PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “RNA Editing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 721 records · Page 40Linked to original sources

ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells.

Double-stranded RNA induces the homology-dependent degradation of cognate mRNA in the cytoplasm via RNA interference (RNAi) but also is a target for adenosine-to-inosine (A-to-I) RNA editing by adenosine deaminases acting on RNA (ADARs). An interaction between the RNAi and the RNA editing pathways in Caenorhabditis elegans has been suggested recently, but the precise mode of interaction remains to be established. In addition, it is unclear whether this interaction is possible in mammalian cells with their somewhat different RNAi pathways. Here we show that ADAR1 and ADAR2, but not ADAR3, avidly bind short interfering RNA (siRNA) without RNA editing. In particular, the cytoplasmic full-length isoform of ADAR1 has the highest affinity among known ADARs, with a subnanomolar dissociation constant. Gene silencing by siRNA is significantly more effective in mouse fibroblasts homozygous for an ADAR1 null mutation than in wild-type cells. In addition, suppression of RNAi effects are detected in fibroblast cells overexpressing functional ADAR1 but not when overexpressing mutant ADAR1 lacking double-stranded RNA-binding domains. These results identify ADAR1 as a cellular factor that limits the efficacy of siRNA in mammalian cells.

Adenosine Deaminase↗

A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains.

Members of the double-stranded RNA- (dsRNA) specific adenosine deaminase gene family convert adenosine residues into inosines in dsRNA and are involved in A-to-I RNA editing of transcripts of glutamate receptor (GluR) subunits and serotonin receptor subtype 2C (5-HT(2C)R). We have isolated hADAR3, the third member of this class of human enzyme and investigated its editing site selectivity using in vitro RNA editing assay systems. As originally reported for rat ADAR3 or RED2, purified ADAR3 proteins could not edit GluR-B RNA at the "Q/R" site, the "R/G" site, and the intronic "hot spot" site. In addition, ADAR3 did not edit any of five sites discovered recently within the intracellular loop II region of 5-HT(2C)R RNAs, confirming its total lack of editing activity for currently known substrate RNAs. Filter-binding analyses revealed that ADAR3 is capable of binding not only to dsRNA but also to single-stranded RNA (ssRNA). Deletion mutagenesis identified a region rich in arginine residues located in the N-terminus that is responsible for binding of ADAR3 to ssRNA. The presence of this ssRNA-binding domain as well as its expression in restricted brain regions and postmitotic neurons make ADAR3 distinct from the other two ADAR gene family members, editing competent ADAR1 and ADAR2. ADAR3 inhibited in vitro the activities of RNA editing enzymes of the ADAR gene family, raising the possibility of a regulatory role in RNA editing.

Adenosine Deaminase↗

Intracellular localization of differentially regulated RNA-specific adenosine deaminase isoforms in inflammation.

Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional process that amplifies the repertoire of protein production. Recently, the induction of this process through up-regulation of the editing enzyme RNA-specific adenosine deaminase 1 (ADAR1) was documented during acute inflammation. Here we report that the inflammation-induced up-regulation of ADAR1 involves differential production and intracellular localization of several isoforms with distinct RNA-binding domains and localization signals. These include the full-length ADAR1 (p150) and two functionally active short isoforms (p80 and p110). ADAR1 p80 starts at a methionine 519 (M519) due to alternative splicing in exon 2, which deletes the putative nuclear localization signal, the Z-DNA binding domain, and the entire RNA binding domain I. ADAR1 p110 is the mouse homologue of the human ADAR1 110-kDa variant (M246), which retains the second half of the Z-DNA binding domain, all RNA binding domains, and the deaminase domain. Additional variations are found in the third RNA binding domain of ADAR1; they are differentially regulated during inflammation, generating isoforms with different levels of activities. Studies in several cell types transfected with ADAR1-EGFP chimeras demonstrated that the p150 and p80 variants are localized in the cytoplasm and nucleolus, respectively. In agreement with this observation, endogenous ADAR1 was identified in the cytoplasm and nucleolus of mouse splenocytes and HeLa cells. Since the ADAR1 variants are differentially regulated during acute inflammation, it suggests that the localization of these variants and of A-to-I RNA editing in the cytoplasm, nucleus, and nucleolus is intracellularly reorganized in response to inflammatory stimulation.

