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PubMed1987

Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity.

Previous experiments have shown that mRNA translation in frog oocytes can be inhibited by the injection of a complementary antisense RNA. Here we explore the use of antisense RNAs to study the functions of localized maternal mRNAs during postfertilization development. While developmental abnormalities were observed in injected fertilized eggs, these abnormalities could not be attributed to the antisense RNA since they were induced at a similar frequency in control embryos. Biochemical tests show that the injected antisense RNA does not form stable hybrids in vivo with its complementary endogenous mRNA. In addition, a novel activity that unwinds RNA:RNA duplexes was found. This activity exists at high levels in eggs and early embryos and is absent or very much diminished in oocytes and late blastula embryos. These results suggest that antisense RNAs may be of limited use in studying the functions of maternal RNAs in Xenopus.

Animals↗
PubMed1980

Transcription and metabolism of RNA from the Drosophila melanogaster heat shock puff site 93D.

Characteristics of the major heat shock puff site 93D and the RNA transcribed from it have been investigated by hybridization to polytene chromosome preparations and to recombinant DNA. By saturation in situ hybridization, the length of the transcribed region at 93D is twice that of the mRNA coding region at the heat shock puff site 87A. From the known length of the heat shock mRNA sequence at 87A, we calculate that the minimum length of the transcribed region at 93D is 9.6 kb (kb = kilobase, i.e., 1,000 nucleotides).--The metabolism of RNA transcribed from 93D has been compared with that of RNA coding for the major heat shock protein hsp70 in cells incubated for one hour at 35 degrees C. Hsp70 mRNA sequences, assayed by hybridization to a specific recombinant DNA probe and by in situ hybridization to 87A, were found in both poly(A)+ and poly(A)- cytoplasmic RNA and were more concentrated in cytoplasmic RNA than in nuclear RNA. In contrast, sequences complementary to 93D, assayed by in situ hybridization, were more concentrated in nuclear than in cytoplasmic RNA. This implies that sequences from 93D exit from the nucleus at a lower rate and/or are turned over in the cytoplasm at a higher rate, than sequences from 87A. Site 93D is also unusual in that its transcribed region is represented in both poly(A)+ and poly(A)- nuclear RNA, even though 93D-complementary RNA in the cytoplasm is predominantly poly(A)-. Finally, only 28-58% of the length of DNA transcribed at 93D is represented in cytoplasmic RNA, indicating that only a portion of the sequences transcribed from 93D are exported from the nucleus. The transcripts from two heat shock loci, 93D and 87A, thus appear to be metabolized in significantly different ways.

Animals↗
PubMed1993

In situ hybridization of virulent canine distemper virus in brain tissue, using digoxigenin-labeled probes.

Only a few hybridization experiments have been performed for detection of canine distemper virus (CDV) nucleic acid sequences in tissue cultures and in various tissues. Those published studies used probes derived from tissue culture-adapted CDV, and hybridization signals were not obtained in the CNS tissue, although infective CDV and viral antigen were detectable in this tissue. We developed probes complementary to virulent CDV and were able to detect viral RNA not only in primary brain cell cultures, but also in brain tissues, by use of in situ hybridization. Sensitivity of the test at least equaled that of immunohistochemistry. We applied digoxigenin-labeled, strand-specific RNA probes complementary to the nucleoprotein-coding viral nucleic acid sequence. Our results indicate that to detect CDV nucleic acid sequences in brain tissues, it is essential to use probes derived from the virulent virus.

Animals↗
PubMed1980

Correlation between splicing sites within an intron and their sequence complementarity with U1 RNA.

We have determined the nucleotide sequence of two short introns (respectively 215 and 90 nucleotides) in the chick alpha 2-collagen (type I) gene as well as parts of the adjacent exons. For one of these introns we find that the 5' end of U1 RNA is complementary not only to the two ends of the intron but also to one end of the intron and sequences inside this intron. These complementarities predict three potential internal splicing sites. By S1 mapping experiments we find three discrete RNA precursors in which different portions of this intron have been deleted. The sizes of the deleted segments are in good agreement with the location of the predicted splicing points inside the intron. The DNA sequence indicates that removal of one portion of the intron should still allow the subsequent elimination of the rest of the intron and the correct splicing of the coding segments located at each end of the intron. The new introns created by the first splicing events contain sequences at each end which are also complementary to U1 RNA. Our data indicate that in the intron which we have examined the sequences at the 3' end of the intron are removed before those at the 5' end.

