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PubMed2006

Genetic algorithm learning as a robust approach to RNA editing site prediction.

BACKGROUND: RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as C --> U editing, appears to exist in a wide range of organisms, but most instances of this form of RNA editing have been discovered serendipitously. With the large amount of genomic and transcriptomic data now available, a computational analysis could provide a more rapid means of identifying novel sites of C --> U RNA editing. Previous efforts have had some success but also some limitations. We present a computational method for identifying C --> U RNA editing sites in genomic sequences that is both robust and generalizable. We evaluate its potential use on the best data set available for these purposes: C --> U editing sites in plant mitochondrial genomes. RESULTS: Our method is derived from a machine learning approach known as a genetic algorithm. REGAL (RNA Editing site prediction by Genetic Algorithm Learning) is 87% accurate when tested on three mitochondrial genomes, with an overall sensitivity of 82% and an overall specificity of 91%. REGAL's performance significantly improves on other ab initio approaches to predicting RNA editing sites in this data set. REGAL has a comparable sensitivity and higher specificity than approaches which rely on sequence homology, and it has the advantage that strong sequence conservation is not required for reliable prediction of edit sites. CONCLUSION: Our results suggest that ab initio methods can generate robust classifiers of putative edit sites, and we highlight the value of combinatorial approaches as embodied by genetic algorithms. We present REGAL as one approach with the potential to be generalized to other organisms exhibiting C --> U RNA editing.

Algorithms↗

PubMed2000

Synthetic oligonucleotides as RNA mimetics: 2'-modified Rnas and N3'-->P5' phosphoramidates.

Significant interest in synthetic DNA and RNA oligonucleotides and their analogues has marked the past two decades of research in chemistry and biochemistry. This attention was largely determined by the great potential of these compounds for various therapeutic applications such as antisense, antigene and ribozyme-based agents. Modified oligonucleotides have also become powerful molecular biological and biochemical research tools that allow fast and efficient regulation of gene expression and gene functions in vitro and in vivo. These applications in turn are based on the ability of the oligonucleotides to form highly sequence-specific complexes with nucleic acid targets of interest. This review summarizes recent advances in the design, synthesis, biochemical and structural properties of various RNA analogues. These comprise 3'-modified oligonucleotide N3'-->P5' phosphoramidates, analogues with modifications at the 2'-position of nucleoside sugar rings, or combinations of the two. Among the properties of the RNA minetics reviewed here are the thermal stability of their duplexes and triplexes, hydrolytic resistance to cellular nucleases and biological activity in in vitro and in vivo systems. In addition, key structural aspects of the complexes formed by the RNA analogues, including interaction with water molecules and ions, are analyzed and presented.

Amides↗

PubMed2003

Synthesis and properties of 2'-O,4'-C-ethylene-bridged nucleic acids (ENA) as effective antisense oligonucleotides.

Novel bicyclo nucleosides, 2'-O,4'-C-ethylene nucleosides and 2'-O,4'-C-propylene nucleosides, were synthesized as building blocks for antisense oligonucleotides to further optimize the 2'-O,4'-C-methylene-linkage of bridged nucleic acids (2',4'-BNA) or locked nucleic acids (LNA). Both the 2'-O,4'-C-ethylene- and propylene-linkage within these nucleosides restrict the sugar puckering to the N-conformation of RNA as do 2',4'-BNA/LNA. Furthermore, ethylene-bridged nucleic acids (ENA) having 2'-O,4'-C-ethylene nucleosides had considerably increased the affinity to complementary RNA, and were as high as that of 2',4'-BNA/LNA (DeltaT(m)=+3 approximately 5 degrees C per modification). On the other hand, addition of 2'-O,4'-C-propylene modifications in oligonucleotides led to a decrease in the affinity to complementary RNA. As for the stability against nucleases, incorporation of one 2'-O,4'-C-ethylene or one 2'-O,4'-C-propylene nucleoside into oligonucleotides considerably increased their resistance against exonucleases to an extent greater than 2',4'-BNA/LNA. These results indicate that ENA is more suitable as an antisense oligonucleotide and is expected to have better antisense activity than 2',4'-BNA/LNA.