Adenosine↗

[Advances in molecular parasitology].

Recent studies on molecular biology of parasites revealed novel mechanisms for the control of expression of parasitic genes. In trypanosomatid protozoa, unusual characteristics of gene regulation, including polycistronic transcription, trans-RNA splicing and RNA editing have been discovered. This review describes the recent progress of RNA editing in trypanosomes, and trans-splicing in both trypanosomes and nematodes. Studies of the editing of mRNAs in trypanosomatid mitochondria indicate the involvement of small guide RNA molecules, which are encoded in the minicircles and/or maxicircles of kinetoplast DNA. A proposed transesterification model for RNA editing suggests an analogous reaction between RNA editing and RNA splicing. In addition, the development of stable transfection system and success of homologous gene targeting in Trypanosoma and Leishmania are reported.

Animals↗

Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition.

RNA editing has been described for organellar genes of protozoa and plants as well as in three cases for nuclear transcripts of mammals. The mitochondrial tRNA for aspartic acid is encoded in the mitochondrial genome of marsupials with the anticodon GCC. However, cDNA from the gene product revealed that the second nucleotide of the anticodon of the tRNA is posttranscriptionally changed to be recognized as an uridine residue. This restores the coding property of the tRNA. Direct sequencing as well as clones of the amplified cDNA indicated that about 50% of the cellular pool of pre-tRNA molecules for aspartic acid is edited. Thus, RNA editing occurs in mammalian mitochondria and can affect the anticodons of tRNAs.

Animals↗

Thyroid hormone regulates hepatic triglyceride mobilization and apolipoprotein B messenger ribonucleic Acid editing in a murine model of congenital hypothyroidism.

Thyroid hormone modulates the expression of numerous genes that in turn regulate lipoprotein metabolism in vivo. We have examined the thyroid hormone-dependent regulation of apolipoprotein B (apoB) RNA editing in a strain of congenitally hypothyroid mice (Pax8(-/-)) that lacks thyroid follicular cells. Neonatal Pax8(-/-) mice demonstrate an approximately 10-fold increase in hepatic triglyceride content associated with a decrease in hepatic apoB RNA editing. Thyroid hormone administration resulted in hepatic triglyceride mobilization in conjunction with an increase in hepatic, but not intestinal, apoB RNA editing and without changing total apoB RNA abundance. ApoB RNA editing is mediated by a multicomponent enzyme complex whose catalytic core contains two proteins, apobec-1 and apobec-1 complementation factor (ACF). Hepatic ACF mRNA and protein abundance decreased in Pax8(-/-) mice, with restoration after thyroid hormone administration, whereas apobec-1 mRNA and protein abundance were unchanged. Immunohistochemical analysis revealed increased staining intensity of ACF within hepatocyte nuclei of treated mice, findings confirmed by Western analysis of isolated nuclei. In vitro RNA editing assays demonstrated that supplementation with recombinant ACF alone restored enzymatic activity of S100 extracts from hypothyroid, Pax8(-/-) mice. These data demonstrate that thyroid hormone modulates murine hepatic lipoprotein metabolism in association with tissue-specific effects on apoB RNA editing mediated through alterations in ACF gene expression.

APOBEC-1 Deaminase↗

Widespread inosine-containing mRNA in lymphocytes regulated by ADAR1 in response to inflammation.

Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification of pre-mRNA catalysed by an RNA-specific adenosine deaminase (ADAR). A-to-I RNA editing has been previously reported in the pre-mRNAs of brain glutamate and serotonin receptors and in lung tissue during inflammation. Here we report that systemic inflammation markedly induces inosine-containing mRNA to approximately 5% of adenosine in total mRNA. Induction was the result of up-regulation of A-to-I RNA editing as both dsRNA editing activity and ADAR1 expression were increased in the spleen, thymus and peripheral lymphocytes from endotoxin-treated mice. Up-regulation of ADAR1 was confirmed in vitro in T lymphocytes and macrophages stimulated with a variety of inflammatory mediators including tumour necrosis factor-alpha and interferon-gamma. A late induction of RNA editing was detected in concanavalin A-activated splenocytes stimulated with interleukin-2 in vitro. Taken together, these data suggest that a large number of inosine-containing mRNAs are produced during acute inflammation via up-regulation of ADAR1-mediated RNA editing. These events may affect the inflammatory and immune response through modulation of protein production.

