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PubMed1996

Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date from prokaryotic and eukaryotic organisms. About 500 small RNA sequences are in our database currently. The sources of individual RNAs and their GenBank accession numbers are also included. The small RNA database can be accessed through the World Wide Web(WWW). Our WWW URL is http://mbcr.bcm.tmc.edu/smallRNA/smallrna. html. The new small RNA sequences published since our last compilation are listed in this paper.

Animals↗
PubMed2025

Genomic subtypes of non-muscle-invasive bladder cancer: guiding immunotherapy decision-making for patients exposed to aristolochic acid.

BACKGROUND: The limited genomic data on non-muscle-invasive bladder cancer (NMIBC) hampers our understanding of its carcinogenesis and development. Specifically, Aristolochic acid (AA), a potent human carcinogenic compound from aristolochia plants and commonly found in Chinese herbal medicine, has been extensively documented as being closely associated with the onset and progression of bladder cancer. However, the field of AA-induced NMIBC remains largely unexplored in terms of its genomic and molecular characteristics, as well as clinical therapeutic strategies. METHODS: To bridge this knowledge gap, we conducted a comprehensive study using a cohort of 81 NMIBC samples. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to obtain detailed genomic and transcriptomic data. We subjected these datasets to genomic analysis and subtype analysis to gain valuable insights into NMIBC. RESULTS: By temporally dissecting mutations in NMIBC specimens, we identified a comprehensive mutational landscape of NMIBC and the associations of these mutations with recurrence-free survival. Additionally, we discerned four genomic subtypes of NMIBC: AA-like, FGFR3/HRAS, FGFR3 & chr9Del, and genome instability (GI). The AA-like subtype presented a high frequency of gene mutations along with a pronounced AA mutagenesis signature of SBS22 (Fisher test: P-value 3.5e-4, OR 25.25) even after temporal dissection. The FGFR3/HRAS subtype exhibited FGFR3 or HRAS mutations with few copy number alterations (CNAs). The FGFR3 & chr9Del subtype was characterized by the co-occurrence of chr9p and chr9q deletions as well as FGFR3 mutations, while the GI subtype showed a high frequency of CNAs. Notably, the AA-like and GI subtypes demonstrated better outcomes after immunotherapy, whereas the FGFR3/HRAS subtype showed poorer outcomes. CONCLUSIONS: Our findings provide novel perspectives on the genomics of NMIBC, unveiling four prominent genomic subtypes, each showing different outcomes following immunotherapy. TRIAL REGISTRATION: No. 2019PHB268-01 (retrospectively registered on February 14, 2020).

Humans↗
PubMed1996

Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences.

RNA editing by adenosine deamination in brain-expressed pre-mRNAs for glutamate receptor (GluR) subunits alters gene-specified codons for functionally critical positions, such as the channel's Q/R site. We show by transcript analysis of minigenes transiently expressed in PC-12 cells that, in contrast to GluR-B pre-mRNA, where the two editing sites (Q/R and R/G) require base pairing with nearby intronic editing site complementary sequences (ECSs), editing in GluR5 and GluR6 pre-mRNAs recruits an ECS located as far as 1900 nucleotides distal to the Q/R site. The exon-intron duplex structure of the GluR5 and GluR6 pre-mRNAs appears to be a substrate of double-stranded RNA-specific adenosine deaminase. This enzyme when coexpressed in HEK 293 cells preferentially targets the adenosine of the Q/R site and of an unpaired position in the ECS which is highly edited in brain.

Adenosine↗
PubMed1981

RNA and macronuclear transcription in the ciliate Stylonychia mytilus.

Nuclear and cytoplasmic RNA of Stylonychia mytilus were analyzed on denaturing polyacrylamide gels. The molecular weight of rRNA precursor molecules is within a range of 2.1 x 10(6) daltons. A comparison between the electrophoretic pattern of nuclear non-ribosomal RNA and cytoplasmic mRNA indicates that a considerable amount of nuclear RNA sequences is of higher molecular weight than cytoplasmic RNA sequences. The molecular weight distribution of cytoplasmic RNA supports the assumption that also in Stylonychia an average sized mRNA molecule contains 1,200-1,500 nucleotides according to a molecular weight of 4 x 10(5) to 5 x 10(5) daltons. The size of the polyadenylic acid fragment of poly-A+ RNA molecules is about 120 nucleotides. The total mass of cytoplasmic RNA is around 7.5/10(10)g/cell, corresponding to 1.2 x 10(7) average sized mRNA molecules per cell. RNA excess hybridization experiments show that 60% of the DNA sequences are transcribed into nuclear RNA and that the cytoplasmic mRNA sequences are homologous to about 40% of macronuclear DNA sequences. There is no indication of different frequency classes within the mRNA. The number of different mRNA species in a Stylonychia cell is 1.2-1.5 x 10(4). On the average each of them is present about 1,000 times in every cell.