Animals↗
PubMed1977

RNA synthesis of vesicular stomatitis virus. VII. Complete separation of the mRNA's of vesicular stomatitis virus by duplex formation.

Full-length virion RNA and complementary mRNA's of vesicular stomatitis virus can be annealed to each other, digested with RNases, and then separated as five unique duplex RNA molecules on polyacrylamide slab gels. Similar RNA duplexes were detected whether mRNA or virion RNA was the radioactive component and whether the mRNA was synthesized in vitro or in vivo. The sharp banding pattern of these RNA molecules was dependent on treatment with RNase T2, suggesting that removal of poly(A) is necessary. Identification of the coding region contained in each RNA duplex was based on their previous identification as single-stranded mRNA on formamide-containing, polyacrylamide gels. Because the two smallest mRNA'S had not been previously separated, their identification was based on their in vitro transcriptional gene order. In the order of increasing mobilities on the slab gels, the RNA duplexes are identified as the hybrid of the region of the genome RNA hybridized to the complementary mRNA coding for the large protein, the glycoprotein, the nucleocapsid protein, the core-associated NS protein, and the matrix protein (L,G,N,NS, and M). Several lines of evidence support the presence of undegraded complete mRNA, excluding poly(A), in these RNA duplexes. Also, the two smallest mRNA's, separated by duplex formation, were denatured, and their individual oligonucleotide fingerprints were determined. From chemical length determinations, the molecular weights of the mRNA, minus poly(A), are 2.78 X 10(5) and 2.5 X 10(5), respectively, for the mRNA's of the NS and M proteins.

Cell Line↗
PubMed1996

Sequence of echinochloa hoja blanca tenuivirus RNA-5.

The sequence is presented of RNA-5 of Echinochloa hoja blanca tenuivirus, a second tenuivirus associated with rice cultivation in Latin America (after rice hoja blanca virus). The RNA is 1334 nucleotides long and contains in the complementary sense RNA a single long open reading frame. The deduced amino acid sequence of this open reading frame shows that it encodes a highly basic and hydrophilic 44 kD protein (pc5) with about 50% similarity to the pc5 protein of maize stripe virus (MStV). This and other features of the RNA are discussed.

Amino Acid Sequence↗
PubMed2000

Hepatitis C virus RNA codes for proteins and replicates: does it also trigger the interferon response?

Hepatitis C virus (HCV) is a positive sense virus with a genomic RNA molecule roughly 9,600 nucleotides in length. The single-stranded genomic RNA has a nontranslated region (NTR) at each end and a long open reading frame (coding region) in between. The 5'NTR and portions of the 3'NTR are the most conserved parts of HCV RNA. These conserved regions contain signals for replication and translation. Much of the 5'NTR is folded into a structure that binds ribosomes. This structure, an internal ribosome entry site, promotes the initiation of protein synthesis and is critical for HCV gene expression. The ribosome binding site may extend into the coding region; its exact boundaries are not known. The open reading frame encodes the HCV polyprotein, which is slightly more than 3,000 amino acids in length. The 3'NTR plays a key role in HCV replication and may also influence the rate of HCV protein synthesis. During replication, the genomic RNA is copied by virally encoded enzymes into a complementary antigenomic RNA, which itself is a template for the synthesis of progeny RNAs. At steady state, genomic strands outnumber antigenomic strands about 10 to 1. HCV RNA replication is thought to take place in the cytoplasm and is an error-prone process. It generates a mixed population of RNA sequences (quasispecies), including mutants that may be more fit than the parental type, less fit, or equally fit (but distinct). Natural selection acts upon the progeny RNAs, causing the population to change and drift. Over time, mutation, selection, and population bottlenecks led to the evolution of varied genotypes. The HCV replication complex is a potential source of double-stranded RNA, a powerful inducer of interferon. Thus, HCV-specific double-stranded RNA may trigger the first steps of innate immunity; however, for unknown reasons, the immune system often fails to clear the infection. The plasticity of the HCV genome and the low level of HCV gene expression may counterbalance any immunostimulatory effects of HCV RNA and allow the virus to escape specific immune responses. Antisense drugs and ribozymes directed against HCV RNA are under investigation. Future interventions may include nucleic acid drugs (antisense and ribozymes) and smaller pharmaceuticals that bind to intricate structures in HCV RNA and HCV-specific double-stranded RNA. Infectious clones of HCV RNA are available. These clones and other systems for expressing HCV proteins pave the way for vaccine development.

