Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78Linked to original sources
PubMed1991

Emergence and possible transmission of amantadine-resistant viruses during nursing home outbreaks of influenza A (H3N2).

Outbreaks of influenza A (H3N2, A/Shanghai/11/87-like) occurred in two partially (60% and 79%) vaccinated nursing home populations in January 1988. A retrospective cohort study using chart review was designed to assess the effectiveness of influenza vaccination and amantadine prophylaxis (100 mg per day) in controlling the outbreaks and to determine the amantadine susceptibility of influenza viruses isolated from case-patients. The point estimate of vaccine efficacy in preventing influenza-like illness was -33% (95% confidence interval -115% to 18%). However, 9% of vaccinated case-patients died within 14 days after onset of influenza-like illness compared with 26% of unvaccinated case-patients (relative risk = 0.4, 95% confidence interval 0.1-1.0). There was no significant difference in illness severity among case-patients who became ill before amantadine prophylaxis was started (n = 84) compared with those who became ill while taking amantadine (n = 34). Four virus isolates obtained before amantadine prophylaxis was started demonstrated 52-68% inhibition by 1 microgram/ml of amantadine; by comparison, six isolates (resistant viruses) obtained from residents who became ill while taking amantadine demonstrated 1-18% inhibition. The resistant viruses had four different RNA sequences in the gene coding for the M2 protein transmembrane region. Three resistant viruses with identical RNA sequences were isolated from residents living in contiguous rooms who had onset of signs and symptoms during a 6-day interval. Further studies are needed to determine how frequently and under what circumstances resistant viruses occur when antiviral agents are used to control institutional influenza A outbreaks. Strategies for antiviral agent administration that limit the emergence and transmission of resistant virus strains may be needed.

Aged↗
PubMed2004

Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments.

We have applied tests for detecting recombination to genes of foot-and-mouth disease virus (FMDV). Our approach estimated summary statistics of linkage disequilibrium (LD), which are sensitive to recombination. Using the genealogical relationships, rate heterogeneity and mutation parameters estimated from individual sets of aligned gene sequences, we simulated matching RNA sequence datasets without recombination. These simulated datasets allowed for recurrent mutations at any site to mimic homoplasy in virus sequence data and allow construction of null distributions for LD parameters expected in the absence of recombination. We tested for recombination in two ways: by comparing LD in observed data with corresponding null distributions obtained from simulated data; and by testing for a negative relationship between observed LD between pairs of polymorphic nucleotide sites and inter-site distance. We applied these tests to six FMDV datasets from four serotypes and found some evidence for recombination in all of them.

Capsid Proteins↗
PubMed2005

Evolution of hepatitis delta virus RNA genome following long-term replication in cell culture.

Previous studies have defined a novel cell culture system in which a modified RNA genome of hepatitis delta virus (HDV) is able to maintain a low level of continuous replication for at least 1 year, using a separate and limited DNA-directed source of mRNA for the essential small delta protein. This mode of replication is analogous to that used by plant viroids. An examination was made of the nucleotide changes that accumulated on the HDV RNA during 1 year of replication. The length of the RNA genome was maintained, except for some single-nucleotide deletions and insertions. There was an abundance of single-nucleotide substitutions, with a 22-fold excess of these being base transitions rather than transversions. Of the detected transitions, at least 70% were consistent with being the consequences of posttranscriptional RNA editing by an adenosine deaminase acting on RNA. The remainder of the changes, including the single-nucleotide insertions and deletions, are likely to be the consequence of misincorporation during transcription. In addition, an intermolecular competition assay was used to show that the majority of the genomes present after 1 year of replication were essentially as competent in replication as the original single HDV RNA sequence that was used to initiate the genome replication. A model is provided to explain how, in this experimental system, the observed single-nucleotide changes were essentially neutral in terms of their effect on the ability of the HDV genome to carry out continued rounds of replication.

Base Sequence↗
PubMed1995

The microbiology and histopathology of human root caries.