Animals↗
PubMed2000

Phylogeny and classification of poison frogs (Amphibia: dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences.

An analysis of partial sequences of the 16S ribosomal rRNA gene (582 bp) of 20 poison frog species (Dendrobatidae) confirmed their phylogenetic relationships to bufonid and leptodactylid frogs. Representatives of the ranoid families and subfamilies Raninae, Mantellinae, Petropedetinae, Cacosterninae, Arthroleptidae, Astylosternidae, and Microhylidae did not cluster as sister group of the Dendrobatidae. Similar results were obtained in an analysis using a partial sequence of the 12S gene (350 bp) in a reduced set of taxa and in a combined analysis. Within the Dendrobatidae, our data supported monophyly of the genus Phyllobates but indicated paraphyly of Epipedobates and Colostethus. Minyobates clustered within Dendrobates, contradicting its previously assumed phylogenetic position. Phobobates species clustered as a monophyletic unit within Epipedobates. Allobates was positioned in a group containing two Colostethus species, indicating that lack of amplexus, presence of skin alkaloids, and aposematic coloration evolved independently in Allobates and the remaining aposematic dendrobatids.

Amphibians↗
PubMed2006

Phylogenetic position of the marine ciliate, Certesia quadrinucleata (Ciliophora; Hypotrichia; Hypotrichida) inferred from the complete small subunit ribosomal RNA gene sequence.

The complete small subunit rRNA (SSrRNA) gene sequence of the rare marine hypotrich, Certesia quadrinucleata Fabre-Domergue, 1885, was determined, and found to be 1752 nucleotides long. The phylogenetic position of this species was deduced using distance matrix, maximum parsimony and maximum likelihood methods. Certesia was consistently demonstrated to be a member of the Aspidisca-Euplotes group and clearly exhibits a very close relationship to the well-known genus Euplotes (99% Bay, 99% LS, 99% NJ, 99% MP). The phylogenetic trees further suggest that: (1) Uronychia and Diophrys, traditionally placed in the family Uronychiidae, branch earlier and share a closer relationship to each other than to other hypotrichs; (2) taxa in Gastrocirrhidae, represented by Euplotidium arenarium, might be an "ancestral" group among "traditional" hypotrichs.

Animals↗
PubMed2002

Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class polyacanthocephala (acanthocephala).

Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala.

Acanthocephala↗
PubMed1994

16S ribosomal RNA gene sequence and phylogeny of toxic Microcystis sp. (cyanobacteria).

The toxigenic and bloom-forming cyanobacterial genus Microcystis contains several ill-defined species. The 16S rDNA for two strains of toxic M. aeruginosa were sequenced and compared to available cyanobacterial, bacterial, and chloroplast 16S rRNA gene information. Phylogeny and the validity of a molecular taxonomy for the genus Microcystis is presented.

Base Sequence↗
PubMed1980

Post-transcriptional regulation of gene expression in guinea pig tissues.

The formation of individual functional mRNA sequences in higher organisms requires many steps in addition to transcription. These include RNA splicing, polyadenylation, base modification, transport from nucleus to cytoplasm and assembly into polyribosomes. Various control mechanisms must also operate. These will function on a quantitative basis to account for the differing frequency of the various classes of cytoplasmic mRNAs, and also on a qualitative basis, because in higher organisms not all the nuclear poly(A)-containing RNA molecules are found in a cytoplasmic poly(A)-containing RNA population from the same tissue. During our studies on the mechanisms controlling the accumulation of the poly(A)-containing RNA sequences which occur with high and moderately high frequency in the cytoplasm of the lactating guinea pig mammary gland, it became apparent that > 75% of the 20,000 or so poly(A)-containing nuclear RNA sequences were not found in the cytoplasmic poly(A)-containing RNA fraction. Here we demonstrate that many of the poly(A)-containing RNA sequences retained in the nucleus of the lactating guinea pig mammary gland are also present in the nucleus and cytoplasm of the liver of the male guinea pig. These observations provide new evidence for a predominant role of post-transcriptional mechanisms in the regulation of structural gene expression in guinea pig tissue.