Genes, Viral↗
PubMed2005

Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA.

BACKGROUND: Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. RESULTS: Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution. CONCLUSION: On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.

Alternative Splicing↗
PubMed2003

Class II transactivator promoter activity is suppressed through regulation by a trophoblast noncoding RNA.

BACKGROUND: Trophoblasts lack expression of all classic major histocompatibility complex (MHC) antigens. Determination of the mechanism involved could provide insight into selective gene suppression and allograft tolerance. Suppression of class II expression in trophoblasts is secondary to dominant negative trans-acting factors that suppress class II transactivator (CIITA) transcription. We recently described a trophoblast-derived noncoding RNA (TncRNA) that suppresses class II expression. We examined the effects of TncRNA on the CIITA promoter, CIITA, and MHC class II expression. METHODS: HeLa clones stably transfected with TncRNA were analyzed for MHC class II and CIITA expression by fluorescence-activated cell sorting, Northern blots, and quantitative polymerase chain reaction. Activity and functional dissection of CIITA promoter IV (pIV) was assessed by transient co-transfection of promoter-reporter constructs. Methylation of pIV was assessed by Southern blots, fluorescence-activated cell sorting, and quantitative polymerase chain reaction. RESULTS: TncRNA suppressed interferon-gamma-induced human leukocyte antigen-DR and CIITA expression in HeLa cells. The mechanism involves inhibition of CIITA pIV through a defined inhibitory domain on the promoter. The mechanism does not involve methylation of the promoter. CONCLUSIONS: A novel method of CIITA suppression is described where a noncoding RNA selectively mediates the suppression of CIITA pIV possibly by complementary RNA-DNA binding to an inhibitory domain on the promoter. Selective suppression of MHC class II could have important implications in allograft tolerance and in developing class II-deficient cells or tissues for the purpose of transplantation or drug delivery systems.

Base Sequence↗
PubMed2003

Gene silencing by expression of hairpin RNA in Lotus japonicus roots and root nodules.

We investigated the efficacy of self-complementary hairpin RNA (hpRNA) expression to induce RNA silencing in the roots and nodules of model legume Lotus japonicus, using hairy root transformation mediated by Agrobacterium rhizogenes. Transgenic lines that express beta-glucuronidase (GUS) by constitutive or nodule-specific promoters were supertransformed by infection of A. rhizogenes harboring constructs for the expression of hpRNAs with sequences complementary to the GUS coding region. GUS activity in more than 60% of the hairy roots was decreased or silenced almost completely. Silencing of the GUS gene was also observed in symbiotic nodules formed on hairy roots in both early and late stages of nodule organogenesis. These results indicate that transient RNA silencing by hairy root transformation provides a powerful tool for loss-of-function analyses of genes that function in roots and root nodules.

Gene Expression Regulation, Developmental↗
PubMed1997

Site-specific introduction of functional groups into phosphodiester oligodeoxynucleotides and their thermal stability and nuclease-resistance properties.

We report here the site-specific introduction of functional groups into phosphodiester oligodeoxynucleotides (ODNs). ODNs containing both 5-( N-aminohexyl)-carbamoyl-2'-deoxyuridine (H), which serves as a tether for the further conjugation of functional groups, and 5-(N,N-dimethylaminohexyl)carbamoyl-2'-deoxyuridine (D), which contributes to the thermal stability of the duplex and to the resistance to nucleolytic hydrolysis by nucleases, were synthesized. Functional groups such as folic acid and palmitic acid were site-specifically introduced into the terminus of the aminohexyl-linker of H. The thermal stability and resistance toward nuclease digestion of the modified ODNs were studied. We found that ODNs containing D and H formed stable duplexes with both the complementary DNA and RNA strands even when a bulky functional group such as folic acid, palmitic acid or cholesterol was attached to the terminus of the amino-linker. We also found that ODN analogues which contained D were more resistant to nucleolytic degradation by exo- and endonuclease than the unmodified ODN. Furthermore, duplexes formed by ODNs containing D and the complementary RNA could elicit RNase H activity.

