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At least 721 records · Page 40Linked to original sources
PubMed1997

The complete sequence of the genomic RNAs of spinach latent virus.

We describe the sequence for the complete genome of spinach latent virus (SpLV). Comparisons of this genome with that of the only other complete genome described for a species within the genus Ilarvirus (citrus leaf rugose virus-CiLRV) indicate that while there are marked differences between the RNA 3 of the two viruses, their respective RNAs 1 and 2 share many similarities. However, the putative 2a protein of SpLV contains a C2H2 type "zinc finger"-like motif located towards the carboxy terminal of the protein which is absent in CiLRV and has not been reported for other members of the family Bromoviridae. A second open reading frame (2b), located at a similar position to that described for the cucumoviruses, occurs in the RNA 2 of both SpLV and CiLRV. The putative coat protein of SpLV is similar to that of citrus variegation virus (CVV) and asparagus virus 2 (AV-2), both members of subgroup 2 of the ilarviruses. We have subsequently demonstrated a serological relationship between SpLV and other viruses in subgroup 2 and suggest that SpLV should be included in this subgroup rather than remain in a separate group (subgroup 6). However, while the putative movement protein of SpLV is remarkably similar to that of AV-2, it shows little relationship with the corresponding protein of CVV and the lack of similarity suggests that a recombination event may have occurred in the past. The relationship between the genera Alfamovirus and Ilarvirus is discussed in the light of the data for the genome of SpLV and recently published information for other members of the genus Ilarvirus.

Amino Acid Sequence↗
PubMed1999

The nucleotide sequence of a chinese isolate of wheat yellow mosaic virus and its comparison with a Japanese isolate. Brief report.

The nucleotide sequences of wheat yellow mosaic virus isolated in China were determined and compared with a Japanese isolate of the same virus. Results showed that the viral genome had 7629 nucleotides for RNA1 and 3639 nucleotides for RNA2, which shared 97. 1% and 94.6% of identities to the RNAs of Japanese isolate. The single open reading frames in RNA1 and RNA2 encoded polyproteins with 2407 amino acids and 903 amino acids respectively, from which ten proteins may be produced by autolytic cleavage processing as the Japanese isolate. Since the sequence of WYMV RNA1 showed identity of less than 70% with that of WSSMV, it is further confirmed that WYMV is a distinct species within Bymovirus.

Base Sequence↗
PubMed2003

A novel splice site mutation in neonatal carnitine palmitoyl transferase II deficiency.

Mitochondrial beta-oxidation of long-chain fatty acids requires the concerted action of three tightly integrated membrane-bound enzymes (carnitine palmitoyltransferase I and II and carnitine/acylcarnitine translocase) that transport them into mitochondria. Neonatal onset of carnitine palmitoyltransferase II (CPT II) deficiency is an autosomal recessive, often lethal disorder of this transport. We describe a novel splice-site mutation in the CPT II gene, found in a Moroccan family, of which four out of five children have died from the neonatal form of CPT II deficiency. Mutation detection studies at the mRNA level in the CPT II gene implied that the affected children were homozygous for the previously reported 534T insertion followed by a 25-bp deletion (encompassing bases 534-558). Studies of genomic DNA, however, revealed all patients to be compound heterozygous for this 534T ins/del 25 mutation, and for a new g-->a splice-site mutation in the splice-acceptor site of intron 2. Because of these findings, prenatal diagnosis was performed in chorionic villi of three new pregnancies. This did not reveal new compound heterozygous genotypes, and, after uneventful pregnancies, all children appeared to be healthy. The new mutation is the first splice-site mutation ever identified in CPT II deficiency. The fact that it was not discovered in the patient's cDNA makes this study another example of the incompleteness of mutation detection at the mRNA level in cases where a mutation leads to aberrant splicing or nonsense-mediated messenger decay.

Carnitine O-Palmitoyltransferase↗
PubMed1993

A procedure for the isolation of specific point mutants of influenza virus.

Procedures were developed for the screening and isolation of RNA viruses that vary from the consensus population by a single point mutation and are present in low abundance. We tested these procedures using a mixture of the vaccine donor line cold-adapted (ca) B/Ann Arbor/1/66 and its wild type (wt) progenitor at a ratio of 1,000:1. A 13-mer oligodeoxynucleotide was prepared as a [32P]-radiolabeled probe which specifically hybridized to wt viral RNA (vRNA) at a region that varied between the ca and wt sequence by a single base at position 1,320 of the PA gene. This probe was able to detect as little as 88 pg of total wt vRNA blotted to nitrocellulose, while giving no positive signal with as much as 1 microgram of total ca vRNA. We were able to isolate virus containing the wt PA gene sequence from the mixed pool of ca and wt viruses by two successive rounds of amplification in embryonated eggs inoculated with a controlled number of infectious virions. During each round of amplification the abundance of the virus containing the wt PA gene sequence was increased about ten-fold. Once a relative abundance of 1:10 was reached, the virus was cloned by plaquing in Madin-Darby canine kidney cells. These procedures, which allow the isolation of specific point mutants, utilize no selective pressure conditions and are suitable for analyzing the phenotypic importance of known mutations in biologically important viruses.