Based on numerous microbiological studies performed over the past several decades, it is clear that mutans streptococci can cause human root caries. S. mutans fulfills the criteria for implicating bacteria in the etiology of a mixed infection. For example, S. mutans is found in high numbers in lesion sites, higher than on sound root surfaces in the same subject. Subjects make elevated antibody levels to S. mutans antigens. The organism produces a number of virulence factors including metabolic acid from dietary sucrose and extracellular polysaccharides which facilitate bacterial colonization of tooth surfaces. Eliminating or reducing the number of S. mutans reduces the number of root caries lesions and can even result in "healing" of incipient lesions. There is also data demonstrating the cariogenic potential of S. mutans in animal models. Clearly, S. mutans fulfills the aforementioned requirements. Further, there is also evidence to implicate Lactobacillus as being important in the pathogenesis of root caries by virtue of its association with S. mutans in these lesions. There is less recent evidence regarding the importance of Actinomyces in this disease. While this microorganism is present in root caries and while animal studies clearly point to their cariogenic potential, more recent studies with few exceptions fail to find much association between Actinomyces and root caries. There is an important caveat, however. The Actinomyces may have subspecies groups which are more highly virulent and more closely involved in the etiology of root caries than other groups. For example, A. viscosus serovar 2 is associated with root caries. This and other subspecies groups may produce certain virulence factors not found within Actinomyces species as a whole. For this group of microorganisms and for other potential pathogens, techniques in molecular biology such as 16S ribosomal RNA sequencing offers the hope of more precisely defining species and unraveling what may be largely problems in bacterial taxonomy. Ribosomal RNA sequencing may reveal taxonomic relationships not apparent with classical phenotypic or serologic analyses. Other molecular methods, such as DNA or RNA probes to specific virulence factors may also reveal relationships between clinical lesions and microorganisms possessing these virulence factors. Finally, there are clearly a number of additional species which may have importance in root surface caries as shown in some studies. These techniques can be used to identify the distribution of novel, even uncultivable bacteria in root caries lesions and in this way establish their role in this important disease.

Actinomyces↗
PubMed2025

Tandem splice acceptor sites: Profiling their relevance to human disease.

PURPOSE: Interpretation of variation, particularly the creation or disruption of tandem splice acceptor sites (NAGNnAG variants), challenges genomic medicine practice. METHODS: We analyzed the creation and disruption of dinucleotide AG sites within ±30 bases of natural splice-acceptor sites in the GRCh37 human reference genome. These results were compared with variant data from the ClinVar and gnomAD databases, as well as with data from 779 National Institutes of Health Undiagnosed Diseases Program study participants. Using RNA sequencing, we assessed the splicing at NAGNnAG variants for 107 of the Undiagnosed Diseases Program participants and compared the empirical data with SpliceAI predictions. RESULTS: Creation or disruption of NAGNnAG sites within 30 bases of the natural splice acceptor are enriched in ClinVar compared with gnomAD; however, such variants in the 2 databases are rarely differentiated by SpliceAI scores. Empirical evaluation via RNA sequencing analysis supported novel acceptor site usage from -21 to +30; splice-altering variants did not predominate in a specific region or have SpliceAI scores invariantly, suggesting increased spliceogenicity. CONCLUSION: NAGNnAG variants within 30 bp of the natural splice acceptor have a high probability of clinical relevance and are poorly contextualized for clinical utility. Their interpretation benefits from empirical evaluation via RNA analysis.

Humans↗
PubMed1996

Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism.

The adenovirus major late arrest site blocks transcription by mammalian RNA polymerase II in vitro downstream of the major late promoter but not the mouse beta-globin promoter. We localized the sequences responsible for anti-arrest to the 5' end of the beta-globin transcript and demonstrated that anti-arrest required that this region of RNA form base pairs with the nascent transcript upstream of the arrest site. Small antisense RNA or DNA oligonucleotides hybridizing upstream of the arrest site also prevented arrest when added in trans. Our results suggest that arrest is accompanied by retraction of the nascent transcript into the interior of the polymerase and that hybridization of the transcript prevents this movement, thereby allowing the polymerase to continue elongation.

Animals↗
PubMed1984

Expression of endogenous murine leukemia virus in transplantable tumor cells and DNA methylation of the viral sequences.

A cell line derived from early passage of a transplantable tumor in athymic mice that initially had been injected with human breast adenocarcinoma cells produced a substantial amount of RNA sequences related to the Kirsten murine leukemia virus. The cell line derived from later passage of transplantation of these tumors diminished viral RNA production. Expression of the viral RNA sequences in these cell lines is inversely correlated with the level of viral DNA methylation in the mouse genome.

Adenocarcinoma↗
PubMed2026

Single-cell transcriptomics reveals that air-liquid interface culture promotes goblet cell differentiation and inhibits glycolysis in organoid cell monolayers.