Animals↗
PubMed2002

Haemophilus segnis polymicrobial and monomicrobial bacteraemia identified by 16S ribosomal RNA gene sequencing.

This paper reports a case of Haemophilus segnis polymicrobial bacteraemia and a case of H. segnis monomicrobial bacteraemia identified by 16S ribosomal RNA gene sequencing. In the first case, a gram-negative aerobic coccobacillus was isolated with Streptococcus intermedius and S. sanguis from the blood culture of a 32-year-old intravenous drug addict with left thoracic empyema. In the second case, a gram-negative aerobic coccobacillus was isolated from the blood culture of an 82-year-old woman with Clostridium difficile colitis and septicaemic shock. Both gram-negative coccobacilli grew on chocolate agar as colonies of 1 mm in diameter after incubation for 24 h at 37 degress C in air with CO2 5%, but only to pinpoint sizes on blood agar under the same incubation conditions. Both strains were factor V-dependent, but not factor X-dependent. For the first isolate, the Vitek system (NHI) showed that it was 56% likely to be Actinobacillus actinomycetemcomitans and 40% Neisseria subflava; whereas the API system (NH) showed that it was 58% likely to be H. aphrophilus/paraphrophilus and 42% H. parainfluenzae. For the second isolate, the Vitek system (NHI) showed that it was 95% likely to be H. influenzae VIII; whereas the API system (NH) showed that it was 58% likely to be H. aphrophilus/paraphrophilus and 42% H. parainfluenzae. 16S rRNA gene sequencing showed that there were four base differences between isolate 1 and H. segnis and two base differences between isolate 2 and H. segnis, indicating that both isolates most closely resembled a strain of H. segnis. Only two cases of H. segnis bacteraemia were found in the English scientific literature, one in a case of infective endocarditis and the other in a case of pancreatic abscess. Including the present two cases, the overall mortality of H. segnis bacteraemia was 50%.

Adult↗
PubMed1996

The RU5 ('R') region from human leukaemia viruses (HTLV-1) contains an internal ribosome entry site (IRES)-like sequence.

RNA fragments containing the complete R region and the beginning of the U5 region ('R') from the human T cell leukaemia virus 1 (HTLV-1) stimulated the translation of the second cistrons in bicistronic mRNAs. The 5' untranslated region from SV40 early genes (SU) which was unable to stimulate translation of second cistrons amplified markedly the internal ribosome entry site (IRES) effect of the HTLV-1 'R' fragments. The 'R' regions from HTLV-1 have therefore properties similar to internal ribosome entry sites (IRES) originally found in picornavirus. The beginning of the U5 region from HTLV-1 contains a polypyrimidine sequence which is known to play an essential role in the IRES activity in picornavirus. The same experiments carried out using the 'R' region from bovine leukaemia virus (BLV) showed that this sequence has at most a weak IRES effect. One retroviruses, HTLV-1 and perhaps others contain therefore an IRES activity. Interestingly, the combined SU 'R' sequence worked efficiently with different cistrons, different promoters and in all tested cell lines, whereas the poliovirus IRES was active in CHO cells but not in the mouse mammary cell line HC11. The SU 'R' sequence may therefore preferably be used to generate active bicistronic mRNAs.

Animals↗
PubMed2025

A probe-based capture enrichment method for detection of A-to-I editing in low abundance transcripts.

Exactly two decades ago, the ability to use high-throughput RNA sequencing technology to identify sites of editing by ADARs was employed for the first time. Since that time, RNA sequencing has become a standard tool for researchers studying RNA biology and led to the discovery of RNA editing sites present in a multitude of organisms, across tissue types, and in disease. However, transcriptome-wide sequencing is not without limitations. Most notably, RNA sequencing depth of a given transcript is correlated with expression, and sequencing depth impacts the ability to robustly detect RNA editing events. This chapter focuses on a method for enrichment of low-abundance transcripts that can facilitate more efficient sequencing and detection of RNA editing events. An important note is that while we describe aspects of the protocol important for capturing intron-containing transcripts, this probe-based enrichment method could be easily modified to assess editing within any low-abundance transcript. We also provide some perspectives on the current limitations as well as important future directions for expanding this technology to gain more insights into how RNA editing can impact transcript diversity.

