PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “RNA, Circular”

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 19 recordsLinked to original sources
PubMed1995

Increase of satellite tobacco ringspot virus RNA initiated by inoculating circular RNA.

A small satellite RNA of tobacco ringspot virus (sTRSV RNA) generates circular and linear molecules of unit length and repetitive sequence, linear multimers during replication. The phosphodiester junction joining the unit satellite RNA sequences in multimeric and circular RNA resisted base-catalyzed cleavage in circles but not in linear dimers. We postulate that junctions of multimeric satellite RNA form during synthesis of the polyribonucleotide chain, whereas those of circular RNA result from a ligation reaction that introduces a group blocking the junction 2'-hydroxyl. To test the relative effectiveness of linear and circular satellite RNAs in initiating replication, we inoculated onto bean (Phaseolus vulgaris cv Black Valentine) the four possible pairs of satellite RNA molecules, one member of each pair having the wild-type sTRSV RNA sequence and the other that of the replicating mutant 51AG/212CU, with each sequence provided as the unit circular or linear form. The relative amounts of wild-type and mutant satellite RNA sequence recovered from progeny virions reflected their relative abundances in the inoculum without regard to whether the sequence was supplied as a linear or a circular molecule. These results are consistent with models for the replication of the satellite RNA in which a circular form of the satellite RNA is a template for rolling circle transcription or is otherwise a replication intermediate or is readily converted to an intermediate. We also show that a circular form of a nonaccumulating satellite RNA mutant induced an increase in a satellite RNA that is endogenous to some tobacco ringspot virus virion preparations, as demonstrated previously for the linear form.

Base Sequence↗
PubMed1997

Effects of nucleotide changes on the ability of hepatitis delta virus to transcribe, process, and accumulate unit-length, circular RNA.

The circular RNA genome of hepatitis delta virus (HDV) can fold into an unbranched rodlike structure. We mutagenized the two ends of this structure and assayed the effects on the ability of the genomes to replicate and accumulate processed RNA transcripts in transfected cells. The top end, defined as that nearest to the 5' end of the putative mRNA for delta antigen, was much more sensitive than the other end, defined as the bottom. Most of the 22 mutants made at the bottom were able to accumulate RNA as well as the wild type. For deletions extending as close as 2 nucleotides (nt) from the predicted domains needed for the two ribozymes, the accumulation levels dropped to <0.1%. In one mutant, 13 nt of HDV was replaced with 57 nt of non-HDV sequences, and accumulation was at 20% of the wild-type level, consistent with the potential of HDV to act as a vector. However, after replacement with a second sequence, accumulation dropped to 1%. For most of the 14 mutants made at the top of the rod, we observed dramatic inhibitory effects. For example, after removal of 3 bp from the stem adjacent to the terminal loop, accumulation dropped to <0.06% of the wild-type genome level. The top region that we considered was adjacent to both the 5' end of the putative mRNA and the domain that has been proposed to contain a promoter for RNA-directed RNA synthesis. The RNA accumulation abilities of certain mutants were tested under additional different experimental conditions. It was found that after longer times, some mutants began to catch up with the wild type. Also, it was found that certain top mutants gave much greater levels of accumulation when transfected into cells containing the small delta antigen. One interpretation of these data is that certain features at the top of the rod are needed for the accumulation of essential delta antigen mRNA species.

Animals↗
PubMed2025

A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression.

Circular RNAs (circRNAs) are essential regulators of cellular processes, but are challenging to study using traditional methods. Overexpression approaches, such as the use of linearized plasmids and viral vectors, often result in high rates of false-positive clones, where cells retain selection markers without expressing the target circRNA. This study addresses this limitation by developing a dual-selection circRNA system designed to enhance the accuracy and reliability of circRNA overexpression. Our system integrates a fluorescent reporter gene upstream of the circRNA expression cassette, under a shared promoter, and a downstream antibiotic resistance marker, allowing for both antibiotic selection and flow cytometric cell-sorting to identify and enrich cells with genuine circRNA expression. We successfully incorporated this system into an inducible lentiviral vector for controlled overexpression in various cell types. The dual-selection circRNA system offers a significant advance for circRNA research and studies of other RNA species where accurate and reliable overexpression is essential.