Faithfully recapitulating the cellular heterogeneity of the intestinal epithelium is essential when using organoid models. Air-liquid interface (ALI) culture has been shown to promote secretory cell differentiation, but its impact on gene expression in each epithelial cell type remains unclear. In this study, we used single-cell RNA sequencing (scRNA-seq) to characterize the cellular heterogeneity of rabbit cecum-derived organoid monolayers grown under immerged or ALI conditions. We then compared these organoid cell type-specific gene expression profiles to a scRNA-seq atlas of the rabbit cecal epithelium in vivo. We selected the rabbit model notably because, unlike mice, it possesses BEST4+ epithelial cells, a newly discovered subset of mature absorptive cells. Our analysis revealed a high degree of transcriptomic similarity between in vivo and organoid-derived stem and transit-amplifying cells. ALI culture markedly enhanced the differentiation of the secretory lineage, especially goblet cells, whose transcriptome closely resembled that of in vivo goblet cells. Furthermore, ALI was the only condition allowing the detection of enteroendocrine cells. BEST4+ cells, however, were absent from organoids in immerged or ALI conditions despite their presence in vivo. In addition, ALI culture led to a consistent downregulation of hypoxia and glycolysis-associated genes across all cell types, which suggests a metabolic shift likely driven by increased oxygen availability in ALI conditions. Cell-cell communication analyses further indicated that ALI more closely mirrored in vivo patterns than immerged condition. Altogether, these results demonstrate that ALI culture allows for better recapitulation of the in vivo cellular heterogeneity and molecular signatures of the intestinal epithelium.NEW & NOTEWORTHY Using single-cell RNA sequencing, this study shows that air-liquid interface (ALI) culture enhances secretory lineage differentiation of intestinal organoid cell monolayers and improves transcriptomic similarity to the native epithelium. ALI reduced hypoxia-associated gene expression and better recapitulates in vivo-like cell-cell interactions, supporting its value for modeling intestinal epithelial heterogeneity in organoids.

Animals↗
PubMed1978

DNA-dependent RNA polymerase II from Acanthamoeba castellanii. Comparison of the catalytic properties and subunit architectures of the trophozoite and cyst enzymes.

The actively growing cells (trophozoites) of the amoeba Acanthamoeba castellanii were found to contain three or perhaps four different forms of class II DNA-dependent RNA polymerase (EC 2.7.7.6). The chromatographic and catalytic properties of all forms of the Acanthamoeba class II polymerases suggest them to be cognates of the class II polymerases previously reported. The predominant form was purified to near homogeneity and its subunit composition determined. Nine different polypeptides were found associated with the purified enzyme: 21 000; 185 000; 140 000; 70 000; 35 000; 21 000; 19 000; 18 500 and 16 200. These polypeptides were interpreted in terms of two class II RNA polymerases which differ in the molecular weight of their largest subunit. When A. castellanii is transferred to a medium lacking nutrients, the cells undergo cellular differentiation resulting in the formation of metabolically inactive cells (cyst formation). During this process there are significant changes in the RNA sequences transcribed. In contrast to this, we find that the chromatographic and catalytic properties of all of the class II RNA polymerases remain unchanged. Further, the subunit architecture of the predominant form(s) of polymerase II is unaltered. These findings suggest that although new RNA sequences are transcribed during encystment their appearance is not a consequence of extensive alterations in the subunit composition of the major class II RNA polymerase.

Amanitins↗
PubMed1978

Recombination between viral and cellular sequences generates transforming sarcoma virus.

A series of sarcoma viruses has been obtained from tumors induced by transformation-defective (td) mutants of the Schmidt-Ruppin strain of Rous sarcoma virus, subgroup A (SR-A). The RNA sequences of these "recovered avian sarcoma viruses" (rASVs) were compared with those of td mutants and of SR-A by oligonucleotide fingerprinting. Of six sarcoma-specific oligonucleotides present in SR-A RNA, three to six were missing in the RNAs of the four td mutants examined. All six isolates of rASV examined have regained these six oligonucleotides. In addition, most rASV RNAs have three new oligonucleotides not present in the RNA either of td mutants or of SR-A. The newly obtained oligonucleotides are located between 800 and 2600 nucleotides from the 3' end of rASV RNA, which corresponds to the src region of SR-A RNA mapped previously. Furthermore, viral RNAs of two td mutants isolated from a clone of rASV lack most src-specific oligonucleotides, including the three new ones. No differences were found among RNAs of td, SR-A, and rASV in the regions outside of src. Our results indicate that RNA sequences that rASVs have acquired from cells in the process of conversion from td virus to transforming virus are mapped within the src region and segregate with the transforming function. Some of the sequences are new and some are identical with those in SR-A RNA.