RNA Editing↗
PubMed1975

Ribonucleotide sequence homology among avian oncornaviruses.

RNA sequence relatedness among avian RNA tumor virus genomes was analyzed by inhibition of DNA-RNA hybrid formation between 3H-labeled 35S viral RNA and an excess of leukemic or normal chicken cell DNA with increasing concentrations of unlabeled 35S viral RNA. The avian viruses tested were Rous associated virus (RAV)-3, avian myeloblastosis virus (AMV), RAV-60, RAV-61, and B-77 sarcoma virus. Hybridization of 3H-labeled 35S AMV RNA with DNA from normal chicken cells was inhibited by unlabeled 35S RAV-0 RNA as effeciently (100%) as by unlabeled AMV RNA. Hybridization between 3H-labeled 35S AMV RNA and DNA from leukemic chicken myeloblasts induced by AMV was suppressed 100 and 68% by unlabeled 35S RNA from AMV and RAV-0, respectively. Hybridization between 3H-labeled RAV-0 and leukemic chicken myeloblast DNA was inhibited 100 and 67% by unlabeled 35S RNA from RAV-0 and AMV, respectively. It appears therefore that the AMV and RAV-0 genomes are 67 to 70% homologous and that AMV hybridizes to RAV-0 like sequences in normal chicken DNA. Hybridization between AMV RNA and leukemic chicken DNA was inhibited 40% by RNA from RAV-60 or RAV-61 and 50% by B-77 RNA. Hybridization between RAV-0 RNA and leukemic chicken DNA was inhibited 80% by RAV-60 or RAV-61 and 70% by B-77 RNA. Hybridization between 3H-labeled 35S RNA from RAV-60 or RAV-61 and leukemic chicken myeloblast DNA was reduced equally by RNA from RAV-60, RAV-61, AMV or RAV-0; this suggests that RNA from RAV-60 and RAV-61 hybridizes with virus-specific sequences in leukemic DNA which are shared by AMV, RAV-0, RAV-60, and RAV-61 RNA'S. Hybridization between 3H-labeled 35S RNA from RAV-61 and normal pheasant DNA was inhibited 100% by homologous viral RNA, 22 TO 26% BY RNA from AMV or RAV-0, and 30 to 33% by RNA from RAV-60 or B-77. Nearly complete inhibition of hybricization between RAV-0 RNA and leukemic chicken DNA by a mixture of AMV and B-77 35S RNAs indicates that the RNA sequences shared by B-77 virus and RAV-0. It appears that different avian RNA tumor virus genomes have from 50 to 80% homology in nucleotide sequences and that the degree of hybridization between normal chicken cell DNA and a given viral RNA can be predicted from the homology that exists between the viral RNA tested and RAV-0 RNA.

Animals↗
PubMed1983

The sequence of RNA segment 1 of influenza virus A/NT/60/68 and its comparison with the corresponding segment of strains A/PR/8/34 and A/WSN/33.

The complete nucleotide sequence of RNA segment 1 of influenza virus A/NT/60/68, corresponding to the PB2 protein, has been determined. It is 2341 nucleotides long, encoding a predicted product of 759 amino acids with a net charge of +27 1/2 at neutral pH. The predicted amino acid sequence has been compared to the equivalent sequences in influenza viruses A/PR/8/34 and A/WSN/33. Evolutionary divergence, assuming a direct lineage from A/PR/8/34 and allowing for "laboratory drift", is 0.08% per year. The alignment of RNA segment 10 of A/NT/60/68 with segments 1 and 3 is completed, confirming that it is a mosaic of regions from these two segments.

Amino Acid Sequence↗
PubMed1997

A variant of Plasmodium ovale; analysis of its 18S ribosomal RNA gene sequence.