Animals↗
PubMed1976

Nucleotide sequences in mouse DNA and RNA specific for Moloney sarcoma virus.

Complementary DNA (cDNA) synthesized by Moloney murine sarcoma virus (M-MSV) was separated into two parts, the first, termed MSV-specific cDNA, composed of nucleotide sequences found only in M-MSV viral RNA, and the second, termed MSV-MuLV common cDNA, composed of nucleotide sequences that were found in both M-MSV and murine leukemia virus (MuLV) VIRAL RNAs. RNA complementary to the MSV-specific cDNA was not found in several other MSV isolates, nor in ecotropic MuLV, mouse mammary tumor virus, or several murine xenotropic oncoviruses. Cellular DNA of several species was examined for the presence of nucleotide sequences complementary to MSV-specific cDNA. Cells transformed by M-MSV did contain MSV-specific cDNA in their DNA. Normal mouse cell DNA apparently contained the majority of MSV-specific nucleotide sequences. Cellular DNA of related species contained proportionally less MSV-specific cDNA. Hybrids of MSV-spedivic cDNA and cellular DNA of related species melted at lower temperatures than hybrids of MSV-specific cDNA and mouse cellular DNA. RNA from normal mouse adult or embryonic cells did not contain detectable nucleotide sequences complementary to MSV-specific cDNA. Transformation of cells with M-msv resulted in transcription of RNA hybridizing with MSV-specific cDNA. Methylcholanthrene-induced mouse sarcomas and cell lines derived from them did not contain RNA complementary to MSV-specific cDNA. Mouse cell lines transformed with avian sarcoma virus or Kirsten MSV-specific cDNA. RNA homologous to MSV-specific nucleotide sequences is measurably present only in cells transformed by M-MSV and not in cells transformed by other biological or chemical agents that also cause sarcomas.

Animals↗
PubMed1984

A gene sequence expressed only in undifferentiated EC, EK cells and testes.

A clone, EC1, has been isolated from a cDNA library prepared from 4-day embryoid bodies formed by suspension culture of PSMB EC cells. This clone has been used to screen a variety of RNA sources including adult tissues, embryonal carcinoma (EC), and endoderm cell lines. A 3-kb poly(A)+ RNA species was found to be present only in undifferentiated EC cells and adult mouse testes. This species was significantly reduced in testes of W/Wv mice compared with wild-type at this locus. Germ cells and their progeny are therefore implicated as the source of the RNA in testes. Hybrid-selected RNA from PSMB could be translated in vitro into a 35-kd protein, but no translatable message was evident in either PYS-2 (parietal), or PSA5-E (visceral) endoderm cell lines. DNA sequencing of the EC1 insert revealed that it is 744 bp in length, the 3' 460 bp of which are in open reading frame. Comparison with known sequences have shown no significant homology. EC1 subclones in M13 have been used to generate single-stranded probes for hybridisation to RNA in situ in tissue sections. Hybridisation of the strand complementary to RNA produces a signal limited to the central regions of embryoid bodies formed on suspension culture of embryo-derived EK cells coinciding with the presence of undifferentiated cells. Probing of a mouse genomic library and Southern blots of liver DNA with EC1 reveals that the gene is present as a single copy.

Amino Acid Sequence↗
PubMed1978

Complete nucleotide sequence of the leader RNA synthesized in vitro by vesicular stomatitis virus.

The complete nucleotide sequence of the leader RNA synthesized in vitro by the Indiana serotype of vesicular stomatitis virus is presented. The sequence was determined by the technique described by Donis-Keller, Maxam and Gilbert (1977) in combination with the standard two-dimensional fingerprint techniques described by Barrell (1971). The leader RNA contains 48 nucleotides variably terminating at the 3' terminus with cytosine (68%) and adenosine at position 47 (32%). Since the leader RNA is complementary to the 3' terminal portion of the viral genome RNA, the first 48 nucleotides from the 3' end of the genome RNA can be decuded. The leader RNA contains repetitive and palindromic sequences with a polypurine sequence at its 3' terminus. The possible role of some of the sequences is discussed.

