosine and adenosine have different base-pairing properties, and thus, editing alters RNA structure, coding potential and splicing patterns. The first ADAR substrates identified were edited in codons, and ADARs were presumed to function primarily in proteome diversification. Although this is an important function of ADARs, especially in the nervous system, editing in coding sequences is rare compared to editing in noncoding sequences. Introns and untranslated regions of mRNA are the primary noncoding targets, but editing also occurs in small RNAs, such as miRNAs. Although the role of editing in noncoding sequences remains unclear, ongoing research suggests functions in the regulation of a variety of post-transcriptional processes.

Section snippets

Basics of RNA editing by ADARs

RNA editing is the alteration of RNA by nucleotide modification, insertion or deletion (for a review, see Ref. [1]). In metazoans, a common type of RNA editing is a nucleotide modification involving the hydrolytic deamination of adenosine (A) to inosine (I). This type of editing is catalyzed by ADARs 2, 3, 4, which target RNA that is completely, or largely, double-stranded. ADARs are likely to be present in all animals and have been studied in squids, worms, flies and mammals. A single organism

Do edited 3’ UTR structures affect cellular localization?

Based on the analysis of synthetic RNAs, an early and attractive hypothesis posited that inosines within an RNA caused nuclear retention by promoting binding to the multifunctional RNA-binding protein p54nrb 27, 28. mRNAs selectively deaminated in codons are clearly translated in the cytoplasm 29, 30, so nuclear retention was proposed to require the nonselective deamination found in noncoding sequences (e.g. UTRs). However, endogenous mRNAs with multiple inosines in their 3’ UTRs have been

Do edited 3’ UTR structures affect translation?

Obviously, one of the best ways to evaluate the effects of inosine on gene expression is to examine mRNAs in animals that lack editing. C. elegans has been used for such studies, as ADARs are not essential for viability in this species [8]. Comparisons of endogenous and reporter mRNAs with structured 3’ UTRs show no difference in mRNA translation between wild type animals and mutants that lack editing [31]. However, these studies revealed that, in both wild type C. elegans and mutants that lack

Do inosines target RNAs for degradation?

Tudor staphylococcal nuclease (Tudor-SN) is a eukaryotic protein associated with diverse processes, including transcription 43, 44, 45, splicing [46], RNA interference (RNAi) [47] and RNA editing [48]. In vitro studies indicate that Tudor-SN specifically binds dsRNA containing runs of IU or UI base-pairs 48, 49. Some studies indicate that Tudor-SN cleaves inosine-containing RNA [50], whereas others indicate that the nuclease function is provided by another, as yet unidentified, factor [48].

Does editing of endogenous small RNAs affect their biological function?

Inosines have been observed in endogenous small RNAs 51, 52, primarily those of the microRNA (miRNA) gene silencing pathway [53]. miRNAs are transcribed from long primary transcripts (pri-miRNAs; Figure 1) that form intramolecular stem–loop structures that are processed into smaller precursor miRNAs (pre-miRNAs) by the RNase III enzyme Drosha. Following Drosha processing, pre-miRNAs are exported from the nucleus and processed into mature miRNAs by Dicer. Mature miRNAs bind with partial

Does inosine in dsRNA affect its processing by Drosha or Dicer?

Almost as soon as dsRNA-mediated gene silencing was discovered, the question arose of whether inosine within dsRNA would affect these pathways [60]. As discussed above, in only one case is there a clear biological function for inosine in a small RNA. However, the results of many in vitro studies, and those that monitor expression of exogenous dsRNA in vivo, provide proof-of-principle evidence that ADARs affect gene silencing.

For example, compared to unedited dsRNA, dsRNA reacted with ADARs in

Do ADARs affect silencing through competition for dsRNA?

Although several in vitro studies show that inosine in dsRNA inhibits its processing to small RNAs, others show that ADARs can antagonize gene silencing simply by binding dsRNA [51]. The first hint that ADARs could cause effects simply by binding dsRNA came from the study of C. elegans transgene silencing [62]. Of the two ADARs in C. elegans, only ADR-2 has the active site residues important for catalysis; thus, worms lacking only adr-2, or both adr-1 and adr-2, have no detectable editing [8].