Acute Disease↗

Apobec-1 and apolipoprotein B mRNA editing.

Apolipoprotein (apo)B mRNA editing is a novel mechanism for the post-transcriptional regulation of gene expression in mammals. It consists of a C-->U conversion of the first base of the codon CAA, encoding glutamine-2153, to UAA, an in-frame stop codon, in apoB mRNA. Since its initial description in 1987, substantial progress has been made in the last few years on the mechanism of editing. Apobec-1, the catalytic component of the apoB mRNA editing enzyme complex, has been cloned. This article begins with an overview of the general biology of apoB mRNA editing. It then provides an in-depth analysis of the structure, evolution and possible mechanism of action of apobec-1. ApoB mRNA editing is the prototype of RNA editing in mammals. What we learn from apoB mRNA editing will be useful in our understanding of other examples of RNA editing in vertebrates which are being described with increasing frequency.

APOBEC-1 Deaminase↗

Editing of human alpha-galactosidase RNA resulting in a pyrimidine to purine conversion.

During a study of the gene coding for alpha-galactosidase (EC 3.2.1.22), the lysosomal enzyme deficient in Fabry's disease, RT-PCR amplification of alpha-galactosidase mRNAs obtained from three different tissues isolated from males revealed a substantial number of clones with a U to A conversion at the nucleotide position 1187. Such a modification of the coding sequence would result in an amino acid substitution in the C-terminal region (Phe396Tyr) of the enzyme. Neither PCR analysis of the genomic sequence nor the RT-PCR amplification of RNA obtained by in vitro transcription of the wild-type cDNA showed this change in the sequence. Multiple genes, pseudogenes are allelic variants were excluded. Hence, we propose RNA editing as a mechanism responsible for this base change in the alpha-galactosidase RNA.

Base Sequence↗

Apolipoprotein B: from editosome to proteasome.

Apolipoprotein (apo) B, the protein component of low-density lipoproteins (LDLs), has been under intense investigation for the last three decades. During the first decade after its initial description, most reports dealt with the physical-chemical characterization of apoB in its natural environment (i.e., intact LDL particles). A few studies dealing with attempts to elucidate the primary structure of apoB were published at this time (Deutsch et al., 1978; Bradley et al., 1980). However, most of these, in retrospect, represented heroic efforts that were doomed to failure because of the huge size and insoluble nature of apoB, once it is separated from its lipid environment. Indeed, during the 1970s, there was no universal agreement on the true molecular weight of the protein, which was not established until sometime into the second decade of apoB research (Yang et al., 1986b). The next 10 years were punctuated by breakthroughs on three different fronts in our understanding of apoB. The first exciting discovery was that apoB exists in two forms, apoB-100 and apoB-48 (Kane et al., 1980; Elovson et al., 1981). The next breakthrough was the elucidation of the primary structure of apoB-100 by a combination of cDNA cloning (Chen et al., 1986; Knott et al., 1986; Yang et al., 1986a) and direct peptide sequencing (Yang et al., 1986a, 1989). This decade of renaissance in apoB research was concluded by the elucidation of the structure of apoB-48. More important in terms of basic cellular molecular biology was the discovery of RNA editing, when apoB-48 was found to be the translation product of an edited apoB mRNA (Chen et al., 1987; Powell et al., 1987). RNA editing had just been described for a kinetoplastid protozoa the year before (Benne et al., 1986). ApoB mRNA editing was the first instance of RNA editing described in a higher eukaryote (Chan and Seeburg, 1995; Grosjean and Benne. 1998). The last decade, which brings us to the present, has been marked by studies that benefited from the breakthroughs of the 1980s. which enabled many different laboratories to examine various aspects of apoB structure, function, and expression. The function of apoB in vivo was analyzed in different animal models (e.g., transgenic animals that overexpress apoB) (Linton et al., 1993; Callow and Rubin, 1995; Veniant et al., 1997) and in knockout animals that have no functional apoB (Farese et al., 1995,1996; Huang et al., 1995,1996). Furthermore, the structure-function relationship of apoB has been investigated in mice that express site-specific apoB mutants (Callow and Rubin, 1995; Veniant et al., 1997: Borén et al., 1998). A breakthrough in a related area led to the identification and cloning of microsomal triglyceride transfer protein (MTP) (Wetterau and Zilversmitt, 1984: Wetterau et al., 1992; Sharp et al., 1993) and the demonstration that MTP is essential for apoB production (Gordon et al., 1994; Leiper et al., 1994). The absence of MTP was found to lead to the complete degradation of apoB, which harks back to an observation in 1987 that, even in the presence of MTP, a substantial proportion of newly synthesized apoB-100 undergoes intracellular degradation before secretion (Borchardt and Davis, 1987). Indeed, the intracellular degradation of apoB-100 is the major determinant of its production rate from the liver, since the transcription of apoB appears to be constitutive and not subject to much regulation (Pullinger et al., 1989). It was in 1996, almost a decade after the first description of apoB's destruction inside the cell, that the proteasome-ubiquitin pathway was found to be the major mechanism for the intracellular degradation of apoB-100 (Yeung et al., 1996). Another important development within the last decade was the cloning of APOBEC-1, the catalytic subunit of the apoB mRNA editing complex (editosome) (Teng et al., 1993). This chapter will review some of the major landmarks in apoB research in the last 10 to 15 years, concentrating mainl