RNA, Circular↗
PubMed1981

The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena.

The Tetrahymena thermophila ribosomal RNA gene contains an intervening sequence (IVS), which is transcribed as part of the precursor RNA and subsequently removed by splicing. We have found previously that the IVS is excised as a 0.4 kb RNA in isolated nuclei. We now report the finding of a novel RNA molecule, which is an electrophoretic variant (EV) of this 0.4 kb IVS RNA. The EV was identified as a form of the IVS RNA by Southern hybridization, RNA fingerprinting and R-loop mapping. A pulse-chase experiment established that in vitro the excised IVS RNA is converted to the EV by a post-splicing event. This conversion is enhanced at 39 degrees C compared to 30 degrees C and is irreversible under our experimental conditions. The EV of the IVS is a circular RNA. This structure was first suggested by its anomalous electrophoretic mobility on denaturing compared to nondenaturing gels. When the EV was prepared for electron microscopy under totally denaturing conditions, 0.4 kb circular molecules were observed. Furthermore, we have converted the circular form to a linear form by limited T1 RNAase digestion. The circular RNA survived treatment with DNAase, protease, glyoxal and various denaturants, which suggests that it is a covalently closed RNA circle.

Animals↗
PubMed2026

Enhancing Lipid Nanoparticle-Mediated Circular RNA and mRNA Expression in the Placenta through Inhibition of IFNAR-JAK-STAT Signaling.

The placenta has emerged as a promising target for RNA lipid nanoparticle (LNP)-based therapies to treat obstetric complications, yet efficient extrahepatic RNA transfection remains a challenge. Here, we identify innate immune signaling as a regulator of placental RNA translation and demonstrate that inhibition of IFN-&#x3b1;/&#x3b2; receptor (IFNAR) and JAK-STAT signaling enhances LNP-mediated transgene expression in the placenta for both messenger RNA (mRNA) and circular RNA (circRNA). While a placenta-tropic LNP enabled robust and durable circRNA expression in trophoblasts in vitro, circRNA translation was substantially decreased in vivo compared to mRNA in pregnant mice. Inhibition of IFNAR-JAK-STAT signaling enhanced circRNA translation up to 12-fold in maternal organs and increased circRNA and mRNA translation in the placenta up to 17.5- and 4-fold, respectively. JAK-STAT inhibition also enhanced translation of therapeutically relevant VEGF-encoding circRNA and mRNA in pregnant mice, suggesting innate immune modulation as a broadly applicable strategy to improve RNA therapeutics during pregnancy.

Female↗
PubMed2025

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

RNA, Circular↗
PubMed1993

RNA circularization reveals terminal sequence heterogeneity in a double-stranded RNA virus.

Double-stranded RNA viruses (dsRNA), termed LRV1, have been found in several strains of the protozoan parasite Leishmania. With the aim of constructing a full-length cDNA copy of the viral genome, including its terminal sequences, a protocol based on PCR amplification across the 3'-5' junction of circularized RNA was developed. This method proved to be applicable to dsRNA. It provided a relatively simple alternative to one-sided PCR, without loss of specificity inherent in the use of generic primers. LRV1 terminal nucleotide sequences obtained by this method showed a considerable variation in length, particularly at the 5' end of the positive strand, as well as the potential for forming 3' overhangs. The opposite genomic end terminates in 0, 1, or 2 TCA trinucleotide repeats. These results are compared with terminal sequences derived from one-sided PCR experiments.

Animals↗
PubMed1992

The strands of both polarities of a small circular RNA from carnation self-cleave in vitro through alternative double- and single-hammerhead structures.

