Hybridization of oligodeoxynucleotide probes to RNA molecules: specificity and stability of duplexes

Heat Shock Affects Mitotic Segregation of Human Chromosomes Bound to Stress-Induced Satellite III RNAs

Heat shock activates the transcription of arrays of Satellite III (SatIII) DNA repeats in the pericentromeric heterochromatic domains of specific human chromosomes, the longest of which is on chromosome 9. Long non-coding SatIII RNAs remain associated with transcription sites where they form nuclear stress bodies or nSBs. The biology of SatIII RNAs is still poorly understood. Here, we show that SatIII RNAs and nSBs are detectable up to four days after thermal stress and are linked to defects in chromosome behavior during mitosis. Heat shock perturbs the execution of mitosis. Cells reaching mitosis during the first 3 h of recovery accumulate in pro-metaphase. During the ensuing 48 h, this block is no longer detectable; however, a significant fraction of mitoses shows chromosome segregation defects. Notably, most of lagging chromosomes and chromosomal bridges are bound to nSBs and contain arrays of SatIII DNA. Disappearance of mitotic defects at the end of day 2 coincides with the processing of long non-coding SatIII RNAs into a ladder of small RNAs associated with chromatin and ranging in size from 25 to 75 nt. The production of these molecules does not rely on DICER and Argonaute 2 components of the RNA interference apparatus. Thus, massive transcription of SatIII DNA may contribute to chromosomal instability.

Detection and identification of Vibrio scophthalmi in the intestinal microbiota of fish and evaluation of host specificity

AIMS

To develop a species-specific probe (VSV3) for the detection of Vibrio scophthalmi in fish intestine and to apply this probe to study the host specificity of V. scophthalmi.

METHODS AND RESULTS

A specific probe (VSV3) based on the variable region V3 of the 16S rRNA gene (rDNA) was designed. Its specificity was tested by DNA-DNA hybridization and by colony hybridization. No cross-hybridization was found. The sensitivity of the probe was tested both by DNA-DNA hybridization and by colony hybridization. The detection limit of V. scophthalmi 16S rDNA was 150 pg or 10 cfu. Vibrio scophthalmi cells were detected in experimental samples constituted by mixed cultures when present in proportions of 1 : 10 and 1 : 100. The VSV3 probe also proved to be reliable for the detection of V. scophthalmi in samples of fish intestine.

CONCLUSIONS

The VSV3 probe can be used for the detection of V. scophthalmi in colony hybridization or DNA-DNA hybridization of amplified 16S rDNA. Preliminary results indicate that V. scophthalmi may present certain host specificity for turbot.

SIGNIFICANCE AND IMPACT OF THE STUDY

The VSV3 probe provides a useful tool for ecological studies.

Suppression of the expression of a pancreatic beta-cell form of the kinesin heavy chain by antisense oligonucleotides inhibits insulin secretion from primary cultures of mouse beta-cells

Granular/vesicular transport is thought to be supported by microtubule-based force-generating adenosine triphosphatases such as kinesin. Kinesin is a motor molecule that has been well studied in brain and other neuronal tissues. Although vesicular transport is important for pancreatic beta-cell secretory activities, the role of kinesin in beta-cell function has not been investigated. It is hypothesized that kinesin functions as a translocator that associates with both microtubules and insulin-containing granules in beta-cells and transports the secretory granules from deep within the cytoplasm, where insulin is synthesized and processed, to the surface of beta-cells upon secretory stimulation. To test this hypothesis, a mouse beta-cell kinesin heavy chain complementary DNA was cloned and sequenced. Kinesin expression in primary cultures of mouse beta-cells then was selectively suppressed by antimouse beta-cell kinesin heavy chain antisense oligonucleotide treatment. Analysis of insulin secretion determined that the basal level of insulin secretion from the treated cells was decreased by 50%. Furthermore, glucose-stimulated insulin release from treated beta-cells was reduced by almost 70% after suppression of kinesin expression by antisense treatment. The findings from this study provide the first direct evidence that kinesin, a microtubule-based motor protein, plays an important role in insulin secretion.