Do ADARs and inosine-containing RNAs have general effects on gene expression?

Eukaryotes express other dsRBPs in addition to those involved in gene silencing [65], and in theory, ADARs could compete with these as well. In fact, ADARs are known to affect the function of the dsRNA-dependent protein kinase PKR, a dsRBP whose kinase activity is activated by binding to viral dsRNA. Once activated, PKR phosphorylates the translation initiation factor, eIF2α, to shut down all translation [66]. Over-expression of ADAR1 decreases PKR activation, leading to a general increase in

Concluding remarks

ADAR editing of RNA alters the information content and structure of cellular RNAs. The first endogenous substrates of ADARs that were identified revealed that editing in codons is essential for generating diverse protein isoforms. Although codon editing is clearly important, it represents only a small fraction of the editing events in the transcriptome. Editing sites in noncoding regions of RNA are vastly more prevalent, and their identification has expanded exponentially the number of known

Acknowledgment

This work was supported by funding to BLB from the National Institutes of Health (GM44073).

References (71)

  • K.V. Prasanth

    Regulating gene expression through RNA nuclear retention

    Cell

    (2005)
  • R.W. Carthew et al.

    Origins and mechanisms of miRNAs and siRNAs

    Cell

    (2009)
  • D.E. Golden

    An inside job for siRNAs

    Mol. Cell

    (2008)
  • B.L. Bass

    Double-stranded RNA as a template for gene silencing

    Cell

    (2000)
  • S.W. Knight et al.

    The role of RNA editing by ADARs in RNAi

    Mol. Cell

    (2002)
  • W. Yang

    ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells

    J. Biol. Chem.

    (2005)
  • Y. Wang et al.

    Adenosine deaminase ADAR1 increases gene expression at the translational level by decreasing protein kinase PKR-dependent eIF-2alpha phosphorylation

    J. Mol. Biol.

    (2009)
  • A.D. Scadden

    Inosine-containing dsRNA binds a stress-granule-like complex and downregulates gene expression in trans

    Mol. Cell

    (2007)
  • J.M. Gott et al.

    Functions and mechanisms of RNA editing

    Annu. Rev. Genet.

    (2000)
  • B.L. Bass

    RNA editing by adenosine deaminases that act on RNA

    Annu. Rev. Biochem.

    (2002)
  • O. Maydanovych et al.

    Breaking the central dogma by RNA editing

    Chem. Rev.

    (2006)
  • K. Nishikura

    Editor meets silencer: crosstalk between RNA editing and RNA interference

    Nat. Rev. Mol. Cell. Biol.

    (2006)
  • Q. Wang

    Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis

    Science

    (2000)
  • M. Higuchi

    Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2

    Nature

    (2000)
  • L.A. Tonkin

    RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans

    EMBO J.

    (2002)
  • R.W. Wagner

    A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs

    Proc. Natl. Acad. Sci. U. S. A.

    (1989)
  • E.Y. Levanon

    Systematic identification of abundant A-to-I editing sites in the human transcriptome

    Nat. Biotechnol.

    (2004)
  • A.G. Polson et al.

    Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase

    EMBO J.

    (1994)
  • K.A. Lehmann et al.

    Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities

    Biochemistry

    (2000)
  • K. Nishikura

    Substrate specificity of the dsRNA unwinding/modifying activity

    EMBO J.

    (1991)
  • H. Lomeli

    Control of kinetic properties of AMPA receptor channels by nuclear RNA editing

    Science

    (1994)
  • C.M. Burns

    Regulation of serotonin-2C receptor G-protein coupling by RNA editing

    Nature

    (1997)
  • C.J. Hanrahan

    RNA editing of the Drosophila para Na(+) channel transcript. Evolutionary conservation and developmental regulation

    Genetics

    (2000)
  • L.L. Chen et al.

    Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats

    Cell Cycle

    (2008)
  • D.P. Morse et al.

    Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA

    Proc. Natl. Acad. Sci. U. S. A

    (1999)
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