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PubMed1998

Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondria small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, approximately 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through the WWW (World Wide Web). Our WWW URL address is: http://mbcr.bcm.tmc. edu/smallRNA/smallrna.html . The new small RNA sequences published since our last compilation are listed in this paper (Table 1).

Animals↗

PubMed1995

Ciliate telomerase RNA structural features.

Telomerase RNA is an integral part of telomerase, the ribonucleoprotein enzyme that catalyzes the synthesis of telomeric DNA. The RNA moiety contains a templating domain that directs the synthesis of a species-specific telomeric repeat and may also be important for enzyme structure and/or catalysis. Phylogenetic comparisons of telomerase RNA sequences from various Tetrahymena spp. and hypotrich ciliates have revealed two conserved secondary structure models that share many features. We have cloned and sequenced the telomerase RNA genes from an additional six Tetrahymena spp. (T. vorax, T. borealis, T. australis, T. silvana, T. capricornis and T. paravorax). Inclusion of these sequences, most notably that from T. paravorax, in a phylogenetic comparative analysis allowed us to more narrowly define structural elements that may be necessary for a minimal telomerase RNA. A primary sequence element, positioned 5' of the template and conserved between all previously known ciliate telomerase RNAs, has been reduced from 5'-(C)UGUCA-3' to the 4 nt sequence 5'-GUCA-3'. Conserved secondary structural features and the impact they have on the general organization of ciliate telomerase RNAs is discussed.

Animals↗

PubMed1995

Complete nucleotide sequence of RNA segment 3 of bluetongue virus serotype 2 (Ona-A). Phylogenetic analyses reveal the probable origin and relationship with other orbiviruses.

The nucleotide sequence of the RNA segment 3 of bluetongue virus (BTV) serotype 2 (Ona-A) from North America was determined to be 2772 nucleotides containing a single large open reading frame of 2703 nucleotides (901 amino acid). The predicted VP3 protein exhibited general physiochemical properties (including hydropathy profiles) which were very similar to those previously deduced for other BTV VP3 proteins. Partial genome segment 3 sequences, obtained by polymerase chain reaction (PCR) sequencing, of BTV isolates from the Caribbean were compared to those from North America, South Africa, India, Indonesia, Malaysia and Australia, as well as other orbiviruses, to determine the phylogenetic relationships amongst them. Three major BTV topotypes (Gould, A.R. (1987) Virus Res. 7, 169-183) were observed which had nucleotide sequences that differed by approximately 20%. At the molecular level, geographic separation had resulted in significant divergence in the BTV genome segment 3 sequences, consistent with the evolution of distinct viral populations. The close phylogenetic relationship between the BTV serotype 2 (Ona-A strain) from Florida and the BTV serotypes 1, 6 and 12 from Jamaica and Honduras, indicated that the presence of BTV serotype 2 in North America was probably due to an exotic incursion from the Caribbean region as previously proposed by Sellers and Maaroof ((1989) Can. J. Vet. Res. 53, 100-102) based on trajectory analysis. Conversely, nucleotide sequence analysis of Caribbean BTV serotype 17 isolates suggested they arose from incursions which originated in the USA, possibly from a BTV population distinct from those circulating in Wyoming.

Amino Acid Sequence↗

PubMed1980

Regulated expression of the prolactin gene in rat pituitary tumor cells.