The sequence of a circular RNA from carnation has been determined and found to consist of 275 nucleotide residues adopting a branched secondary structure of minimum free energy. Both plus and minus strands of this RNA can form the hammerhead structures proposed to mediate the in vitro self-cleavage of a number of small infectious plant RNAs and the transcript of satellite 2 DNA from the newt. Minus full- and partial-length transcripts of the carnation circular RNA including the hammerhead structure showed self-cleavage during transcription and after purification, indicating the involvement of a single-hammerhead structure in the self-cleavage reaction. In the case of the plus transcripts only a dimeric RNA, but not a monomeric one, self-cleaved efficiently during transcription and after purification, strongly supporting the implication in this process of a double-hammerhead structure theoretically more stable than the corresponding single cleavage domain. However, a plus monomeric transcript self-cleaved after purification at a slow rate in a concentration-independent reaction which most probably occurs through an intramolecular mechanism. Comparative sequence analysis has revealed that the circular RNA from carnation shares similarities with some representative members of the viroid and viroid-like satellites RNAs from plants, suggesting that it is a new member of either these two groups of small pathogenic RNAs.

Base Sequence↗
PubMed1994

Synthesis of circular RNA in bacteria and yeast using RNA cyclase ribozymes derived from a group I intron of phage T4.

Studies on the function of circular RNA and RNA topology in vivo have been limited by the difficulty in expressing circular RNA of desired sequence. To overcome this, the group I intron from the phage T4 td gene was split in a peripheral loop (L6a) and rearranged so that the 3' half intron and 3' splice site are upstream and a 5' splice site and 5' half intron are downstream of a single exon. The group I splicing reactions excise the internal exon RNA as a circle (RNA cyclase ribozyme activity). We show that foreign sequences can be placed in the exon and made circular in vitro. Expression of such constructs (RNA cyclase ribozymes) in Escherichia coli and yeast results in the accumulation of circular RNA in these organisms. In yeast, RNA cyclase ribozymes can be expressed from a regulated promoter like an mRNA, containing 5' leader and 3' trailer regions, and a nuclear pre-mRNA intron. RNA cyclase ribozymes have broad application to questions of RNA structure and function including end requirements for RNA transport or function, RNA topology, efficacy of antisense or ribozyme gene control elements, and the biosynthesis of extremely long polypeptides.

Bacteriophage T4↗
PubMedDate not supplied

The hepatitis delta (delta) virus possesses a circular RNA.

Hepatitis delta (delta) virus (HDV), a satellite virus of the hepatitis B virus (HBV), causes a severe form of viral hepatitis in humans. Here we present evidence based on electron microscopy and electrophoretic behaviour that HDV contains a single stranded circular RNA molecule. This is the first animal virus identified with a circular RNA genome. Circular RNAs have only been found in plant viruses. We have obtained a partial complementary DNA clone representing approximately 25% of the total genome of HDV. Analysis of this cDNA revealed similarity to two plant viruses that may explain the origin of the virus.

Base Sequence↗
PubMed1997

Exon skipping and circular RNA formation in transcripts of the human cytochrome P-450 2C18 gene in epidermis and of the rat androgen binding protein gene in testis.

The cytochrome P-450 2C18 gene was found by reverse transcription-PCR to represent the most abundantly expressed gene of the P-450 2C subfamily in human epidermis. However, in addition to the canonical mRNA of nine exons, transcripts that have skipped exon 4 or 5, exons 4, 5, and 6, or exons 4, 5, 6, and 7 were also identified in this tissue. Remarkably, circular RNA transcripts synthesized by the joining of the donor and acceptor splice sites of the same exon were detected in human epidermis for exons 4 and 5. Moreover, molecules composed of exons 4, 5, and 6 with the donor splice site of exon 6 joined to the acceptor splice site of exon 4 or composed of exons 4, 5, 6, and 7 with the donor splice site of exon 7 joined to the acceptor splice site of exon 4 were also found to be present in this tissue. In rat testis, a similar analysis allowed the detection of a circular RNA molecule composed of exons 6 and 7 of the androgen binding protein (ABP) gene, with the donor splice site of exon 7 joined to the acceptor splice site of exon 6, and of an ABP mRNA which had skipped exons 6 and 7. These results apparently substantiate the hypothesis that alternative pre-mRNA splicing has the potential to generate not only mRNAs that lack one or more exons but also circular RNA molecules that are composed of the exons that are skipped. However, additional 2C18 circular species containing various combinations of exons were also detected in human epidermis, and an exon 6-skipped ABP mRNA molecule was identified in rat testis. This observation is interpreted as indicative that at low frequency, numerous circular RNA formation and exon skipping events may occur, allowing the joining of a variety of different combinations of exons. Moreover, the relative stability of these molecules is apparently the key factor that determines the relative ease of their detection.