APOBEC-1 Deaminase↗

Mutations at specific atp6 codons which cause human mitochondrial diseases also lead to male sterility in a plant.

Defects in the human mitochondrial genetic system result in some diseases. These disorders are the result of rearrangements or point mutations in mitochondrial genes. In higher plants mutations and rearrangements in the mitochondrial DNA are believed to cause cytoplasmic male sterility (CMS), a mitochondrially inherited inability to produce viable pollen. In sorghum, formation of CMS is strongly correlated with anther-specific loss of mitochondrial atp6 RNA editing. Here we show that this loss of atp6 RNA editing mimics point mutations at codons that cause severe disorders in humans. We conclude that (i) loss of RNA editing in sorghum anthers probably causes CMS, (ii) similarities exist in the onset of mitochondrial dysfunction in plant and human tissues, and (iii) the evolutionary appearance of RNA editing provided a mechanism to compensate for otherwise lethal point mutations.

Amino Acid Sequence↗

Trypanosoma brucei RBP16 is a mitochondrial Y-box family protein with guide RNA binding activity.

Trypanosoma brucei mitochondria possess a unique mechanism of mRNA maturation called RNA editing. In this process, uridylate residues are inserted and deleted posttranscriptionally into pre-mRNA to create translatable messages. The genetic information for RNA editing resides in small RNA molecules called guide RNAs (gRNAs). Thus, proteins in direct contact with gRNA are likely to catalyze or influence RNA editing. Herein we characterize an abundant gRNA-binding protein from T. brucei mitochondria. This protein, which we term RBP16 (for RNA-binding protein of 16 kDa), binds to different gRNA molecules. The major determinant of this interaction is the oligo(U) tail, present on the 3'-ends of gRNAs. RBP16 forms multiple, stable complexes with gRNA in vitro, and immunoprecipitation experiments provide evidence for an association between RBP16 and gRNA within T. brucei mitochondria. Mature RBP16 contains a cold shock domain at the N terminus and a C-terminal region rich in arginine and glycine. The presence of the cold shock domain places RBP16 as the first organellar member of the highly conserved Y-box protein family. The arginine and glycine rich C terminus in combination with the cold shock domain predicts that RBP16 will be involved in the regulation of gene expression at the posttranscriptional level.

Amino Acid Sequence↗

Identification and regulation of protein components of the apolipoprotein B mRNA editing enzyme. A complex event.

Apolipoprotein B (apoB) gene expression is regulated by transcriptional, posttranscriptional, and translational mechanisms in both small intestinal enterocytes and hepatocytes of all mammals. This review focuses on the posttranscriptional regulation of apoB gene expression-specifically, an enzymatic modification to the nuclear transcript referred to as C to U RNA editing. C to U RNA editing, the process responsible for the production of apoB-48, is an exquisitely precise process that targets a single nucleotide in over 14,000. RNA editing requires regulated interactions between core enzyme components whose identity is known and regulatory factors, most of which have yet to be fully characterized. This review summarizes information relevant to those transacting factors that are essential for editing activity (core factors) as well as those interacting partners (regulatory factors) whose physiological role in RNA editing is yet to be fully defined.