Three novel functional variants of human U5 small nuclear RNA

We have identified and characterized three new variants of U5 small nuclear RNA (snRNA) from HeLa cells, called U5D, U5E, and U5F. Each variant has a 2,2,7-trimethylguanosine cap and is packaged into an Sm-precipitable small nuclear ribonucleoprotein (snRNP) particle. All retain the evolutionarily invariant 9-base loop at the top of stem 1; however, numerous base changes relative to the abundant forms of U5 snRNA are present in other regions of the RNAs, including a loop that is part of the yeast U5 minimal domain required for viability and has been shown to bind a protein in HeLa extracts. U5E and U5F each constitute 7% of the total U5 population in HeLa cells and are slightly longer than the previously characterized human U5 (A, B, and C) species. U5D, which composes 5% of HeLa cell U5 snRNAs, is present in two forms: a full-length species, U5DL, and a shorter species, U5DS, which is truncated by 15 nucleotides at its 3' end and therefore resembles the short form of U5 (snR7S) in Saccharomyces cerevisiae. We have established conditions that allow specific detection of the individual U5 variants by either Northern blotting (RNA blotting) or primer extension; likewise, U5E and U5F can be specifically and completely degraded in splicing extracts by oligonucleotide-directed RNase H cleavage. All variant U5 snRNAs are assembled into functional particles, as indicated by their immunoprecipitability with anti-(U5) RNP antibodies, their incorporation into the U4/U5/U6 tri-snRNP complex, and their presence in affinity-purified spliceosomes. The higher abundance of these U5 variants in 293 cells compared with that in HeLa cells suggests possible roles in alternative splicing.

Three novel functional variants of human U5 small nuclear RNA

We have identified and characterized three new variants of U5 small nuclear RNA (snRNA) from HeLa cells, called U5D, U5E, and U5F. Each variant has a 2,2,7-trimethylguanosine cap and is packaged into an Sm-precipitable small nuclear ribonucleoprotein (snRNP) particle. All retain the evolutionarily invariant 9-base loop at the top of stem 1; however, numerous base changes relative to the abundant forms of U5 snRNA are present in other regions of the RNAs, including a loop that is part of the yeast U5 minimal domain required for viability and has been shown to bind a protein in HeLa extracts. U5E and U5F each constitute 7% of the total U5 population in HeLa cells and are slightly longer than the previously characterized human U5 (A, B, and C) species. U5D, which composes 5% of HeLa cell U5 snRNAs, is present in two forms: a full-length species, U5DL, and a shorter species, U5DS, which is truncated by 15 nucleotides at its 3' end and therefore resembles the short form of U5 (snR7S) in Saccharomyces cerevisiae. We have established conditions that allow specific detection of the individual U5 variants by either Northern blotting (RNA blotting) or primer extension; likewise, U5E and U5F can be specifically and completely degraded in splicing extracts by oligonucleotide-directed RNase H cleavage. All variant U5 snRNAs are assembled into functional particles, as indicated by their immunoprecipitability with anti-(U5) RNP antibodies, their incorporation into the U4/U5/U6 tri-snRNP complex, and their presence in affinity-purified spliceosomes. The higher abundance of these U5 variants in 293 cells compared with that in HeLa cells suggests possible roles in alternative splicing.

Detection of immobilised Murray Valley encephalitis virus RNA using oligonucleotide probes with varying degrees of mismatch

The design of oligonucleotides used for hybridisation studies often utilises available sequence information of the type strain of a particular virus. If hybridisation studies, using such oligonucleotides, are carried out with field isolates of the same virus, the problem of base pair mismatches and consequent difficulties in detection may arise. This study examined the effect of base pair mismatches on the hybridisation between membrane-bound Murray Valley encephalitis virus (MVE) RNA derived from various strains and deliberately mismatched oligonucleotide probes. Under conditions of very low stringency, probes containing up to 5 mismatches were able to detect MVE RNA, but not yeast RNA. Under washing conditions of increased stringency, hybridisation could be detected between MVE virus RNA and probes with only 3 to 4 mismatches. However, the extent of this interaction was dependent on the number and type of mismatches and their relative sequence position.