Androgen-Binding Protein↗
PubMed2026

A newly established reverse genetic system for a circular RNA virus reveals new requirements for infection and its biocontrol potential.

Ambiviruses are fungal-infecting circular RNA viruses that uniquely combine viroid-like and viral features, yet the function of their conserved ORF-B protein and their effects on hosts remain unknown, hindered by the lack of a reverse genetics system. Here, we constructed the first infectious cDNA clone of an ambivirus, Fusarium graminearum ambivirus 1 (FgAV1), using a head-to-tail dimer placed downstream of a fungal promoter. FgAV1 was horizontally transmitted via hyphal anastomosis to virus-free Fusarium graminearum strains. Notably, a reverse-oriented dimer construct was also infectious and transmissible. Targeted mutagenesis revealed that both ORF-A- and ORF-B-encoded proteins and the presence of embedded ribozymes are indispensable for ambivirus replication. Our results further demonstrate that FgAV1 infection triggers a fungal RNAi response, extending the antiviral role of host sRNAs to circular RNA viruses. Furthermore, FgAV1 infection suppressed fungal growth and significantly reduced the virulence of F. graminearum on wheat. These findings provide novel insights into ambivirus replication and their potential in fungal pathogen biocontrol.

RNA Viruses↗
PubMed1997

A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities.

The sequence of 451 nucleotides of a cherry small circular RNA (csc RNA1) associated with a cherry disease has been determined. Both csc RNA1 and its complementary strand can form hammerhead structures similar to those found previously in other plant and animal small RNAs. In the branched secondary structure of lowest free energy of csc RNA1, the sequences involved in the hammerhead structures, which comprise approximately one-fourth of this RNA, are found opposite each other, forming part of a rod-like segment. Plus- and minus-strand full-length transcripts of csc RNA1 self-cleaved during transcription and after purification, as predicted by the hammerhead structures, which are stable and very probably act as single hammerhead structures. The minus-strand hammerhead structure of csc RNA1 is exceptional in having a central loop with only 11 conserved nucleotides, a situation previously observed in only one other natural hammerhead structure. Both hammerhead structures of csc RNA1 are also peculiar in having an A instead of a C preceding the self-cleavage sites. The in vivo concentration of the plus strand of csc RNA1 is only slightly higher than that of its complementary strand, and significant fractions of both strands are extracted from the tissue in the form of a complex. csc RNA1 has sequence similarities to viroids and especially to some viroid-like satellite RNAs; they also share some characteristics of their corresponding hammerhead structures with these satellite RNAs. These observations, together with the association in symptomatic tissue of csc RNA1 with a set of presumably viral double-stranded RNAs, suggest that csc RNA1 is a new viroid-like satellite RNA.

Base Sequence↗
PubMed1991

Ribonuclease T1 generates circular RNA molecules from viroid-specific RNA transcripts by cleavage and intramolecular ligation.

A 406 nucleotide long potato spindle tuber viroid (PSTVd)-specific linear RNA transcript was synthesized in vitro and subjected to limited digestion with ribonuclease (RNase) T1. Under certain conditions this guanosine-specific endoribonuclease proved to be capable of processing the longer-than-unit-length, precursor-like viroid RNA transcript by cleaving out a linear 358 nucleotide long product and ligating that to a circular RNA molecule. The new finding that RNase T1 acts as an RNA processing enzyme and, in particular, as an RNA 'circulase' can be explained by the unique structural preconditions inherent in the viroid-specific substrate and by the well characterized two-step cleavage mechanism of the enzyme. These in vitro potentials of RNase T1 suggest that also in vivo procaryotic and eucaryotic RNases with a similar reaction mechanism might not only be involved in RNA degradation and trimming, but also in processing, ligation and recombination of RNA.

Base Sequence↗
PubMed1988

Isolation of three viroids and a circular RNA from grapevines.