Animals↗
PubMed1992

A cis-acting element within the hepatitis A virus 5'-non-coding region required for in vitro translation.

Every picornavirus studied thus far has a sequence within the 5'-non-coding region that is required for internal ribosome binding and translation of the polyprotein. In an attempt to identify this region in hepatitis A virus we constructed a truncated hepatitis A virus (HAV) cDNA clone that contains the entire 736 bp 5' non-coding region (5'-NCR) and 754 base pairs of the viral capsid coding region (P1) under control of the SP6 promoter. In vitro transcription and translation of this transcript in a rabbit reticulocyte lysate yielded a protein product of about 29 kDa as analyzed by autoradiography following sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). A series of mutations of this construct have defined a minimal sequence between bases 347 and 734 in the 5'-NCR that is required for efficient in vitro translation. The deleted constructs (D 523-734 and D 632-734) showed a reduced ability to translate in the rabbit reticulocyte lysate system in comparison with the full-length 5'-NCR construct, pH1489. The translation of these deleted constructs was artificially restored by the addition of a 5'-terminal methylated cap structure, m7GpppG, to the RNA. This increase in translational efficiency could be competed away with cap analog (m7GDP) thus indicating that this region is required for cap-independent internal ribosome binding for HAV translation.

Base Sequence↗
PubMed2006

Comparison of test systems for RNAinterference.

RNAinterference (RNAi) has developed within a short time from an area of basic research occupied by a few experts to a widely used technical tool for reverse genetics, which is expected to have a broad utility not only in research, but also in medical and diagnostic applications. Despite its widespread use, the application of RNAi is often hampered because a difference of only a few nucleotides in the sequence of the target RNA can change the efficiency of a small interfering RNA (siRNA) from high to zero, and publicly available design tools for siRNAs are not yet perfect. We therefore developed and compared RNAi test systems based on different promoters, reporters, and target sequences. Here, we show that fluorescence-based test systems have obvious disadvantages compared to luciferase-based test systems and that some combinations of promoter, reporter, and target sequences, although currently in use, are not well suited for testing RNAi effects.

Base Sequence↗
PubMed2006

LoPPS: a long PCR product sequencing method for rapid characterisation of long amplicons.

Here, we propose an optimised protocol (LoPPS, long PCR product sequencing) which allows the fast, cost-attractive, and high-throughput sequencing of long PCR products. LoPPS constitutes an alternative to the primer-walking technology which is expensive and time consuming but remains the current standard procedure. It is based on the ultrasonic shearing, polishing, and cloning of PCR or RT-PCR products and is compatible with 96- or 384-well microplate systems in which bacterial growth, preparation of plasmid DNA, and sequencing can be automated. We present results obtained from 24 different RT-PCR products (2.5-4.8 kbp long) obtained from various RNA viruses and fully sequenced using LoPPS. The method proved to be robust and fast. It was successfully used on a low amount of DNA and allowed each target nucleotide position to be controlled twice or more, with a final cost which is one-third of that of primer-walking.

DNA↗
PubMedDate not supplied

Identification of new small non-coding RNAs from tobacco and Arabidopsis.

Small non-coding RNAs (ncRNAs) have typically been searched in fully sequenced genomes using one of two approaches-experimental or computational. We developed a mixed method, using both types of information, which has the advantage of applying bio-computing methods to actually expressed sequences. Our method allowed the identification of new small ncRNAs in Arabidopsis thaliana and in the unfinished genome of Nicotiana tabacum. We constructed a N. tabacum cDNA library from small RNAs ranging from 20 to 30 nucleotides (nt). The sequences from 73 unique clones were compared to the A. thaliana genome and to all plant sequences using a pattern-matching approach (program Patbank). Thus, we selected 15 clones from the library corresponding mostly to A. thaliana or N. tabacum non-coding sequences. By Northern blot analyses, we confirmed the presence of most RNA candidates in Arabidopsis and in Nicotiana sylvestris with a size range of 21-100 nt. To gain more insight into the possible genesis of 21-24 nt sequences, stable folding of sRNAs with their flanking regions were predicted with the software MIRFOLD dedicated to the folding of microRNAs (miRNA). Stable hairpins structures were observed for some putative miRNAs.

Arabidopsis↗
PubMed2005

Linear indices of the 'macromolecular graph's nucleotides adjacency matrix' as a promising approach for bioinformatics studies. Part 1: prediction of paromomycin's affinity constant with HIV-1 psi-RNA packaging region.

The design of novel anti-HIV compounds has now become a crucial area for scientists around the world. In this paper a new set of macromolecular descriptors (that are calculated from the macromolecular graph's nucleotide adjacency matrix) of relevance to nucleic acid QSAR/QSPR studies, nucleic acids' linear indices. A study of the interaction of the antibiotic Paromomycin with the packaging region of the HIV-1 psi-RNA has been performed as example of this approach. A multiple linear regression model predicted the local binding affinity constants [Log K (10(-4) M(-1))] between a specific nucleotide and the aforementioned antibiotic. The linear model explains more than 87% of the variance of the experimental Log K (R = 0.93 and s = 0.102 x 10(-4) M(-1)) and leave-one-out press statistics evidenced its predictive ability (q2 = 0.82 and s(cv) = 0.108 x 10(-4) M(-1)). The comparison with other approaches (macromolecular quadratic indices, Markovian Negentropies and 'stochastic' spectral moments) reveals a good behavior of our method.