Detection of Mycoplasma bovis and Mycoplasma agalactiae by oligonucleotide probes complementary to 16S rRNA

The partial sequences of 16S rRNA from Mycoplasma bovis and M. agalactiae were determined by dideoxynucleotide sequencing using reverse transcriptase. Two oligonucleotides complementary to different evolutionary variable regions of 16S rRNA from these two species were synthesized. The oligonucleotides were end-labelled with 32P and used as probes in filter hybridization experiments with different bovine, caprine and ovine mycoplasmas as samples. One of the probes, complementary to a sequence of the V8-region of both M. bovis and M. agalactiae, did not cross-hybridize to any bovine, caprine or ovine mycoplasmas except M. bovigenitalium and M. californicum. This probe is thus not useful for analysis of bovine samples, but can be used for detection of M. agalactiae in samples from goats and sheep, since M. bovigenitalium and M. californicum have never been isolated from these hosts and M. bovis only occasionally. The other probe, complementary to a sequence of the V6-region of M. bovis, gave some cross-hybridization with M. agalactiae but not with bovine mycoplasmas. M. agalactiae has never been isolated from cattle and this probe is therefore useful for rapid screening of bovine samples for M. bovis.

U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6

To understand how the U5 small nuclear ribonucleoprotein (snRNP) interacts with other spliceosome components, its structure and binding to the U4/U6 snRNP were analyzed. The interaction of the U5 snRNP with the U4/U6 snRNP was studied by separating the snRNPs in HeLa cell nuclear extracts on glycerol gradients. A complex running at 25S and containing U4, U5, and U6 but not U1 or U2 snRNAs was identified. In contrast to results with native gel electrophoresis to separate snRNPs, this U4/U5/U6 snRNP complex requires ATP to assemble from the individual snRNPs. The structure of the U5 RNA within the U5 snRNP and the U4/5/6 snRNP complexes was then compared. Oligonucleotide-targeted RNase H digestion identified one RNA sequence in the U5 snRNP capable of base pairing to other nucleic acid sequences. Chemical modification experiments identified this sequence as well as two other U5 RNA sequences as accessible to modification within the U5 RNP. One of these regions is a large loop in the U5 RNA secondary structure whose sequence is conserved from Saccharomyces cerevisiae to humans. Interestingly, no differences in modification of free U5 snRNP as compared to U5 in the U4/U5/U6 snRNP complex were observed, suggesting that recognition of specific RNA sequences in the U5 snRNP is not required for U4/U5/U6 snRNP assembly.

Deoxynucleotide-containing oligoribonucleotide duplexes: stability and susceptibility to RNase V1 and RNase H

Oligoribonucleotide duplexes containing one to four 2'-deoxynucleotide residues were used as substrates for ribonuclease V1 and RNase H. Either deoxyadenosine and/or deoxythymidine were incorporated into the duplex, 5'GGCCGGAUCCGCGC3'-5'GCGCGGAUCCGGCC3' by substitution of the appropriate deoxynucleoside triphosphate into a transcription reaction with T7 RNA polymerase. The melting temperature, Tm, of the duplex (1.8 microM in strands in 50 mM NaCl) containing only ribonucleotides was 79.9 degrees C. Substitution of deoxyadenosine in both strands of the duplex lowered the Tm by 2.4 degrees C. Substitution of deoxythymidine had no measurable effect on the Tm. Comparison of RNase V1 digestion patterns of fully ribonucleotide and deoxy-substituted duplexes suggest that any distortion is localized to the site of the substitution. An oligoribonucleotide containing two deoxy residues directs specific cleavage of RNA by E. coli RNase H. Structural requirements for cleavage are proposed for RNase V1 and RNase H.

Identification of Vibrio anguillarum in fish by using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe

16S rRNA from seven different Vibrio anguillarum strains was partially sequenced and compared. From this sequence information we could design a 25-base-long oligonucleotide and use it as a specific probe for identification of V. anguillarum. This was determined by RNA-DNA colony hybridization and slot-blot hybridization. Strong, specific hybridization to the probe was observed for all V. anguillarum strains tested. Furthermore, no cross-hybridization could be seen against five other bacterial species. The detection limit was 5 x 10(3) bacteria per ml. It was even possible to detect V. anguillarum, by slot-blot hybridization, directly in a homogenized kidney from a fish that had died of vibriosis. The partial sequence information revealed small but significant differences between strains of the same species. These sequence differences are sufficiently significant to allow serotyping on the RNA level. Comparing strains of different serotypes revealed a 10-base and an 11-base difference in V. anguillarum serotypes O8 and O9, respectively, in a 122-base partial sequence.