Analysis of nucleic acids from grapevine tissues by two-dimensional gel electrophoresis demonstrated the presence of two bands of circular RNA. The smaller RNA contained about 300 nucleotide residues and was identified as hop stunt viroid by nucleotide sequencing. The larger RNA band was a mixture of species and contained similar amounts of two components, referred to as RNA 1a and RNA 1b, and in addition a trace amount of citrus exocortis viroid (CEV) which became detectable only after inoculation of the mixture to tomato. The identity of CEV was determined by probe hybridization and nucleotide sequencing. Both RNAs 1a and 1b are distinct from CEV and have estimated sizes larger than those of CEV and other viroids reported so far. RNA 1a preparations were infectious in cucumber and in tomato and the recovered viroid had unique properties. We have provisionally named this viroid Australian grapevine viroid. Evidence for the autonomous replication of RNA 1b was not obtained.

Base Sequence↗
PubMed1998

Self-cleaving circular RNA associated with rice yellow mottle virus is the smallest viroid-like RNA.

We report the sequence, structural features, and self-cleaving activity of the small circular RNA (sc-RNA) associated with rice yellow mottle sobemovirus (RYMV). At 220 nucleotides, the RYMV sc-RNA represents the smallest naturally occurring viroid-like RNA currently documented in the literature. It is similar to other circular satellite RNAs (sat-RNAs) and viroids in being G-C-rich with a high level of self-complementarity. The predicted native structure is essentially a rod with one branched terminus. A region of the RYMV sc-RNA, constituting 24% of the sequence, exhibits 89% identity to the sat-RNA associated with the Australasian isolates of lucerne transient streak sobemovirus. This region is also structurally similar in all three RNAs in that it forms the left terminus of each rod. Dimeric runoff transcripts of cloned RYMV sc-RNA undergo efficient autocatalytic in vitro cleavage in the (+) but not the (-) polarity. Analysis of the (+) sequence indicates the presence of a hammerhead ribozyme resembling that of carnation small retroviroid-like RNA and the genomic satellite transcript of newt. Inefficient cleavage of (+) monomeric transcripts, and a short stem III in the hammerhead, are features consistent with a double-hammerhead mode of self-cleavage. The presence of sat-RNA and retroviroid-like structures within a single RNA suggests a possible role for the RYMV sc-RNA as an evolutionary intermediate between these subviral RNAs.

Base Sequence↗
PubMed1998

The mouse formin (Fmn) gene: abundant circular RNA transcripts and gene-targeted deletion analysis.

BACKGROUND: Mutations in the mouse formin (Fmn) gene result in limb deformities and incompletely penetrant renal aplasia. A molecular genetic approach was taken to characterize novel circular RNAs from the Fmn gene and to understand the developmental effects of gene-targeted mutations. MATERIALS AND METHODS: RT-PCR and ribonuclease protection analyses were done to characterize the circular RNA transcripts arising from the Fmn gene. Two lines of mice with gene-targeted deletions of specific Fmn exons, namely exon 4 or exon 5, were generated and analyzed. RESULTS: In our analysis of formin cDNAs, we discovered a class of transcripts in which the exon order is reversed such that downstream exons are joined to the acceptor end of a specific exon that lies 5' to them in the genome. RT-PCR and ribonuclease protection analyses indicate that these transcripts are circular and are the major transcripts arising from this locus in adult brain and kidney. To gain insight into the biological function of these transcripts, we have systematically deleted the relevant exons using gene-targeted homologous recombination. The resulting mice fail to produce circular transcripts, but appear to produce normal amounts of the linear RNA isoforms from this locus. While these deficient mice have normal limbs, they display variably penetrant renal aplasia characteristic of other mutant formin alleles. CONCLUSIONS: Our results demonstrate novel circular transcripts arising from the Fmn gene. Moreover, their high levels of expression suggest that they are not products of aberrant splicing events, but instead, may play important biological roles. Mice with gene-targeted deletions of Fmn exons 4 or 5 lack these circular transcripts and have an incompletely penetrant renal agenesis phenotype. While the biologic function of circular Fmn RNA transcripts is not entirely known, our work suggests their possible involvement in kidney development.

Animals↗