Prolactin (PRL) gene expression in three strains of GH cells (rat pituitary tumor cells) has been quantitated by measurement of: (a) intracellular and extracellular PRL, (b) cytoplasmic translatable PRL-specific mRNA (mRNAPRL), and (c) molecular hybridization of cytoplasmic poly(A) RNA to cDNAPRL (DNA complementary to mRNAPRL). Three GH cell lines utilized in this investigation were a PRL-producing (PRL+) strain, GH4C1, a PRL nonproducing 5-bromo-deoxyuridine resistnat (PRL- BrdUrdr) strain, F1BGH12C1, and a new strain, 928-9b, derived by fusion of PRL+ cells with a nuclear monolayer of the PRL-, BrdUrdr GH cell strain. PRL production is a characteristic of 928-9b cells, but the level of PRL production (2-4 micrograms/mg protein/24 h) is much lower than that of the PRL+ strain, GH4C1 (15-25 micrograms/mg protein/24 h). Levels of cytoplasmic translatable mRNAPRL and cytoplasmic PRL-RNA sequences quantitated with a cDNAPRL probe were also much lower in 928-9b as compared to the PRL+ parent. PRL-RNA sequences could not be detected in the PRL- strain. Thyrotopin-releasing hormone (TRH) stimulates PRL synthesis about threefold and inhibit a growth hormone (GH) synthesis 72% in the PRL+ strain. TRH has no effect on the synthesis of either PRL or GH in the 928-9b strain, although TRH receptors could be detected in these cells. Stimulation of PRL synthesis in the PRL+ strain by TRH could be correlated with increases in levels of cytoplasmic translatable mRNAPRL and increases in cytoplasmic PRL-RNA sequences. These results demonstrate that the graded expression of the PRL gene at the basal level, and in response to TRH, is caused by the regulated production of specific mRNA, i.e., mRNAPRL in these three GH cell strains.

Animals↗

PubMed2001

trans-acting inhibition of genomic RNA dimerization by Rous sarcoma virus matrix mutants.

The genomic RNA of retroviruses exists within the virion as a noncovalently linked dimer. Previously, we identified a mutant of the viral matrix (MA) protein of Rous sarcoma virus that disrupts viral RNA dimerization. This mutant, Myr1E, is modified at the N terminus of MA by the addition of 10 amino acids from the Src protein, resulting in the production of particles containing monomeric RNA. Dimerization is reestablished by a single amino acid substitution that abolishes myristylation (Myr1E-). To distinguish between cis and trans effects involving Myr1E, additional mutations were generated. In Myr1E.cc and Myr1E-.cc, different nucleotides were utilized to encode the same protein as Myr1E and Myr1E-, respectively. The alterations in RNA sequence did not change the properties of the viral mutants. Myr1E.ATG- was constructed so that translation began at the gag AUG, resulting in synthesis of the wild-type Gag protein but maintenance of the src RNA sequence. This mutant had normal infectivity and dimeric RNA, indicating that the src sequence did not prevent dimer formation. All of the src-containing RNA sequences formed dimers in vitro. Examination of MA-green fluorescent protein fusion proteins revealed that the wild-type and mutant MA proteins Myr1E.ATG-, Myr1E-, and Myr1E-.cc had distinctly different patterns of subcellular localization compared with Myr1E and Myr1E.cc MA proteins. This finding suggests that proper localization of the MA protein may be required for RNA dimer formation and infectivity. Taken together, these results provide compelling evidence that the genomic RNA dimerization defect is due to a trans-acting effect of the mutant MA proteins.

Alleles↗

PubMed1992

Dugbe Nairovirus M RNA: nucleotide sequence and coding strategy.

The coding assignments of the medium-sized (M) RNA segment of the Dugbe (DUG) virus (Nairovirus, Bunyaviridae) were investigated. The complete nucleotide sequence of 4888 nucleotides (nt) contained one long open reading frame in the viral complementary RNA, extending from an AUG start codon at nt 48-50 to a stop codon at nt 4701-4703 (numbered from the 5' terminus of vcRNA). Comparison of the terminal sequences with the ends of the DUG S segment revealed sequence identity between the first nine nucleotides of both segments. No sequence homologies were found with the M segments of other members of the Bunyaviridae, or with their polypeptide products. Expression of portions of the DUG M open reading frame in Escherichia coli demonstrated the carboxyl terminal region of the M open reading frame codes for the G1 structural glycoprotein, which is the target for neutralising antibodies. Confirmation of this assignment was obtained by sequencing the amino terminus of the G1 protein. Two nonstructural glycoproteins which share epitopes with G1 were identified in virus-infected cells, one of which (85 kDa) is processed over a period of several hours to produce G1. The G2 coding region was located upstream of the G1 sequence. The region between the carboxyl terminus of G2 and the 5' end of the long open reading frame apparently encodes a nonstructural protein of about 70 kDa, which is a precursor of the G2 protein.

