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At least 109 records · Page 6Linked to original sources
PubMed2007

Illuminating the silence: understanding the structure and function of small RNAs.

RNA interference (RNAi) is triggered by double-stranded RNA helices that have been introduced exogenously into cells as small interfering (si)RNAs or that have been produced endogenously from small non-coding RNAs known as microRNAs (miRNAs). RNAi has become a standard experimental tool and its therapeutic potential is being aggressively harnessed. Understanding the structure and function of small RNAs, such as siRNAs and miRNAs, that trigger RNAi has shed light on the RNAi machinery. In particular, it has highlighted the assembly and function of the RNA-induced silencing complex (RISC), and has provided guidelines to efficiently silence genes for biological research and therapeutic applications of RNAi.

Animals↗
PubMed1991

Modulation of B2 containing small RNAs during induced differentiation of murine erythroleukemia cells.

We identified a B2 repetitive element approximately 1.9kb down stream from mouse p53 coding gene. This element was then used as a probe to investigate the expression of B2 containing RNA during the induced differentiation of murine erythroleukemia (MEL) cells. This probe revealed two nuclear and one cytoplasmic RNA species. Nuclear small RNAs had a biphasic variation: a decrease followed by a reaccumulation. The cytoplasmic species was essentially non polysomal, and disappeared after the induced differentiation. The presented results suggest that the regulation of these RNAs is associated to cell proliferation and differentiation respectively.

Animals↗
PubMed2025

Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms: implications for pathogenesis in avocado sunblotch disease.

Avocado sunblotch viroid (ASBVd) is a structured RNA molecule responsible for sunblotch disease of avocado, characterised by distinct chloroses of fruit, leaves, and stems. Despite its impact on avocado, the mechanism by which ASBVd elicits sunblotch symptoms remains unknown. Previous studies on other avsunviroids have shown that viroid-derived small RNAs (vd-sRNAs) with specific sequence mutations can trigger leaf chlorosis via RNA silencing of host genes. Building on this knowledge, we aimed to shed light on the molecular basis of ASBVd pathogenesis by analysing ASBVd sequence variants and ASBVd-sRNAs from bleached and asymptomatic leaf tissues of sunblotch-affected avocado trees. Sequencing of ASBVd clones revealed that variants carrying the pathogenic determinant for bleaching were present in both green and yellow leaf tissues. Next-generation sequencing (NGS) identified ASBVd-sRNAs that varied in abundance between symptomatic and asymptomatic leaf tissues, correlating with viroid titre. We discovered 64 vd-sRNAs spanning the pathogenic region of the ASBVd genome, which were almost exclusively found in yellow tissues. The ASBVd-sRNAs containing the bleaching-associated mutation were predicted to target numerous avocado transcripts for degradation, with 25 of these transcripts significantly downregulated in bleached tissues. Notably, one of these genes, encoding a chloroplastic protein, demonstrated strong evidence of ASBVd-sRNA-guided RNA silencing, presenting a promising candidate for future research into the molecular trigger for ASBVd-induced bleaching symptoms. This study is the first to investigate ASBVd-sRNAs in bleached leaves using NGS. Our findings support the role of RNA silencing in sunblotch symptom development and reveal a unique silencing trigger compared to other avsunviroids.

Persea↗
PubMed1983

Two small RNAs encoded by Epstein-Barr virus can functionally substitute for the virus-associated RNAs in the lytic growth of adenovirus 5.

Adenovirus (Ad) serotypes 2 and 5 synthesize large amounts of two low molecular weight RNAs designated virus-associated (VA) 1 and 2. Recently, genetic and biochemical approaches have been used to show that Ad2 VA1 RNA is required for efficient translation of viral mRNAs produced at late times after infection. Primate cells harboring the Epstein-Barr virus genome (EBV) synthesize large amounts of two low molecular weight RNAs: EBER1 and EBER2. Striking similarities of gene organization have been noted between the genes coding for Ad5 VA RNAs and the EBV EBERs [Rosa, M. D., Gottlieb, E., Lerner, M. R. & Steitz, J. A. (1981) Mol. Cell. Biol. 1, 785-796]. To examine whether the EBRs can functionally substitute for the VA RNAs for the lytic growth of Ad5, we have constructed an Ad5 substitution mutant in which the two VA RNA genes have been deleted and replaced by an EBV DNA segment coding for the two EBERs. The resulting Ad5 mutant synthesizes large amounts of the EBERs and is viable. Thus, two small RNAs of EBV origin, having primary and secondary structures different from those of the VA RNAs, can functionally substitute for the VA RNAs in the lytic growth of Ad5. These results are discussed in the context of mechanism of function of the VA RNAs.