Base Sequence↗
PubMed1993

Posttranscriptional repression of Escherichia coli OmpF protein in response to redox stress: positive control of the micF antisense RNA by the soxRS locus.

The soxRS regulon is a cornerstone of the adaptive defense systems of Escherichia coli against oxidative stress. Unexpectedly, activation of this regulon also enhances bacterial resistance to multiple antibiotics that seem unrelated to oxygen radicals. We previously correlated this multiple antibiotic resistance with a reduced rate of synthesis of the OmpF outer membrane porin that does not affect the OmpC or OmpA porins. Studies presented here, with operon and gene fusions of ompF to lacZ, show that the soxRS-dependent repression of OmpF is achieved posttranscriptionally. We also show posttranscriptional repression of OmpF mediated by the soxQ1 mutation, which maps to the marA locus. These repressions are dependent on the micF gene, which encodes a small RNA partially complementary to the 5' end of the ompF message. Northern (RNA) blotting experiments show that micF transcription is strongly inducible by the superoxide-generating agent paraquat in a manner that depends completely on the soxRS locus. The soxR-constitutive and soxQ1 mutations elevate the expression of micF in the absence of redox stress. However, the antibiotic resistance mediated by a soxR-constitutive mutation was only partially reversed upon deletion of micF. The soxRS regulon therefore includes other components that contribute to general antibiotic resistance, although the relation of this phenotype to oxidative stress remains to be established.

Bacterial Outer Membrane Proteins↗
PubMed2000

Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).

DNA.RNA hybrid duplexes are substrates of RNase H and reverse transcriptase. The crystal structure of a hybrid duplex, d(5'-CTCTTCTTC-3').r(5'-gaagaagag-3') (the uppercase letters indicate DNA and lowercase letters RNA), with a polypurine RNA strand and a complementary DNA strand has been determined at 1.8 A resolution. The structure was refined first at 1.9 A by XPLOR and subsequently by CNS at 1.8 A. The hybrid is found in a standard A-form conformation with all the sugars in the C3'-endo puckering. The 5'-terminal base dC of the DNA strand was clearly visible in the electron density map of the present structure, in contrast to the previously reported structure d(TTCTTBr(5)CTTC).r(gaagaagaa) where the 5'-terminal base dT was not visible, leaving the terminal rA unpaired. Thus, the comparison of the terminal base pairs, C.g versus T.a, in the two hybrid crystal structures provides information on the stability of these base pairs in hydrogen bonding (three versus two) and base stacking interactions. The differences in the terminal base pairs produce different kinks in the two structures. Minor groove widening is observed in the present structure at a distinctive kink in the lower half of the duplex, in contrast to the small widening of the minor groove and a very slight bend in the upper half of the T.a structure.

Base Composition↗
PubMedDate not supplied

[Antiviral effect of various oligonucleotide derivatives, complementary to tick-born encephalitis virus RNA].

Antiviral effect of two nucleotides complementary to tick-borne encephalitis (TBE) virus genome and their derivatives was compared to that of noncomplementary oligonucleotides. All the tested reagents influenced TBE multiplication in cell culture, this manifesting by various degrees of suppression of the cytopathic effect of the virus. Intact oligonucleotides, both complementary and noncomplementary to TBE, reduced virus titer by 2-4 orders, whatever the concentration of oligonucleotide. In some experiments a higher virus-inhibiting effect of complementary oligonucleotides (by 3-4 orders) was observed vs. noncomplementary (by 1-2 orders). Moreover, different oligonucleotide derivatives suppressed virus multiplication in porcine embryo kidney cell culture. In parallel with investigation of virus-inhibitory effect of oligonucleotides in cell culture, their effects on the synthesis of virus-specific and cellular proteins was studied. Screening of oligonucleotide derivatives by capacity to suppress biosynthesis and multiplication of virus in cell culture showed the highest efficacy of reaction-capable and cholesterol derivatives.

Animals↗