APOBEC-1 Deaminase↗

Purification of a functional enzymatic editing complex from Trypanosoma brucei mitochondria.

Kinetoplastid mitochondrial RNA editing, the insertion and deletion of U residues, is catalyzed by sequential cleavage, U addition or removal, and ligation reactions and is directed by complementary guide RNAs. We have purified a approximately 20S enzymatic complex from Trypanosoma brucei mitochondria that catalyzes a complete editing reaction in vitro. This complex possesses all four activities predicted to catalyze RNA editing: gRNA-directed endonuclease, terminal uridylyl transferase, 3' U-specific exonuclease, and RNA ligase. However, it does not contain other putative editing complex components: gRNA-independent endonuclease, RNA helicase, endogenous gRNAs or pre-mRNAs, or a 25 kDa gRNA-binding protein. The complex is composed of eight major polypeptides, three of which represent RNA ligase. These findings identify polypeptides representing catalytic editing factors, reveal the nature of this approximately 20S editing complex, and suggest a new model of editosome assembly.

Animals↗

Advances in Precision Editing Therapies for Alpha-1 Antitrypsin Deficiency.

Genome and RNA editing modalities have revolutionized precision gene therapy, offering a safer alternative to traditional gene replacement approaches. Alpha-1 antitrypsin deficiency (AATD) is a compelling model for precision medicine because the disease mechanism is well defined-mutations in a single gene are responsible for both liver and lung pathology. In this review, we summarize the current preclinical and clinical efforts for AATD, with an emphasis on genome and RNA editing strategies.

Humans↗

Opposing effects of polyadenylation on the stability of edited and unedited mitochondrial RNAs in Trypanosoma brucei.

Mitochondrial RNAs in Trypanosoma brucei undergo posttranscriptional RNA editing and polyadenylation. We previously showed that polyadenylation stimulates turnover of unedited RNAs. Here, we investigated the role of polyadenylation in decay of edited RPS12 RNA. In in vitro turnover assays, nonadenylated fully edited RNA degrades significantly faster than its unedited counterpart. Rapid turnover of nonadenylated RNA is facilitated by editing at just six editing sites. Surprisingly, in direct contrast to unedited RNA, turnover of fully edited RNA is dramatically slowed by addition of a poly(A)20 tail. The same minimal edited sequence that stimulates decay of nonadenylated RNA is sufficient to switch the poly(A) tail from a destabilizing to a stabilizing element. Both nucleotide composition and length of the 3' extension are important for stabilization of edited RNA. Titration of poly(A) into RNA degradation reactions has no effect on turnover of polyadenylated edited RNA. These results suggest the presence of a protective protein(s) that simultaneously recognizes the poly(A) tail and small edited element and which blocks the action of a 3'-5' exonuclease. This study provides the first evidence for opposing effects of polyadenylation on RNA stability within a single organelle and suggests a novel and unique regulation of RNA turnover in this system.

Animals↗

Specific cleavage of pre-edited mRNAs in trypanosome mitochondrial extracts.

RNA editing in Trypanosoma brucei is a posttranscriptional processing event that results in the addition and deletion of uridine residues within several mitochondrial mRNAs. We have examined reactions involving pre-edited precursor RNAs in vitro. In this study, we report specific cleavage of pre-edited cytochrome b (CYb), cytochrome oxidase subunit II (COII), and cytochrome oxidase subunit III (COIII) mRNAs when incubated with T. brucei mitochondrial extracts. The pre-edited CYb RNA was cleaved near the 3'-most uridine addition sites, within the region where editing would be expected to commence. Pre-edited COII mRNA was similarly cleaved adjacent to its small editing domain, while pre-edited COIII RNA was cleaved at multiple sites in the region where uridine addition and deletion occurs in vivo. In contrast, edited versions of CYb, COII, and COIII RNAs were not cleaved within the editing domains. Such differential cleavage of the edited and pre-edited forms of these mRNAs suggests either a direct involvement in RNA editing or involvement in another aspect of mitochondrial gene expression requiring cleavage of pre-edited RNAs.

Animals↗

Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem.

Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.

Acylation↗