Alkenes↗

PubMed1991

Enzymatic activity of poliovirus RNA polymerase mutants with single amino acid changes in the conserved YGDD amino acid motif.

RNA-dependent RNA polymerases contain a highly conserved region of amino acids with a core segment composed of the amino acids YGDD which have been hypothesized to be at or near the catalytic active site of the molecule. Six mutations in this conserved YGDD region of the poliovirus RNA-dependent RNA polymerase were made by using oligonucleotide site-directed DNA mutagenesis of the poliovirus cDNA to substitute A, C, M, P, S, or V for the amino acid G. The mutant polymerase genes were expressed in Escherichia coli, and the purified RNA polymerases were tested for in vitro enzyme activity. Two of the mutant RNA polymerases (those in which the glycine residue was replaced with alanine or serine) exhibited in vitro enzymatic activity ranging from 5 to 20% of wild-type activity, while the remaining mutant RNA polymerases were inactive. Alterations in the in vitro reaction conditions by modification of temperature, metal ion concentration, or pH resulted in no significant differences in the activities of the mutant RNA polymerases relative to that of the wild-type enzyme. An antipeptide antibody directed against the wild-type core amino acid segment containing the YGDD region of the poliovirus polymerase reacted with the wild-type recombinant RNA polymerase and to a limited extent with the two enzymatically active mutant polymerases; the antipeptide antibody did not react with the mutant RNA polymerases which did not have in vitro enzyme activity. These results are discussed in the context of secondary-structure predictions for the core segment containing the conserved YGDD amino acids in the poliovirus RNA polymerase.

Amino Acid Sequence↗

PubMed1993

Absence of immature mast cells in the skin of Ws/Ws rats with a small deletion at tyrosine kinase domain of the c-kit gene.

Ws/Ws rats have a small deletion at the tyrosine kinase domain of the c-kit gene, and practically no mast cells were detectable when the tissues were stained with alcian blue. Because alcian blue stains proteoglycans, there is a possibility that immature mast cells that do not contain a sufficient amount of proteoglycans are not detectable by this method. We examined this possibility by using other markers of mast cells. The histamine content in the skin of Ws/Ws rats was 0.3% that of control normal (+/+) rats. Because the number of alcian blue-positive mast cells in the skin of Ws/Ws rats was also 0.3% that of +/+ rats, histamine in the skin seemed to be concentrated to alcian blue-positive mast cells. Mast cells in the skin of +/+ rats express messenger RNA of Fc epsilon RI beta-subunit and c-kit protein. Because c-kit messenger RNA was normally expressed at least in the brain of Ws/Ws rats despite the small deletion, we examined the expression of Fc epsilon RI beta-subunit and c-kit messenger RNA in the skin and stomach of Ws/Ws rats by reverse transcriptase modification of polymerase chain reaction. Expression of either Fc epsilon RI beta-subunit or c-kit messenger RNA in the skin and stomach of Ws/Ws rats was estimated to be less than 1% that of +/+ rats. Moreover no Fc epsilon RI beta-subunit-expressing and no c-kit-expressing cells were detectable in the skin of Ws/Ws rats by in situ hybridization histochemistry. The present result suggests the absence of immature mast cells in tissues of Ws/Ws rats.

Animals↗

PubMed2006

The length of the transcript encoded from the Kcnq1ot1 antisense promoter determines the degree of silencing.

The underlying mechanisms linking antisense RNA, chromatin architecture and gene expression have not been fully elucidated. Here we show that long transcripts encoded from the Kcnq1ot1 antisense promoter silence the flanking genes more efficiently than short antisense transcripts. Interestingly, the antisense RNA-mediated deposition of inactive chromatin-specific histone modifications was higher with the longer antisense transcripts than with the shorter antisense transcripts. The kinetic studies of expression and chromatin remodeling of overlapping and nonoverlapping genes in response to antisense transcription revealed that the overlapping gene was rapidly silenced due to decrease in the occupancy of basal transcription machinery and simultaneous enrichment of its promoter with inactive chromatin modifications. The nonoverlapping gene, initially enriched with histone modifications specific to active chromatin, was subsequently silenced. Surprisingly, the flanking sequences were initially enriched with H3K9 monomethylation, as compared to di- and trimethylation, with a subsequent shift to trimethylated H3K9 enrichment. Our data provide a new perspective into antisense RNA-mediated gene silencing, and, more importantly, provide an explanation for why the antisense transcripts encoded from imprinting control regions are of significant length.