Amino Acid Sequence↗

PubMed2005

Moments of the Boltzmann distribution for RNA secondary structures.

We here present a dynamic programming algorithm which is capable of calculating arbitrary moments of the Boltzmann distribution for RNA secondary structures. We have implemented the algorithm in a program called RNA-variance and investigate the difference between the Boltzmann distribution of biological and random RNA sequences. We find that the minimum free energy structure of biological sequences has a higher probability in the Boltzmann distribution than random sequences. Moreover, we show that the free energies of biological sequences have a smaller variance than random sequences and that the minimum free energy of biological sequences is closer to the expected free energy of the rest of the structures than that of random sequences. These results suggest that biologically functional RNA sequences not only require a thermodynamically stable minimum free energy structure, but also an ensemble of structures whose free energies are close to the minimum free energy.

Algorithms↗

PubMed1992

Identification of intermolecular RNA cross-links at the subunit interface of the Escherichia coli ribosome.

32P-Labeled 70S ribosomes and polysomes were isolated from cultures of Escherichia coli and treated with the cross-linking reagent bis(2-chloroethyl)methylamine. Intermolecular 16S-23S RNA cross-linked complexes were separated from other products of the cross-linking reactions by a two-step sucrose density gradient centrifugation procedure and subjected to oligodeoxynucleotide-directed partial nuclease digestions with RNase H. Cross-linked RNA fragments released by such directed digests were resolved by two-dimensional gel electrophoresis and analyzed using classical oligonucleotide fingerprinting techniques. Two distinct intermolecular cross-links between the 16S and 23S RNA could be localized in this manner, involving positions 1408-1411 and 1518-1520 in the 16S RNA sequence and positions 1912-1920 in the 23S RNA sequence. These data provide the first direct topographical links between the RNA of the 30S and 50S subunits in the functional ribosome and, together with previous topographical data concerning the three-dimensional folding of the rRNA, demonstrate that there is a tight cluster at the ribosomal interface both of sites implicated in ribosomal function and of posttranscriptionally modified nucleotides in the rRNA.

Base Sequence↗

PubMed1982

Oligonucleotide mapping: evaluation of its sensitivity by computer-simulation.

A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides obtained from random RNA sequences can be estimated. The computer simulations also permit estimation of the number of large oligonucleotides which remain unchanged as random variations are introduced into a random RNA sequence. In addition, computer analysis also provides a means of estimating statistical confidence limits to be used in a quantitative comparison of fingerprints of different RNA molecules. The model shows that two RNA sequences which differ overall by 1%, 5% or 10% share, on average, only 85%, 50% or 25%, respectively, of their large oligonucleotides. Thus, the use of fingerprint analysis is recommended only when closely related RNAs or regions of RNAs are compared (sequence homology greater than 90%).

Base Sequence↗

PubMed1997

Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer.

We showed previously that ASF/SF2, a member of the SR protein family of splicing factors, can activate a splicing enhancer element composed of high-affinity ASF/SF2 binding sites. To determine whether other SR proteins can behave similarly, we selected a high-affinity RNA-binding site (B1) for the SR protein SRp40. Strikingly, the success of this selection was completely dependent on phosphorylation of the RS domain, as unphosphorylated SRp40 failed to select specific sequences. We show that three copies of B1 function as a strong splicing enhancer, activating an intron with suboptimal splicing signals in nuclear extracts. Enhancer activity in S100 extracts (which lack SR proteins) required SRp40 and a nuclear fraction previously found to be required for ASF/SF2-dependent splicing. Importantly, enhancer activity was lost when SRp40 was replaced by ASF/SF2 or SC35, and SRp40 was the only classical SR protein found to be associated with the enhancer. Together, our results indicate that phosphorylation-dependent, sequence-specific RNA binding can impart unique activities to individual SR proteins.

Binding Sites↗

PubMed1996

DNA and RNA oligomer sequences from the 3' noncoding region of the chicken glutamine synthetase gene from intramolecular hairpins.

