Recognition of double‐stranded RNA by proteins and small molecules

Carlson, Coby B.; Stephens, Olen M.; Beal, Peter A.

doi:10.1002/bip.10413

Cited by 56 publications

(54 citation statements)

References 111 publications

(114 reference statements)

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“…Further support for this hypothesis was observed with mice lacking ADAR1 expression, where editing at the ADAR2-selective D site was increased (25). Molecular recognition of dsRNA is a key event for numerous biological pathways, including the trafficking, editing, and maturation of cellular RNA, the interferon-mediated antiviral response, and RNA interference (11,16,64). A lack of sequence-specific binding for members of the dsRBD-containing family (20,51) suggests that ADAR2 may bind to a wide variety of dsRNA substrates, thus competing with the functions of other dsRNA-binding proteins within the cell.…”

Section: Discussionmentioning

confidence: 90%

Altered RNA Editing in Mice Lacking ADAR2 Autoregulation

Feng¹,

Sansam²,

Singh³

et al. 2006

Molecular and Cellular Biology

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ADAR2 is a double-stranded-RNA-specific adenosine deaminase involved in the editing of mammalian RNAs by the site-selective conversion of adenosine to inosine. Previous studies from our laboratory have demonstrated that ADAR2 can modify its own pre-mRNA to create a proximal 3 splice site containing a noncanonical adenosine-inosine dinucleotide. Alternative splicing to this proximal acceptor adds 47 nucleotides to the mature ADAR2 transcript, thereby resulting in the loss of functional ADAR2 protein expression due to premature translation termination in an alternate reading frame. To examine whether the editing of ADAR2 transcripts represents a negative autoregulatory strategy to modulate ADAR2 protein expression, we have generated genetically modified mice in which the ability of ADAR2 to edit its own pre-mRNA has been selectively ablated by deletion of a critical sequence (editing site complementary sequence [ECS]) required for adenosine-to-inosine conversion. Here we demonstrate that ADAR2 autoediting and subsequent alternative splicing are abolished in homozygous ⌬ECS mice and that ADAR2 protein expression is increased in numerous tissues compared to wild-type animals. The observed increases in ADAR2 protein expression correlate with the extent of ADAR2 autoediting observed with wild-type tissues and correspond to increases in the editing of ADAR2 substrates, indicating that ADAR2 autoediting is a key regulator of ADAR2 protein expression and activity in vivo.The conversion of adenosine to inosine (A to I) by RNA editing is a widespread posttranscriptional modification resulting from the hydrolytic deamination of selective adenosine residues that alters the nucleotide sequence of RNA transcripts from that encoded by genomic DNA. The majority of well-characterized A-to-I editing events involve nonsynonymous codon changes in mRNA sequences, resulting in the production of proteins with altered functional properties. In mammals, the most prominent examples of A-to-I editing have been described for transcripts encoding ionotropic glutamate receptor subunits (GluR), a voltage-gated potassium channel subunit (K v 1.1), and the 2C subtype of the serotonin receptor (5-HT 2C R), which lead to the production of channels with altered electrophysiological and ion permeation properties (6,27,37,38,43,54) and receptors with decreased G-protein coupling efficiency (5,10,46). A-to-I modifications have also been described for nontranslated RNA species and noncoding regions of RNA transcripts, suggesting that such RNA modifications may also affect other aspects of RNA function, including splicing, trafficking, translation efficiency, and transcript stability (1,7,35,42,45).The enzymes responsible for the site-specific deamination of A to I in mRNA transcripts are known as adenosine deaminases that act on RNA (ADARs) (2, 3, 34, 53). For mammals, three ADAR proteins (ADAR1, ADAR2, and ADAR3) and their corresponding genes have been identified (12,28,36,44). ADAR1 and ADAR2 have been shown to be ubiquitously expressed (44,50,59) an...

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Section: Discussionmentioning

confidence: 90%

Altered RNA Editing in Mice Lacking ADAR2 Autoregulation

Feng¹,

Sansam²,

Singh³

et al. 2006

Molecular and Cellular Biology

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“…This view is supported by the observation that purified p53 protein could not discriminate between RNAs in vitro even when the RNAs displayed dramatically different apparent affinities for p53 in yeast. Three sequence-nonspecific RNA-binding proteins were compared with p53: the E. coli S12 ribosomal protein (Coetzee et al 1994), the double-stranded RNA-binding domain of the double-stranded RNA-dependent protein kinase (Carlson et al 2003), and the zinc finger domain of the HIV-1 nucleocapsid protein (Kanevsky et al 2005). Both S12 and HIV-1 NC have been discussed as ''RNA chaperones,'' an activity that has also been mentioned for p53.…”