Cell Line, Tumor↗

PubMed2006

SUMO modification of Sam68 enhances its ability to repress cyclin D1 expression and inhibits its ability to induce apoptosis.

Sam68 (Src associated in mitosis; 68 kDa) is an RNA-binding protein and substrate of Src family kinases. It is thought to play a role in cell cycle progression. Overexpression of Sam68 in fibroblasts was reported to have two separable functions dependent on its ability to bind RNA--cell cycle arrest or the induction of apoptosis. Post-translational modification with SUMO (small ubiquitin-like modifier) is common to many transcription factors and can regulate protein localization, stability and function. Here we show Sam68 to be modified by SUMO, and demonstrate that the SUMO E3 ligase (PIAS1) (protein inhibitor of activated STAT1) can enhance Sam68 sumoylation. Lysine 96, the first lysine in the amino-terminal region of Sam68, was found to be the major SUMO acceptor site. Mutation of the SUMO acceptor lysine to arginine enhanced the ability of Sam68 to induce apoptosis but inhibited its ability to act as a transcriptional inhibitor of cyclin D1 expression. A SUMO-1 Sam68 fusion protein, on the other hand, inhibited the ability of Sam68 to induce apoptosis but was a strong repressor of cyclin D1 expression. Thus, SUMO may be an important regulator of Sam68 function in cell cycle progression.

Adaptor Proteins, Signal Transducing↗

PubMed1978

[RNA synthesis in the isolated nuclei of nerve cells treated with acetylcholine].

Acetylcholine modified the incorporation of radioactive precursors 3H-uridine-5-triphosphate, 14C-uridine and 14C-cytidine in RNA of nuclei isolated from the rat brain. This modification has two tendencies: either the activation or the suppretion. The character of the nuclear reaction depends upon the season and animal population. In the presence of actinomycin D (5.10(-5) M), acetylcholine does not influence the precursor incorporation into the nuclear RNA. In the system that involves nuclei+soluble cytoplasmic fraction acetylcholine exerts an effect that is opposite to that when the nuclei are alone. These results suggest that acetylcholine action is mediated by a cytoplasmic factor. Actinomycin D in the presence of cytoplasmic fraction did not influence effects of acetylcholine.

Acetylcholine↗

PubMed1987

Relationship between nuclear ADP-ribosylation and RNA transcription in calf and human thyroid.

ADP-ribosylation is a posttranslational modification of proteins that has been related to many cellular events, such as DNA replication and repair, cell proliferation and differentiation. The present studies were performed in order to explore the possible relationship between nuclear protein ADP-ribosylation and RNA transcription in the thyroid gland. Inhibition of RNA transcription by alpha-amanitin and actinomycin D caused a decrease in ADP-ribosylation of 27 and 17%, respectively. Nicotinamide caused a dose-related inhibition of ADP-ribosylation, which was highest at 2 mM (around 90%). At this dose nicotinamide inhibited total RNA transcription by 46%, while the activity due to RNA polymerase II decreased by 50% and that related to RNA polymerases I+III dropped by 24%. These results suggest that inhibition of total nuclear protein ADP-ribosylation is accompanied by a parallel decrease in RNA transcription. Since our previous work has shown that TSH stimulates both nuclear ADP-ribosylation and RNA transcription it may be concluded that these activities follow parallel changes within the thyroid. When the same activities were assayed in normal human and in glands bearing follicular adenoma, RNA polymerase II was increased 4 fold in the latter group, without change in nuclear ADP-ribosylation. These results would suggest that a mechanism, distinct from ADP-ribosylation, may also be involved in the regulation of RNA transcription. This latter might be altered under this pathologic condition.