Animals↗
PubMed1983

The nucleotide sequence of Bacillus subtilis tRNA genes.

Clones carring Bacillus subtilis tRNA genes were isolated from a lambda 816 library. A recombinant phage lambda 816-BS83 which was hybridized effectively with unfractionated tRNA probes contained a 3-kb fragment. By a Southern's blot analysis, it was found that tRNA genes were located in Eco RI-Hinc II region of this fragment. Sequence determination revealed the presence of a cluster of four tRNA genes in this region. The gene organization was as follows: tDNALys-9bp-tDNAGlu-81bp-tDNAAsp-30bp-tDNAPhe. The RNA sequences expected from tDNALys and tDNAPhe were identical with the reported RNA sequences. Two tRNA genes, tDNALys and tDNAAsp encoded the CCA sequence of 3'-terminal region, but the other two, tDNAGlu and tDNAPhe did not. A promoter-like sequence which corresponds to the sigma 55-recognition site was found in a region about 100bp upstream from tDNALys.

Bacillus subtilis↗
PubMed2004

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

MOTIVATION: RNA structure motifs contained in mRNAs have been found to play important roles in regulating gene expression. However, identification of novel RNA regulatory motifs using computational methods has not been widely explored. Effective tools for predicting novel RNA regulatory motifs based on genomic sequences are needed. RESULTS: We present a new method for predicting common RNA secondary structure motifs in a set of functionally or evolutionarily related RNA sequences. This method is based on comparison of stems (palindromic helices) between sequences and is implemented by applying graph-theoretical approaches. It first finds all possible stable stems in each sequence and compares stems pairwise between sequences by some defined features to find stems conserved across any two sequences. Then by applying a maximum clique finding algorithm, it finds all significant stems conserved across at least k sequences. Finally, it assembles in topological order all possible compatible conserved stems shared by at least k sequences and reports a number of the best assembled stem sets as the best candidate common structure motifs. This method does not require prior structural alignment of the sequences and is able to detect pseudoknot structures. We have tested this approach on some RNA sequences with known secondary structures, in which it is capable of detecting the real structures completely or partially correctly and outperforms other existing programs for similar purposes. AVAILABILITY: The algorithm has been implemented in C++ in a program called comRNA, which is available at http://ural.wustl.edu/softwares.html

Algorithms↗
PubMed1993

Identification of an RNA binding site for human thymidylate synthase.

Previous studies from this laboratory have shown that human TS mRNA translation is regulated by its protein product in a negative autoregulatory manner. In this paper, we identify an RNA binding site for TS protein located within the first 188 nt of TS RNA. A 36-nt RNA sequence contained within this 188-nt fragment, corresponding to nt 75-110 and including the translational initiation site, binds TS protein with an affinity similar to that of both the full-length and the 188-nt TS RNA sequences. Variant RNAs with either a deletion or a mutation at the translational initiation region are unable to compete for TS protein binding. UV crosslinking studies reveal that an RNA fragment of approximately 36 nt is protected from RNase T1 digestion by TS protein binding. A second TS protein-binding site is localized within the protein-coding region corresponding to nt 434-634. These findings demonstrate a specific interaction between human TS protein and its TS RNA and identify an RNA binding site that includes the translational initiation site.

Base Sequence↗
PubMed2025

HMGA2 links morphological evolution and microenvironment dynamics to systemic therapy response in clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) exhibits significant heterogeneity due to morphological changes and tumor microenvironment dynamics, influencing systemic therapy responses. While the role of high-mobility group AT-hook 2 (HMGA2) in tumor progression has been implicated in other cancers, its significance in ccRCC remains unclear. This study investigates the role of HMGA2 in these processes and its clinical impact. METHODS: Spatial transcriptomics (ST) was performed on primary ccRCC samples to investigate expression trajectories associated with HMGA2 expression and morphological evolution. In metastatic ccRCC cohorts treated with systemic therapy, immunohistochemistry and bulk RNA sequencing data were analyzed to evaluate molecular and clinical features in relation to HMGA2. Single-cell RNA sequencing (scRNA-seq) data were used to explore immune cell populations and their interactions. Based on these findings, multiplex immunohistochemistry (mIHC) assessed spatial distribution, cell-cell interactions, and pathological responses of key immune populations. RESULTS: HMGA2 expression was associated with aggressive morphological patterns, such as solid sheets and rhabdoid/sarcomatoid. ST revealed a progressive increase in HMGA2 expression along the morphological trajectory, marked by a shift from clear to eosinophilic cytoplasm, with eccentric nuclei and prominent nucleoli, and loss of vascular architecture. HMGA2-high tumors exhibited aggressive phenotypes driven by cell cycle, epithelial-mesenchymal transition, and inflammatory signaling pathways. Clinically, patients with high HMGA2 had worse progression-free survival but responded better to immune checkpoint inhibitor combination (Combo-ICI) therapy than to tyrosine kinase inhibitor monotherapy. To assess the immune landscape, scRNA-seq data revealed that HMGA2-high tumors were enriched with progenitor exhausted CD8+ T cells (Tpex), along with increased frequencies of conventional dendritic cell type 1 (cDC1) and inflammatory cDC type 2, which were found to interact with Tpex via ICAM-1. mIHC confirmed that Tpex were enriched among Combo-ICI responders in HMGA2-high tumors, with higher densities and closer proximity to ICAM-1+ cDC1. CONCLUSIONS: These findings suggest that dynamic HMGA2 expression contributes to morphological evolution and modulates immune responses through enhanced Tpex-cDCs engagement, serving as a potential marker for systemic therapy response in ccRCC. However, additional experimental studies are required to validate these mechanisms.