Anti-Bacterial Agents↗
PubMed2011

Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.

Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, Xiphophorus maculatus and Xiphophorus couchianus, and their F(1) interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈5-10 million years ago, were identified about every 700 bp. Using 6524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F(1) interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the in silico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F(1) interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression.

Alleles↗
PubMed2006

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.

We sequenced approximately 400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV-primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs).

Animals↗
PubMed2006

Sweating the small stuff: microRNA discovery in plants.

The class of small RNAs known as microRNAs (miRNAs) has a demonstrated role in the negative regulation of gene expression in both plants and animals. These small molecules have been shown to play a critical role in a wide range of developmental and physiological pathways. Although hundreds of different miRNAs have now been identified using cloning and computational approaches, characterization of their targets and biological roles has been more limited. New sequencing technologies promise to accelerate the sequencing of small RNAs and additional genetic and genomic strategies are being applied to assess their regulatory function on RNA targets. These technologies will enable the identification of large numbers of small RNAs from diverse species, and comparative genomics approaches based on these data are likely to identify additional miRNAs. Combined with bioinformatics and experimental approaches to separate miRNAs from short-interfering RNAs (siRNAs), the pace of miRNA discovery is likely to accelerate, leading to an improved understanding of miRNA function and biological significance.

MicroRNAs↗
PubMed2005

On realizing shapes in the theory of RNA neutral networks.

It is known (Reidys et al., 1997b. Bull. Math. Biol. 59(2), 339-397) that for any two secondary structures S,S' there exists an RNA sequence compatible with both, and that this result does not extend to more than two secondary structures. Indeed, a simple formula for the number of RNA sequences compatible with secondary structures S,S' plays a role in the algorithms of Flamm et al. (2001. RNA 7, 254-265) and of Abfalter et al. (2003. Proceedings of the German Conference on Bioinformatics, ) to design an RNA switch. Here we show that a natural extension of this problem is NP-complete. Unless P=NP, there is no polynomial time algorithm, which when given secondary structures S1,...,S(k), for k4, determines the least number of positions, such that after removal of all base pairs incident to these positions there exists an RNA nucleotide sequence compatible with the given secondary structures. We also consider a restricted version of this problem with a "fixed maximum" number of possible stars and show that it has a simple polynomial time solution.

Algorithms↗
PubMed2004

AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation.

Deleterious 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions are introduced into nucleic acids by methylating agents. It was recently demonstrated that the E. coli AlkB protein and a human homolog, hABH3, can demethylate these lesions both in DNA and RNA. To elucidate the biological significance of the RNA repair, we have tested whether such repair can rescue the function of chemically methylated RNA. We demonstrate that a methylation-induced block in translation of an mRNA can be readily relieved by treatment with AlkB and hABH3 prior to translation. Furthermore, we show that chemical methylation of tRNAPhe inhibits aminoacylation and translation, but that the inhibition can be reversed by AlkB and hABH3. AlkB-mediated repair of 1-meA in tRNA was also observed in E. coli in vivo. Our data demonstrate that AlkB proteins can mediate functional recovery of RNA exposed to methylation damage, supporting the notion that RNA repair is important.

AlkB Homolog 1, Histone H2a Dioxygenase↗
PubMed2006

The receptor for branch-site docking within a group II intron active site.

The distinguishing feature of group II introns, and the property that links them with spliceosomal catalysis, is their ability to undergo splicing through branching. In this reaction, the 2'-hydroxyl group of a specific adenosine within intron domain 6 serves as the nucleophile for attack on the 5' splice site. We know less about branching than any other feature of group II intron catalysis, largely because the receptor structure for activating the branch site is unknown. Here, we identify the intronic region that binds the branch site of a group IIB intron. Located in domain 1, close to receptors for intron domain 5 and both splice sites, we demonstrate that the branch-site receptor is a functional element required for transesterification. Furthermore, we show that crosslinked branch sites can carry out both steps of splicing, suggesting that the conformational state of the intron core is set early and that it persists throughout the entire splicing process.

Binding Sites↗
PubMed2004

Evidence for codon bias selection at the pre-mRNA level in eukaryotes.

We investigated codon usage patterns across eukaryotic exons. We have shown that in humans codon preference varies with distance from the splice sites. This is consistent with the distribution of RNA elements involved in splicing regulation. Our results provide the first evidence that selection at the pre-mRNA level influences codon usage in humans. We also show that systematic trends in codon usage are found in other eukaryotes, suggesting that pre-mRNA level selection for codon usage could be a widespread phenomenon in organisms that undergo RNA splicing.

Animals↗