ADP Ribose Transferases↗

PubMed2005

The GTP binding protein Obg homolog ObgE is involved in ribosome maturation.

Obg proteins belong to a subfamily of GTP binding proteins, which are highly conserved from bacteria to human. Mutations of obgE genes cause pleiotropic defects in various species but the function remained unclear. Here we examine the function of ObgE, the Obg homolog in Escherichia coli. The growth rate correlates with the amount of ObgE in cells. Co-fractionation experiments further suggest that ObgE binds to 30S and 50S ribosomal subunits, but not to 70S ribosome. Pull-down assays suggest that ObgE associates with several specific ribosomal proteins of 30S and 50S subunits, as well as RNA helicase CsdA. Purified ObgE cosediments with 16S and 23S ribosomal RNAs in vitro in the presence of GTP. Finally, mutation of ObgE affects pre-16Sr-RNA processing, ribosomal protein levels, and ribosomal protein modification, thereby significantly reducing 70S ribosome levels. This evidence implicates that ObgE functions in ribosomal biogenesis, presumably through the binding to rRNAs and/or rRNA-ribosomal protein complexes, perhaps as an rRNA/ribosomal protein folding chaperone or scaffold protein.

Cytosol↗

PubMed1979

Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage phi 29 DNA.

By using a modification of the BAC spreading method for mounting the DNA for electron microscopy, partial denaturation maps of protein-free phi 29 DNA and of phi 29 DNA containing protein p3 were obtained. In phi 29 p3-DNA1 the protein does not seem to influence the melting of the ends of the molecules. The comparison of the partial denaturation map and the B. subtilis RNA polymerase binding sites indicates that five of the seven early promoters (A1, A2, A3, B2 and C2) are located in A-T rich DNA regions whereas the other two early promoters (B1 and C1) are located in less A-T rich sites.

Bacillus subtilis↗

PubMed1992

In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs.

A method to investigate the structure of RNA molecules within intact plant tissues has been developed. The RNA structures are analyzed using dimethyl sulfate (DMS), which modifies substituents of adenine and cytosine residues within single-stranded regions of RNA molecules. Reactive sites are identified by primer extension analysis. Using this procedure, an analysis of the secondary structure of the cytoplasmic 18S ribosomal RNA in soybean seedling leaves has been completed. DMS modification data are in good agreement with the phylogenetic structure predicted for soybean 18S rRNA. However, there are a few notable exceptions where residues thought to be involved in double-stranded regions in all 18S rRNAs are strongly modified in soybean leaf samples. These data taken together with the phylogenetic structure suggest that alternate structures may exist in vivo. The further applicability of this technique is demonstrated by comparing the modification pattern obtained in vivo to that obtained in vitro for a particular mRNA molecule encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. The results obtained are compared to a predicted minimum energy secondary structure. The data indicate that the conformation of RNA molecules within the cell may not be reflected in a structural analysis of purified mRNA molecules.

Base Composition↗

PubMed2003

Full-length cDNA synthesis for long-distance RT-PCR of large mRNA transcripts.

Reverse transcription of mRNA often leads to the synthesis of partial, non-full-length cDNAs. Methods to facilitate reverse transcription across RNA regions of secondary structure, as well as enzyme modifications to eliminate RNase H activities inherent to reverse transcriptase enzymes, have been previously reported. However, because all reverse transcriptases have high error rates of polymerization, the misincorporation of nucleotides can also cause the reverse transcriptase to stumble. Hence, even in the absence of RNA secondary structure and RNase H activity, the synthesis of full-length cDNA from long mRNA transcripts still remains a challenge. We describe here the coupling of a 3'-->5' exonuclease function during reverse transcription. The incorporation of a proofreading activity, when used in conjunction with denaturant buffers and RNase H-deficient reverse transcriptases, can successfully generate full-length cDNAs of up to 15 kb.

DNA↗

PubMedDate not supplied

Nucleoside modifications affect the structure and stability of the anticodon of tRNA(Lys,3).

NMR spectroscopy was used to determine the solution structures of RNA oligonucleotides comprising the anticodon domain of tRNA(Lys,3). The structural effects of the pseudouridine modification at position 39 were investigated and are well correlated with changes in thermodynamic parameters. The loop conformation differs from that seen in tRNA(Phe) and provides an explanation of the critical role of modification in this tRNA.