Adenoviruses, Human↗
PubMed1994

Detection of Epstein-Barr virus small RNAs in routine paraffin sections using non-isotopic RNA/RNA in situ hybridization.

The Epstein-Barr virus (EBV) is associated with an increasing range of reactive and neoplastic lesions. There is a need for a sensitive and specific method for detecting latent EBV in routine histological sections. We report the use of a highly sensitive paraffin section RNA/RNA in situ hybridization (ISH) technique using digoxigenin-labelled antisense riboprobes for demonstrating EBV encoded small RNAs (EBERs), EBV gene products that are transcribed in abundance during latent EBV infection. We applied EBER-ISH to 846 paraffin embedded specimens, including cases of reactive lymphoid hyperplasia (n = 28), infectious mononucleosis (16), Burkitt's lymphoma (44), immunodeficiency-associated lymphomas in transplant recipients (9) and AIDS patients (128), Hodgkin's disease (130), CD30 antigen positive lymphomas (106), peripheral T-cell lymphomas (104), sporadic B-cell non-Hodgkin's lymphomas (162), undifferentiated nasopharyngeal carcinoma (86), salivary gland lymphoepithelioma (11), and oral hairy leukoplakia (5). Strong, reproducible EBER staining was seen in EBV latently infected cells in archival surgical biopsy and autopsy specimens. EBER-ISH is specific, has a sensitivity comparable to that of the polymerase chain reaction, and is now the method of choice for the in situ detection of latent EBV infection.

Animals↗
PubMed1996

The SLA RNA gene of Trypanosoma brucei is organized in a tandem array which encodes several small RNAs.

We have recently identified the Spliced Leader Associated RNA (SLA RNA) which is implicated in pre-messenger RNA splicing in Trypanosoma brucei by virtue of its interaction with the 5' splice site of the trans spliced spliced leader RNA (SL RNA) in vivo. Southern analyses reveal that the SLA RNA gene is found in a tandem array of 10-11 copies per haploid genome in T. brucei. Each repeat unit in the array encodes three additional small RNAs of unknown function. RNA polymerase inhibition studies are consistent with transcription of all four genes by the same polymerase, but do not clearly differentiate between RNA polymerases II and III. The SLA RNA has homologs in other kinetoplastid protozoa and we have determined the sequence from two additional species. Trypanosoma cruzi and Crithidia fasciculata. Features of both secondary structure and sequence are conserved in these organisms. One conserved element, 5'-UGUAGUG-3', has the potential to base-pair to the SL RNA upstream of the 5' splice site. This potential interaction is consistent with the sites of SL RNA to SLA RNA psoralen cross-linking in vivo [1].

Animals↗
PubMed1995

Seminomas positive for Epstein-Barr virus by the polymerase chain reaction: viral RNA transcripts (Epstein-Barr-encoded small RNAs) are present in intratumoral lymphocytes but absent from the neoplastic cells.

A possible role of Epstein-Barr virus (EBV) in the pathogenesis of testicular germ cell neoplasms has been suggested repeatedly, but direct evidence for an association of testicular cancer with EBV is lacking. We examined 26 cases of classical seminoma, two spermatocytic seminomas, and 12 cases of nonseminomatous or combined germ cell tumors for the presence and cellular location of EBV with a combined approach using the polymerase chain reaction and nonradioactive in situ hybridization for EBV-encoded small RNAs (EBER1/2). After exclusion of cases without amplifiable DNA, 4/21 (19%) seminomas, but none of the other tumors, were positive for EBV by polymerase chain reaction. In situ hybridization for EBER1/2 showed rare positive lymphocytes, probably latently infected B-cells, in two of these four EBV-positive cases. No EBER-positive tumor cells were found in any of the analyzed tumors. The occurrence of EBV-positive lymphoid cells was not correlated to the frequency of intratumoral lymphocytes, including B-cells, which were present in seminomas in significant numbers. Our study demonstrates the absence of EBV from the neoplastic cells of testicular germ cell tumors and makes a direct role of EBV in the development of these malignancies improbable. Whether the presence of EBER-positive lymphocytes in some seminomas simply reflects the normal occurrence of latently infected cells in lymphoid tissue of seropositive individuals or is influenced by local factors remains to be determined.

Antibodies, Monoclonal↗
PubMed2000

Epstein-Barr virus small RNAs potentiate tumorigenicity of Burkitt lymphoma cells independently of an effect on apoptosis.