The DNA sequence of the chicken glutamine synthetase gene contains an A.T-rich stretch of approximately 1500 base pairs in the 3' noncoding regions of exon 7 [Pu, H., & Young, A. P. (1989) Gene 18, 169-175]. Within this region several palindromic sequences occur that could conceivably form intramolecular structures. One such perfect inverted repeat sequence resides between positions 2605 and 2623. To investigate the hairpin-forming potential for this sequence, optical and calorimetric melting and gel electrophoresis studies have been performed on the following synthetically prepared DNA and RNA oligomer subsequences: DNA, 5'd-T-T-T-T-T-T-A-A-T-A-A-T-T-A-A-A-A-A-A-3'; and RNA, 5'r-U-U-U-U-U-U-A-A-U-A-A-U-U-A-A-A-A-A-A-3'. The DNA strand corresponds to the coding strand sequence while the RNA strand represents the transcribed mRNA. Results of melting analysis of these 19-base, partially self-complementary strands performed in 115 mM Na+ yielded evaluations of their thermodynamic transition parameters. These values are consistent with the melting of unimolecular structures, presumably hairpins. Thermodynamic parameters evaluated by analysis of the optical melting transitions assuming a two-state model and measured directly by differential scanning calorimetry agreed within experimental error. Therefore, melting behavior of the hairpins is all-or-none like. The DNA hairpin is slightly more stable than the RNA hairpin with melting enthalpy delta H0 = 41.2 +/- 3.8 kcal/mol and entropy delta S0 = 133 +/- 11 cal/K.mol (eu) compared to delta H0 = 32.0 +/- 6.0 kcal/mol and entropy delta S0 = 105 +/- 20 eu for the RNA. Gel electrophoretic analysis of these oligomers alone and in various mixtures with their DNA and RNA complementary strands was also performed. Consistent with interpretations of melting results, these experiments revealed both strands alone preferentially form intramolecular hairpin structures. In mixtures in which their complementary strands are in vast molar excess (stoichiometric ratios > 10:1), the intramolecular structures are converted to intermolecular duplexes. For the DNA and RNA strands examined, the conversion is not complete until over a 1000-fold excess of the complementary strand is added. Semiquantitative analysis of gel electrophoretograms enabled evaluations of the relative free energies of the hairpin and duplex states as a function of complementary strand concentration. With the finding that these sequences preferentially form hairpins, potential roles these structures could play in regulatory activities are considered.

Animals↗

PubMed2003

The partial sequence of RNA 1 of the ophiovirus Ranunculus white mottle virus indicates its relationship to rhabdoviruses and provides candidate primers for an ophiovirus-specific RT-PCR test.

A 4018 nucleotide sequence was obtained for RNA 1 of Ranunculus white mottle virus (RWMV), genus Ophiovirus, representing an incomplete ORF of 1339 aa. Amino acid sequence analysis revealed significant similarities with RNA polymerases of viruses in the family Rhabdoviridae and a conserved domain of 685 aa, corresponding to the RdRp domain of those in the order Mononegavirales. Phylogenetic analysis indicated that the genus Ophiovirus is not related to the genus Tenuivirus or the family Bunyaviridae, with which it has been linked, and probably deserves a special taxonomic position, within a new family. A pair of degenerate primers was designed from a consensus sequence obtained from a relatively conserved region in the RNA 1 of two members of the genus, Citrus psorosis virus (CPsV) and RWMV. The primers, used in RT-PCR experiments, amplified a 136 bp DNA fragment from all the three recognized members of the genus, i.e. CPsV, RWMV and Tulip mild mottle mosaic virus (TMMMV) and from two tentative ophioviruses from lettuce and freesia. The amplified DNAs were sequenced and compared with the corresponding sequences of CPsV and RWMV and phylogenetic relationships were evaluated. Assays using extracts from plants infected by viruses belonging to the genera Tospovirus, Tenuivirus, Rhabdovirus and Varicosavirus indicated that the primers are genus-specific.