Anticodon↗

PubMed1988

The preparation of poly(A)+mRNA from the hagfish slime gland.

The isolation of translatable poly(A)+mRNA from the slime glands of the Pacific hagfish, Eptatretus stouti, is not possible by the commonly used procedures because of the viscous slime that is formed when the contents of the glands are hydrated. This paper reports on a procedure developed to overcome this problem. Briefly, the tissue was powdered in liquid nitrogen, mixed with sodium lauroylsarcosine and proteinase K and lyophilized. The lyophilized powder was then mixed with 0.3 mm diameter glass beads, thoroughly ground and wetted with buffer and digested at 37 degrees C. The RNA from the digest was recovered by ultracentrifugation through a CsCl cushion. Further purification of the RNA was accomplished by the usual methods with slight modifications.

Animals↗

PubMed1983

Inhibition of vesicular stomatitis virus RNA synthesis by 2',3'-dideoxycytidine 5'-triphosphate.

The ability of the compound 2',3'-dideoxycytidine 5'-triphosphate (ddCTP) to serve as an inhibitor of viral RNA synthesis was examined using an in vitro system that supports vesicular stomatitis virus (VSV) protein synthesis, transcription and replication. Viral RNA synthesis was inhibited by 87 and 98% of control, respectively, in reactions containing 1 mM- and 10 mM-ddCTP in place of CTP. VSV RNA replication and transcription were inhibited equally by ddCTP. At a concentration of 1 mM-ddCTP, there was no inhibitory effect on viral protein synthesis; at 10 mM-ddCTP, total protein synthesis was inhibited by 30% as compared to control reactions. The presence of ddCTP had no effect on the size or relative molar amounts of each protein synthesized as analysed by electrophoresis on polyacrylamide gels. This is the first report describing a compound that will inhibit VSV RNA synthesis in vitro without compromising the concurrent synthesis and modification of proteins.

Deoxycytosine Nucleotides↗

PubMed1980

Mutations in a nonessential viral gene permit bacteriophage T4 to form plaques on Escherichia coli valS ts relA.

During viral development bacteriophage T4 modifies the valyl-transfer RNA synthetase of its host Escherichia coli, but the function of the modification has remained elusive. A strain of Escherichia coli has now been identified which is nonpermissive for wild-type bacteriophage T4, but permissive for bacteriophage mutants impaired in the modification reaction. A comparison with other bacteria suggests that nonpermissiveness is due to synthesis of a thermolabile valyl-transfer RNA synthetase and relaxed control of RNA accumulation.

Escherichia coli↗

PubMed2004

Sequential histone modifications at Hoxd4 regulatory regions distinguish anterior from posterior embryonic compartments.

Hox genes are differentially expressed along the embryonic anteroposterior axis. We used chromatin immunoprecipitation to detect chromatin changes at the Hoxd4 locus during neurogenesis in P19 cells and embryonic day 8.0 (E8.0) and E10.5 mouse embryos. During Hoxd4 induction in both systems, we observed that histone modifications typical of transcriptionally active chromatin occurred first at the 3' neural enhancer and then at the promoter. Moreover, the sequential distribution of histone modifications between E8.0 and E10.5 was consistent with a spreading of open chromatin, starting with the enhancer, followed by successively more 5' intervening sequences, and culminating at the promoter. Neither RNA polymerase II (Pol II) nor CBP associated with the inactive gene. During Hoxd4 induction, CBP and RNA Pol II were recruited first to the enhancer and then to the promoter. Whereas the CBP association was transient, RNA Pol II remained associated with both regulatory regions. Histone modification and transcription factor recruitment occurred in posterior, Hox-expressing embryonic tissues, but never in anterior tissues, where such genes are inactive. Together, our observations demonstrate that the direction of histone modifications at Hoxd4 mirrors colinear gene activation across Hox clusters and that the establishment of anterior and posterior compartments is accompanied by the imposition of distinct chromatin states.

Animals↗