The tumorigenic potential of the Burkitt lymphoma (BL) cell line Akata is dependent on the restricted latency program of Epstein-Barr virus (EBV) that is characteristically maintained in BL tumors. Within these cells, EBV-mediated inhibition of apoptosis correlates with an up-regulation of BCL-2 levels in concert with a down-regulation in c-MYC expression that occurs under growth-limiting conditions. Here we addressed whether EBV's effects on apoptosis and tumorigenicity are mediated by the EBV small RNAs EBER-1 and EBER-2. Stable expression of the EBERs in EBV-negative Akata BL cells, at levels comparable to those in EBV-positive cells, significantly enhanced the tumorigenic potential of EBV-negative BL cells in SCID mice, but did not fully restore tumorigenicity relative to EBV-positive Akata cells. Furthermore, wild-type or greater levels of EBER expression in EBV-negative Akata cells did not promote BL cell survival. These data therefore suggest that EBV can contribute to BL through at least two avenues: an EBER-dependent mechanism that enhances tumorigenic potential independent of a direct effect on apoptosis, and a second mechanism, mediated by an as-yet-unidentified EBV gene(s), that offsets the proapoptotic consequences of deregulated c-MYC in BL.

Animals↗
PubMed1982

Small nuclear RNAs from Drosophila KC-H cells; characterization and comparison with mammalian RNAs.

Small molecular weight nuclear RNAs were extracted from cultured Drosophila KC-H cells and characterized by their electrophoretic mobilities in 5--15% gradient acrylamide gels or in 10% acrylamide-7 M urea gels. Comparison between the electrophoretic profiles of these SnRNAs with those from human and mouse cells revealed striking similarities and allowed for assignation of band nomenclatures as established for mammalian cells. Comparison of mobilities in the two gel systems also permitted correspondence between the different nomenclatures established by various groups for this class of RNAs, as well as an approximate estimate of their molecular sizes.

Animals↗
PubMed2006

Identification of microRNAs and other small RNAs from the adult newt eye.

PURPOSE: MicroRNAs (miRNAs) are capable of controlling gene expression by targeting complimentary sequences in many mRNAs. Thus, a small number of miRNAs are capable of regulating expression of many different genes. miRNAs have been found in all animals from Drosophila to human and they are highly conserved. This work was undertaken in order to identify such RNAs in the newt eye. METHODS: Cloning of these RNAs was attempted after isolating and fractionating total RNA from the adult newt eye. A gel slice ranging from about 15 to 30 nucleotides in length was cut and the extracted RNA was cloned after several processes involving reverse transcription and linker addition. For expression analysis and verification during the process of lens regeneration we used as a probe mir-124a. RESULTS: Several microRNAs, piRNAs and other small RNAS were identified. Some of them have eye specific gene targets in other species, but for many a function in the eye remains to be attributed. Expression of miR-124a showed an interesting regulation in the lens regeneration-competent dorsal iris. CONCLUSIONS: The cloned miRNAs and other small RNAs are the first to be reported for this animal and might bear significance in regulating processes that are unique to the newt eye, i.e., regeneration of the lens and retina.

Animals↗
PubMed1980

Stimulation of transcription of chromatin by specific small nuclear RNAs.

Small molecular weight nuclear RNAs (SnRNA) purified from the chromatin of SV40-transformed W138 human fibroblasts have been found to stimulate transcription of chromatin in homologous isolated nuclei as well as in nuclei of untransformed human and monkey cells. Stimulation in normal cell nuclei involves an increase in both initiation sites and rate of elongation of RNA chains. Fractionation of the SnRNA in polyacrylamide gradient slab gels revealed that the "active" RNA was 160-175 nucleotides in length.

Cell Line↗
PubMed1993

A novel protein encoded by small RNAs of parvovirus B19.

A second small ORF contained within the parvovirus B19 genome has been shown to direct synthesis of a small 7.5-kDa protein. These results extend our previous studies in which we identified a family of 11-kDa proteins (J. St. Amand, C. Beard, K. Humphries, and C.R. Astell, Virology 183, 133-142, 1991; J. St. Amand and C.R. Astell, Virology, 192, 121-131, 1993). The presumed ORF encoding the 7.5-kDa protein was discovered on the left side of the viral genome and was identified by expression of the protein and in vitro mutagenesis. Two small RNA transcripts of B19 virus were demonstrated to be able to direct the synthesis of this 7.5-kDa protein by in vitro translation using rabbit reticulocyte lysates. Expression of 7.5-kDa protein was also observed in COS-7 cells transfected with a plasmid containing the B19 genome as well as in human peripheral mononucleocytes infected with B19 virus. In both cases the 7.5-kDa protein was detected by immunoprecipitation of cell lysates with polyclonal antibodies raised against a synthetic peptide corresponding to a portion of the predicted protein sequence. These data partially reveal the function of the abundant small RNA transcripts produced by parvovirus B19.