Humans↗
PubMed2002

cis-acting sequences of Bacillus subtilis pyrG mRNA essential for regulation by antitermination.

Expression of the Bacillus subtilis pyrG gene, which encodes CTP synthetase, is repressed by cytidine nucleotides. Regulation involves a termination-antitermination mechanism acting at a transcription terminator located within the 5' untranslated pyrG leader sequence. Deletion and substitution mutagenesis of a series of pyrG'-lacZ transcriptional fusions integrated into the B. subtilis chromosome demonstrated that only the terminator stem-loop and two specific 4- to 6-nucleotide RNA sequences were required for derepression of pyrG by starvation for cytidine nucleotides. The first sequence, GGGC/U, comprises the first four nucleotides at the 5' end of the pyrG transcript, and the second, GCUCCC, forms the first six nucleotides of the 5' strand of the terminator stem. All of the nucleotides lying between the two required RNA sequences can be deleted without loss of regulation. We propose that an as-yet-unidentified regulatory protein binds to these two RNA segments and prevents termination of transcription in the pyrG leader region when intracellular CTP levels are low.

5' Untranslated Regions↗
PubMed1976

Preferential synthesis of viral late RNA by nuclei isolated from SV40 lytically infected cells.

Nuclei from SV40-infected monkey cells were isolated late in lytic infection and their cell-free transcriptional activity was characterized. 3H-RNA synthesized in vitro was hybridized to excess quantities of separated SV40 DNA strands which were each covalently bound to Sepharose. It was found that 3-5% of the newly synthesized RNA is virus-specific and that the plus-strand DNA, coding for late RNA sequences, is transcribed at a rate about 15 times higher than that of the minus-strand DNA, which codes for early RNA sequences. This indicates that transcriptional control has a major role in determining the relative abundancy of early and late RNA classes in lytically infected cells.

Amanitins↗
PubMed1984

Intracellular site of U1 small nuclear RNA processing and ribonucleoprotein assembly.

We have investigated the intracellular site and posttranscriptional immediacy of U1 small nuclear RNA processing and ribonucleoprotein (RNP) assembly in HeLa cells. After 30 or 45 min of labeling with [3H]uridine, a large amount of U1-related RNA radioactivity in the cytoplasm was found by using either hypotonic or isotonic homogenization buffers. The pulse-labeled cytoplasmic U1 RNA was resolved as a ladder of closely spaced bands running just behind mature-size U1 (165 nucleotides) on RNA sequencing gels, corresponding to a series of molecules between one and at least eight nucleotides longer than mature U1. They were further identified as U1 RNA sequences by gel blot hybridization with cloned U1 DNA. The ladder of cytoplasmic U1 RNA bands reacted with both RNP and Sm autoimmune sera and with a monoclonal Sm antibody, indicating a cytoplasmic assembly of these U1 RNA-related molecules into complexes containing the same antigens as nuclear U1 RNP particles. The cytoplasmic molecules behave as precursors to mature nuclear U1 RNA in both pulse-chase and continuous labeling experiments. While not excluding earlier or subsequent nuclear stages, these results suggest that the cytoplasm is a site of significant U1 RNA processing and RNP assembly. This raises the possibility that nuclear-transcribed eucaryotic RNAs are always processed in the cell compartment other than that in which they ultimately function, which suggests a set of precise signals regulating RNA and ribonucleoprotein traffic between nucleus and cytoplasm.

Autoantibodies↗