U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6

To understand how the U5 small nuclear ribonucleoprotein (snRNP) interacts with other spliceosome components, its structure and binding to the U4/U6 snRNP were analyzed. The interaction of the U5 snRNP with the U4/U6 snRNP was studied by separating the snRNPs in HeLa cell nuclear extracts on glycerol gradients. A complex running at 25S and containing U4, U5, and U6 but not U1 or U2 snRNAs was identified. In contrast to results with native gel electrophoresis to separate snRNPs, this U4/U5/U6 snRNP complex requires ATP to assemble from the individual snRNPs. The structure of the U5 RNA within the U5 snRNP and the U4/5/6 snRNP complexes was then compared. Oligonucleotide-targeted RNase H digestion identified one RNA sequence in the U5 snRNP capable of base pairing to other nucleic acid sequences. Chemical modification experiments identified this sequence as well as two other U5 RNA sequences as accessible to modification within the U5 RNP. One of these regions is a large loop in the U5 RNA secondary structure whose sequence is conserved from Saccharomyces cerevisiae to humans. Interestingly, no differences in modification of free U5 snRNP as compared to U5 in the U4/U5/U6 snRNP complex were observed, suggesting that recognition of specific RNA sequences in the U5 snRNP is not required for U4/U5/U6 snRNP assembly.

Isolation of an active gene encoding human hnRNP protein A1. Evidence for alternative splicing

Heterogeneous nuclear ribonucleoprotein (hnRNP) core protein A1 is a major component of mammalian hnRNP 40 S particles. We describe the structure of an active A1 gene and report on the partial characterization of the A1 gene family. About 30 A1-specific sequences are present per haploid human genome: 15 such sequences were isolated from a human genomic DNA library. Many corresponded to pseudogenes of the processed type but by applying a selection for actively transcribed regions we isolated an active A1 gene. The gene spans a region of 4.6 x 10(3) base-pairs and it is split into ten exons that encode the 320 amino acid residues of the protein. The amino acid sequence derived from the exon sequences is identical with that deduced from cDNA and reported for the protein. One intron exactly separates the two structural domains that constitute the protein. Each of the two RNA-binding domains in protein A1 is encoded by one exon. Experimental evidence indicates that the A1 gene can encode for more than one protein by alternative splicing. The gene is preceded by a strong promoter that contains at least two CCAAT boxes and two possible Sp1 binding sites, but it lacks a TATA box.

Techniques for using antisense oligodeoxyribonucleotides to study gene expression

Molecular biology is providing powerful tools for cloning and sequencing genes. The more difficult task is that of ascribing functions to the specific DNA sequences that appear to code for proteins, the "open reading frames," or of regulating the expression of known genes in biological systems in order to determine their contributions to cellular functions. The classical genetic approach of making mutants is difficult in eukaryotic systems, with the exception of yeasts and viruses, and has proved of limited utility. A promising approach to this problem has been to introduce into either the in vitro assay or tissue culture system oligodeoxyribonucleotides with nucleotide sequences complementary to the protein coding or "sense" sequence, usually referred to as "antisense" oligonucleotides. The term MATAGEN (MAsking TApe for Gene ExpressioN) has also been used for these compounds, which appear to inhibit gene expression predominantly by hybridization arrest of translation. Interest in the use of antisense molecules for the study of gene expression and regulation has increased dramatically in the past few years. The demonstrated utility of the antisense oligomer in both in vitro and tissue culture assays, the increased availability of nucleotide sequence data as well as improvements in nucleic acid sequencing techniques, and the automation of synthetic procedures for their preparation have made studies using these molecules more practical. This review focuses on short oligodeoxyribonucleotides, which offer important stability and synthetic advantages over the use of antisense RNA transcripts, and is intended as an introduction to practical approaches in the use of antisense oligodeoxyribonucleotides in biological systems. For synthetic techniques, the reader is referred to the individual references cited.

cDNA cloning of human hnRNP protein A1 reveals the existence of multiple mRNA isoforms

Protein A1 is one of the major component of mammalian ribonucleoprotein particles (hnRNP). Human protein A1 cDNA cloning and sequencing revealed the existence of at least two protein isoforms. Among the cDNAs examined, sequence differences were found both in the structural portion, leading to aminoacid changes (Tyr to Phe or Arg to Lys) and in the non translated 3'-region where two T-stretches of different length were observed. Interestingly one of the aminoacid substitutions falls into a consensus sequence common to many RNA binding proteins. Northern blot analysis of poly A+ RNAs from five human tissues revealed two mRNA forms of 1500 and 1900 n due to alternative polyadenylation. Analysis of genomic DNA showed at least 30 A1-specific sequences, some of which correspond to processed pseudogenes. These results suggest that protein A1 is encoded by a multigene family.