Section: Discussion P53 Binds Rna In Yeastmentioning

confidence: 99%

Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system

Riley

Cassiday

Kumar

et al. 2006

RNA

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The p53 tumor suppressor protein is a homotetrameric transcription factor whose gene is mutated in nearly half of all human cancers. In an unrelated screen of RNA/protein interactions using the yeast three-hybrid system, we inadvertently detected p53 interactions with several different RNAs. A literature review revealed previous reports of both sequence-specific and -nonspecific interactions between p53 and RNA. Using yeast three-hybrid selections to identify preferred RNA partners for p53, we failed to identify primary RNA sequences or obvious secondary structures required for p53 binding. The cationic p53 C-terminus was shown to be required for RNA binding in yeast. We show that while p53 strongly discriminates between certain RNAs in the yeast three-hybrid assay, the same RNAs are bound equally by p53 in vitro. We further show that the p53 RNA-binding preferences in yeast are mirrored almost exactly by a recombinant tetrameric form of the HIV-1 nucleocapsid (NC) protein thought to be a sequence-nonspecific RNA-binding protein. However, the possibility of specific RNA binding by p53 could not be ruled out because p53 and HIV-1 NC displayed certain differences in RNA-binding preference. We conclude that (1) p53 binds RNA in vivo, (2) RNA binding by p53 is largely sequence-nonspecific in the yeast nucleus, (3) some structure-specific RNA binding by p53 cannot be ruled out, and (4) caution is required when interpreting results of RNA screens in the yeast threehybrid system because sequence-dependent differences in RNA folding and display can masquerade as sequence-dependent differences in protein recognition.

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“…There are several excellent reviews regarding the topic of how proteins bind sequence specifically to single-stranded RNA (2, 30, 85) and a more recent report regarding binding to double-stranded sequences (17). Indeed, several reports in the recent literature suggest that RNA secondary structure plays an important role in binding.…”

Section: Effects Of Rna Secondary Structure On Binding Of Rna Splicinmentioning

confidence: 99%

Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process

Buratti

Baralle

2004

Molecular and Cellular Biology

380

302

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Pre-mRNA splicing in eukaryotes requires joining together the nucleotides of the various mRNA-coding regions (exons) after recognizing them from the normally vastly superior number of non-mRNA-coding sequences (introns). For three excellent reviews on general splicing and its regulation, refer to references 14, 62, and 70. In eukaryotes, the vast majority of splicing processes are catalyzed by the spliceosome, a very complex RNA-protein aggregate which has been estimated to contain several hundred different proteins in addition to five spliceosomal snRNAs (1,54,62,63,81,109). These factors are responsible for the accurate positioning of the spliceosome on the 5Ј and 3Ј splice site sequences. The reason why so many factors are needed reflects the observation that exon recognition can be affected by many pre-mRNA features such as exon length (5, 97), the presence of enhancer and silencer elements (8, 62), the strength of splicing signals (45), the promoter architecture (29,55), and the rate of RNA processivity (86). In addition, the general cellular environment also exerts an effect, as recent observations suggest the existence of extensive coupling between splicing and many other gene expression steps (69) and even its modification by external stimuli (96).In the midst of all this complexity, it has also been proposed that pre-mRNA secondary structures can potentially influence splicing activity. However, despite a steady increase of reports invoking their effects on splicing regulation, the last specific review on this subject is now more than 10 years old (3). Here, we propose to address again this specific issue in the current perspective of the general field. Before we do this, however, we have to answer a basic question. DO PRE-mRNAS PRESENT SECONDARY STRUCTURE IN VIVO?Two properties of RNA molecules cannot be denied: their natural tendency to form highly stable secondary and tertiary structures in vitro and in vivo (9, 27, 39) and the observation that alterations in these structures represent a well-known regulatory mechanism for many RNA cellular processes (60).In this particular respect, however, a question that still remains to be addressed conclusively regards the presence of secondary structures in pre-mRNAs in vivo. That this existence may not simply be taken for granted comes from early experimental evidence. In fact, it was suggested that in vitro evidence regarding the possible influence of RNA structure on splicing (94) could not be accurately reproduced in vivo (95). The reason why this should be so goes back to the classical concept that RNA is coated in vivo by proteins. In fact, heterogeneous ribonucleoprotein particles have been known since early studies and the major protein family involved, the hnRNP proteins, are very abundant in mammalian cells. These RNAprotein interactions may well prevent mRNAs from folding in stable secondary structures (34) (Fig. 1a). For this reason, it was hypothesized that, following transcription, pre-mRNA may be allowed only a very limited timespan to fold (36)....

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Recognition of double‐stranded RNA by proteins and small molecules

Cited by 56 publications

References 111 publications

Altered RNA Editing in Mice Lacking ADAR2 Autoregulation

Altered RNA Editing in Mice Lacking ADAR2 Autoregulation

Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system

Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process

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