Amino Acid Sequence↗

PubMed1982

The 5.8S RNA gene sequence and the ribosomal repeat of Schizosaccharomyces pombe.

We have characterized the rRNA gene repeat in Schizosaccharomyces pombe. This repeat, which does not contain the 5S RNA gene, is found in a 10.4 kb HindIII DNA fragment. We have determined the nucleotide sequences of the S. pombe 5.8S RNA gene and intergenic spacers from two different 10.4 kb DNA fragments. Analysis of isolated total cellular 5.8S RNA revealed the presence of eight species of 5.8S RNA, differing in the number of nucleotides at the 5'-end. The eight 4.8S RNA species vary in length from 158 to 165 nucleotides. Apart from the heterogeneity observed at the 5'-end, the sequence of the eight 5.8S RNA species appears to be identical and is the same sequence as coded for by the 5.8S genes. The gene sequence shows great homology to the 5.8S RNA genes or S. cerevisiae and N. crassa. Most of the base differences are confined to the highly variable stem though to be involved in co-axial helix stacking with the 25S RNA, where base pairing is nearly identical despite the sequence differences. Secondary structure models are examined in light of 5.8S RNA oligonucleotide conservation across species from yeasts to higher eukaryotes.

Ascomycota↗

PubMed1978

Equivalent expression of endogenous murine leukemia virus-related genes in C3H/10T1/2 cells and chemically transformed derivative cells.

The possibility that chemical carcinogens may induce enhanced expression of endogenous C-type RNA tumor virus genes in the absence of intact virus particle production has been partially tested in a model system. Thie was accomplished by measuring the abundance and diversity of murine leukemia virus-related RNA sequences associated with the polyribosome fraction of nontransformed C3H/10T1/2 clone 8 cells and a 3-methylcholanthrene-transformed derivative clone. Although both clones are virus nonproducers, they were found to contain significant amounts of polyadenylate-containing murine leukemia virus-related RNA sequences; however, both the types and quantities of such sequences appear indistinguishable in both clones. These results suggest that expression of the corresponding gene sequences into RNA is not related to the maintenance of the transformed state in these chemically transformed cells.

Base Sequence↗

PubMed1991

Conflicting phylogenetic hypotheses for the parasitic platyhelminths tested by partial sequencing of 18S ribosomal RNA.

Partial sequencing of the 18S ribosomal RNA in nine parasitic and one free-living species of platyhelminth was used to test hypotheses on the phylogenetic relationships among the major groups. The eucestodes, amphilinideans, gyrocotylideans and monopisthocotylideans appeared as a monophyletic assemblage in a cladistic analysis of the data, with a very close association between the gyrocotylideans and monopisthocotylideans. The polyopisthocotylidean monogeneans were paraphyletic to the monopisthocotylideans. The digeneans appeared to be a sister group to the monogeneans and eucestodes, while the temnocephalidean was closely related to the free-living polyclad.

Animals↗

PubMed2025

Paradoxical Effect of Myosteatosis on the Immune Checkpoint Inhibitor Response in Metastatic Renal Cell Carcinoma.