We report here a new variant of human malaria parasite found by comparison of diagnostic results obtained from a new DNA diagnostic method named microtiter plate-hybridization (MPH) and traditional microscopic method. Total five cases of malaria were diagnosed as microscopy-positive but MPH-negative; one case was found in epidemiological research in Vietnam and four cases were obtained from imported malaria in Japan. Although they were quite similar to typical P. ovale morphologically in microscopy, sequence analysis of PCR-amplified DNA fragment revealed that their 18S ribosomal RNA gene sequence was different from published sequence of P. ovale. Combination of MPH and microscopic examination provides us a new method for detection of a new type of malaria parasite which is difficult to distinguish morphologically.

Animals↗
PubMed1994

Evolution of secondary structure in the family of 7SL-like RNAs.

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserved from prokaryotes to distant eukaryotic species. Yet only in primates and rodents did this molecule give rise to retroposing Alu and B1 RNAs and to apparently functional BC200 and 4.5S RNAs. To understand this transition and the underlying molecular events, we examined, by comparative analysis, the evolution of RNA structure in this family of molecules derived from 7SL RNA. RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats were derived from their genomic consensus sequences taken from the literature and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data on 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropositionally active RNAs are conserved among Alu and B1 subfamilies in different genomes. In RNAs that do not proliferate by retroposition these motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by specific interactions with proteins; these functions were either useful for the host or served the selfish propagation of RNA templates within the host genome.

Animals↗
PubMed1977

Sequence analysis of protamine mRNA from the rainbow trout. Depurination and nearest neighbor analysis of protamine cDNA.

Protamine cDNA, which was a full length copy of protamine mRNA was labeled during its synthesis by using deoxynucleoside [alpha-32P]triphosphates. Depurination analysis showed that there were 19 different pyrimidine oligonucleotides in protamine cDNA, some of which contained isomeric sequences. The stoichiometry of the pyrimidine oligonucleotides indicated that, while some sequences probably occur in each of the protamine mRNA components, other sequences are clearly absent from one or more of the components. Several of the pyrimidine oligonucleotides had sequences consistent with the amino acid sequences of the rainbow trout protamines. The longest oligopyrimidine tract, C7T4, had a complementary RNA sequence of AGGAGAGGAGG, a stoichiometry of close to 1, and fitted the amino acid sequence Arg-Arg-Gly-Gly which occurs near the COOH terminus of each of three major protamine components. Other pyrimidine oligonucleotides analyzed were complementary to RNA sequences from the noncoding region of protamine mRNA. There appears to be no preferential use of one particular arginine codon or set of codons. Of the 21 to 22 arginine codons in protamine mRNA no less than 7 and no more than 12 are of the CGX series. The other two codons, AGA and AGG, both occur but not in a series of more than two together. This indicates that the RNA sequences coding for the arginine tracts tend to contain a mixture of arginine codons. Nearest neighbor frequency analysis of protamine cDNA gives a low value for the frequency of the CpG doublet, despite its occurrence in four out of the six arginine codons. This is in accordance with the observation that the sequence CpG is surprisingly rare in vertebrate DNA and in the RNA transcribed from it.

Animals↗
PubMedDate not supplied

Incorporation of an artificial protease and nuclease at the HIV-1 Tat binding site of trans-activation responsive RNA.

The synthesis of a C-5 modified uridine phosphoramidite which contains a primary amino group protected with Fmoc is described. During cleavage and deprotection of chemically synthesized RNA, the Fmoc protecting group is removed to yield a free amino group at a predetermined position in the RNA sequence that can be covalently modified with any reporter group, small structural probes, and biological molecules. This modified uridine phosphoramidite was used to incorporate a reactive primary amino group at position 24 in the HIV-1 Tat binding site of a trans-activation responsive (TAR) RNA sequence during chemical syntheses. Modified RNA phosphoramidite was incorporated into RNA oligomers with more than 97% coupling efficiencies. RNA containing modified uridine was cleaved from the support, deprotected, and desalted according to standard procedures. After deprotection and gel purification, nuclease digestion and HPLC analysis were performed to confirm the incorporation of C-5-aminouridine into the RNA sequence. The effect of modified uridine on TAR RNA structure was analyzed by CD spectroscopy and protein binding assays. Site-specific incorporation of EDTA was accomplished by treating primary amine bearing TAR RNA with an isothiocyanato derivative of nitrobenzyl-EDTA.

Amino Acid Sequence↗