Amino Acid Sequence↗
PubMed1985

Isolation and partial characterization of U1-U6 small RNAs from Bombyx mori.

We have used a variety of techniques to characterize the U-series small nuclear RNAs from the posterior silk gland of Bombyx mori. Six molecular species have been identified which correspond to the vertebrate U1-U6 RNAs by the following criteria: (a) presence of the RNAs in ribonucleoprotein particles which can be immunoprecipitated by lupus Sm antisera; (b) presence of a 2,2,7-trimethylguanosine cap, as assayed by immunoprecipitation with anti-2,2,7-trimethylguanosine IgG; (c) size, as assayed by acrylamide/urea gel electrophoresis using HeLa cell U-RNA markers; and (d) primary nucleotide sequence, as determined by chemical/enzymatic cleavage of end-labeled molecules. The high conservation of primary sequence (66-81% homology based on partial sequences) relative to the corresponding vertebrate U-RNAs has permitted unambiguous identification of each molecule. With the exception of two subspecies of U3 RNA, the U-snRNAs of Bombyx exhibit a striking conservation of secondary structure relative to the proposed structures of the U-RNAs of vertebrates. This conservation is best exemplified by several compensatory base alterations that result in the maintenance of hairpin structures. These are particularly evident in U1 and U5 RNAs. Bombyx U3 is interesting in that two subspecies (of a total of four that were sequenced) diverge considerably in sequence (and presumably in structure) relative to the U3 RNA of vertebrates. The most abundant U-RNAs in the posterior silk gland appear to be U1 and U2, while U3-U6 are present in relatively small amounts.

Animals↗
PubMed1996

The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions.

We have discovered that all known yeast and vertebrate small nucleolar RNAs (snoRNAs), except for the MRP/7-2 RNA, fall into two major classes. One class is defined by conserved boxes C and D and the other by a novel element: a consensus ACA triplet positioned 3 nt before the 3' end of the RNA. A role for the ACA box is snoRNA stability has been established by mutational analysis of a yeast ACA snoRNA (snR 11). Full function of the box depends on the integrity of an adjacent upstream stem. All members of the yeast ACA family are associated with the GAR1 protein. Binding of this or another common small nucleolar ribonucleoprotein particle protein is predicted to be a critical entry point to snoRNA posttranscriptional life, including precise formation of the snoRNA 3' end.

Animals↗
PubMed1991

EAP, a highly conserved cellular protein associated with Epstein-Barr virus small RNAs (EBERs).

Human B lymphocytes latently infected with Epstein-Barr virus (EBV) synthesize very large amounts (5 x 10(6)/cell) of two small nuclear RNAs called EBERs (Epstein-Barr encoded RNAs). These RNAs are of unknown function and, like many RNA polymerase III (Pol III) transcripts, bind the La autoantigen. We have discovered that the EBERs also associate with a second highly abundant host-encoded protein designated EAP (EBER associated protein). Human EAP is a small (14,777 dalton, 128 amino acid) polypeptide that binds both EBER 1 and EBER 2. EAP is also found in association with one or both of two analogous virally-encoded RNAs found in baboon cells infected with herpesvirus papio (HVP). We have devised a purification procedure for EAP and have cloned its cDNA from a human placental cDNA library using amino acid sequence data and the polymerase chain reaction (PCR). The predicted amino acid sequence of EAP shows a strong resemblance (77% identity) to an endodermal, developmentally regulated sea urchin protein called 217 (Dolecki et al., 1988). EAP contains a potential nuclear localization signal and a highly acidic carboxy terminus, but does not display marked similarity to any other RNA binding proteins.

Amino Acid Sequence↗
PubMed2003

Enhanced gene silencing by the application of multiple specific small interfering RNAs.

Small interfering RNA duplexes (siRNA) induce gene silencing in various eukaryotic cells, although usually in an incomplete manner. Using chemically synthesized siRNAs targeting the HIV-1 co-receptor CXCR4 or the apoptosis-inducing Fas-ligand (FasL), co-transfection of cells with two or more siRNA duplexes targeting different sites on the same mRNA resulted in an enhanced gene silencing compared with each single siRNA. This was shown in the down-regulation of protein and mRNA expression, and functionally in the inhibition of CXCR4-mediated HIV infection and of FasL-mediated cell apoptosis. Transfection efficiency determined for the FasL-specific siRNAs was dose-dependent and varied among the siRNAs tested, but was not the main reason for the enhanced gene silencing.

Apoptosis↗
PubMed2004

The long hand of the small RNAs reaches into several levels of gene regulation.

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.

Animals↗