BACKGROUND: Treatment for metastatic renal cell carcinoma (mRCC) has shifted from tyrosine kinase inhibitor (TKI) therapy to immune checkpoint inhibitor (ICI)-based therapy, improving outcomes but with variable individual responses. This study investigated the prognostic implications of pretreatment low skeletal muscle mass (LSMM) and myosteatosis in patients with mRCC undergoing first-line ICI-based therapies, comparing outcomes between PD-1 inhibitor + CTLA-4 inhibitor and PD-1 inhibitor + TKI, incorporating single-cell RNA sequencing. METHODS: A retrospective analysis was performed on 90 patients with mRCC treated with ICI-based therapies between November 2019 and March 2023. Patients were grouped based on whether they received PD-1 inhibitor + CTLA-4 inhibitor or PD-1 inhibitor + TKI combinations. LSMM was defined as skeletal muscle index below 40.8 cm2/m2 for men and 34.9 cm2/m2 for women. Myosteatosis was defined using skeletal muscle density, with cut-off values < 41 HU for BMI < 25 kg/m2 and < 33 HU for BMI ≥ 25 kg/m2. Progression-free survival (PFS) and overall survival (OS) were compared using Kaplan-Meier curves and multivariable models. Single-cell RNA sequencing was performed on pretreatment samples to compare the immune microenvironment between patients with and without myosteatosis. RESULTS: The study cohort (26.7% female; median age: 60.5 years) included 59 patients (65.6%) treated with PD-1 inhibitor + CTLA-4 inhibitor and 31 patients (34.4%) treated with PD-1 inhibitor + TKI. LSMM was present in 18.9% of patients, and myosteatosis in 41.1%, with comparable proportions across groups. During follow-up, 29 patients (32.2%) died: 16 in the PD-1 inhibitor + CTLA-4 inhibitor group and 13 in the PD-1 inhibitor + TKI group. The overall 1-year mortality rate was 22.2%, and PFS rate was 53.3%. Myosteatosis predicted poor OS (HR, 5.389; p = 0.008) and PFS (HR, 2.930; p = 0.022) in the PD-1 inhibitor + TKI group but was protective for PFS (HR, 0.461; p = 0.049) in the PD-1 inhibitor + CTLA-4 inhibitor group. LSMM did not significantly affect outcomes in either group. Single-cell RNA sequencing revealed higher CTLA-4 expression in regulatory T cells and more effector memory CD8+ T cells in patients with myosteatosis, whereas patients without myosteatosis had more anti-tumoural non-classical monocytes. CONCLUSIONS: Myosteatosis negatively impacts OS and PFS in patients with mRCC treated with PD-1 inhibitor + TKI therapy but is protective for PFS in those treated with PD-1 inhibitor + CTLA-4 inhibitor therapy. Altered checkpoint expression and immune cell composition associated with myosteatosis may contribute to these differential responses.

Humans↗

PubMed1986

Elevated amounts of a 7S nuclear RNA with sequence homology to a tumor virus promoter in transformed and tumorigenic cells.

A small nuclear RNA (7S-K) from cultured mammalian cells has been shown, in previous studies, to have the characteristics expected of a gene regulatory molecule, i.e., a tissue- and species-specific stimulatory activity for initiation of transcription of protein-coding genes. Moreover, in simian virus 40 (SV40)-transformed mouse cells, this RNA was shown, by S1-analysis, to bear an extensive homology to the SV40 promoter, suggesting that it acts by base-pairing to DNA in this region to facilitate the formation of the transcription-initiation complex. In order to investigate whether or not this homology is restricted to SV40-transformed cells and in any way related to transformation, a series of normal and transformed cell lines were examined for the degree of homology between their 7S-K RNAs and the SV40 promoter. Results show that the amount of 7S-K RNA hybridizable to the promoter varies as a direct function of the established degree of tumorigenic activity of the cells and is not dependent on the presence of SV 40 sequences. Taken together with the known overexpression of some cellular oncogenes in tumor tissues, these results suggest that this particular RNA may be involved in stimulating transcription of, at least, some of these genes.

Animals↗

PubMed1975

A kinetic estimation of base sequence complexity of nuclear poly(A)-containing RNA in mouse Friend cells.

Complementary DNA (cDNA) has been transcribed by viral reverse transcriptase from poly(A)-containing nuclear RNA prepared from growing mouse Friend cells (clone M2). Annealing experiments with this cDNA have demonstrated that a large proportion of the poly(A) tracts in M2 cell nuclear RNA are adjacent to RNA sequences which are transcribed from nonrepetitive DNA in the mouse genome. The kinetics of hybridization of cDNA to template RNA indicate that nuclear poly(A)-containing RNA consists of at least two abundance classes, the more complex of which is transcribed from approximately 3 percent of the genome. Thus there are at least 5 times more unique DNA sequences represented in nuclear polyadenylated RNA than in polysomal polyadenylated RNA. Moreover, there is evidence for posttranscriptional mechanisms which alter the relative concentrations of some (at least) gene transcripts between nucleus and cytoplasm.

Adenine Nucleotides↗