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J Sri-Widada

Publications and source records attributed to J Sri-Widada.

14 recordsLinked to original sources
PubMed1990

Presence of a differentially expressed U3A RNA variant in mouse. Structure and evolutive implications.

A U3 RNA variant has been identified in mouse, the abundance of which relative to the previously characterized major form (U3B) appears to vary to a large extent depending upon the cell origin. Its partial sequence analysis shows that it is clearly related to the U3A form previously described in rat. Sequence comparisons suggest that the separation of the two forms of U3 genes now found in rat and mouse represent a relatively ancient event in rodent evolution. While mouse U3B RNA is encoded by four clustered genes, the U3A variant is encoded by a unique gene. Both mouse U3 RNAs differ substantially in primary structure (more than 10% divergence). Although rodent U3 RNAs exhibit a largely similar secondary structure, a specific difference between the A and B form can nevertheless be observed.

Animals↗
PubMed1988

Analysis of double-stranded poly(A).poly(U) molecules by reversed-phase high-performance liquid chromatography.

The behaviour of different batches of synthetic Poly(A).Poly(U) in reversed-phase high-performance liquid chromatography (HPLC) was studied. They consist of large molecules mainly in the form of a double strand. Differences in the elution patterns were correlated with properties detected by conventional methods such as electrophoresis, centrifugation, fusion analysis or enzymatic digestions. Under the present conditions, contamination by products and precursors used during synthesis was detectable, but was absent in most of the preparations. The differences in elution patterns between batches appear to be correlated with the size of the molecules synthesized. The chromatograms suggested that Poly(A).Poly(U) molecules contain single-strand portions at least transiently. The presence of such portions was confirmed by enzymatic digestion with S1 nuclease. The rapidity, reproducibility and ease of reversed-phase HPLC qualify this technique as a tool for routine analysis.

Chromatography, High Pressure Liquid↗
PubMed1986

A human auto-immune antibody specifically recognizing initiator methionine tRNA from yeast and higher eucaryotes.

Analysis of sera from 168 patients with autoimmune disorders revealed that one patient with Sjôgren's syndrome produced antibodies against deproteinized initiator methionine tRNA in addition to those against La protein. This anti-tRNAimet recognizes also tRNAimet from yeast but not from Phaseolus vulgaris chloroplasts (bean) or E. coli. It appears therefore that the epitope could be located in the TF loop in which an A residue in position 60 and the AUCG sequence are the only common features in yeast and human tRNAimet.

Autoantibodies↗
PubMed1986

RNA-protein organization of U1, U5 and U4-U6 small nuclear ribonucleoproteins in HeLa cells.

Small nuclear ribonucleoproteins (snRNPs) containing U1 and U5 snRNAs from HeLa cells have been fractionated using a combination of isopycnic centrifugation in cesium chloride and ion-exchange chromatography on DEAE-Sepharose. The procedure is based on the extreme stability conferred upon snRNPs by Mg2+ enabling them to withstand the very high ionic strength that prevails in cesium chloride. U1 snRNP prepared by this method contains all nine major proteins (68K, A, B, B', C, D, E, F, G) corresponding to those previously identified by immunoprecipitation and is therefore precipitable by anti-RNP and anti-Sm antibodies. U5 snRNP purified in this way contains the common D to G proteins and is also enriched in a 25 X 10(3) Mr protein that may be U5 snRNP-specific. The core-resistant U5 snRNA sequence (nucleotide 84 to 3' OH) covered by D to G proteins is extended by only six nucleotides. A similar situation is seen in U4-U6 snRNP, which we have obtained in a sufficiently pure form to examine protected sequences. However, the core-resistant sequence of U4 (nucleotide 116 to 3' OH) in U4-U6 snRNP is extended by 37 nucleotides, suggesting that the protein composition of this particle could be more complex than that of U5 snRNP. The ribonucleoprotein organization of snRNPs is summarized and discussed in view of our current knowledge on snRNA sequences protected by proteins.

Base Sequence↗
PubMed1984

Mg2+ induces a sharp and reversible transition in U1 and U2 small nuclear ribonucleoprotein configurations.

When U1 and U2 small nuclear ribonucleoproteins (snRNPs) purified by a procedure which preserves their immunoprecipitability by autoimmune antibodies (Hinterberger et al., J. Biol. Chem. 258:2604-2613, 1983), were submitted to extensive digestion with micrococcal nuclease, we found that their degradation pattern was sharply dependent upon magnesium concentration, indicating that they undergo a profound structural modification. At low Mg2+ (less than or equal to 5 mM), both particles only exhibit a core-resistant structure previously identified as being common to all but U6 snRNAs (Liautard et al., J. Mol. Biol. 162: 623-643, 1982). At high Mg2+ (greater than or equal to 7 mM), U1 and U2 snRNPs behave differently from one another. In U1 snRNP, most U1 snRNA sequence is protected, except for the 10 5'-terminal nucleotides presumably involved in splicing and a short sequence between nucleotides 102 and 108. Another region spanning nucleotides 60 to 79 is only weakly protected. This structural modification was demonstrated to be reversible. In U2 snRNP, the U2 snRNA sequence remains exposed in its 5' part up to nucleotide 92, and the 3'-terminal hairpin located outside the core structure becomes protected.

Base Sequence↗
PubMed1983

Interaction of snRNAs with rapidly sedimenting nuclear sub-structures (hnRNPs) from HeLa cells.

We have shown previously (Liautard et al., 1982, J. Mol. Biol., 162, 623-643) that digestion with micrococcal nuclease under drastic conditions of a pure U1 snRNP, as well as a mixture containing U2, U1, U4, U5 and U6 snRNPs, gives rise to resistant RNA fragments derived from all but U6 snRNAs. As an attempt to elucidate the way in which snRNPs are attached to their native structure, the same approach was applied to hnRNP which are known to contain snRNP (Guimont-Ducamp et al., 1977, Biochimie, 59, 755-758). Micrococcal nuclease digestion of hnRNPs yielded a population of 15-50 nucleotides long resistant fragments of snRNAs. Sequence analyses showed that all fragments previously identified in core snRNPs were also present. Only U2 and U5 snRNAs were further protected as a result of their association with the hnRNP complex (from the cap to nucleotide 32 for U2 and from nucleotide 22 to nucleotide 70 for U5). No additional protected fragment derived from U1, U4 and U6 snRNAs was found. This finding confirms that the 5' terminal region of U1 snRNP remains available for base-pairing interaction with the premessenger RNA, as predicted by the model of Lerner et al. (Nature, 1980, 283, 220-224).

Base Sequence↗
PubMed1982

Mouse DNA sequences complementary to small nuclear RNA U1.

A mouse genomic library was screened for sequences complementary to U1 nuclear RNA. Out of the eight clones tested, none contained more than one copy of U1. Six of them were identical and one of those (clone 0U1-XIII) was further analyzed. This latter clone contained no other gene for discrete species of small size RNA in the 8 Kb EcoRI fragment encoding U1. A 248 bp Bg1II fragment from 0U1-XIII encompassing the full length of U1 as well as flanking regions on both sides has been subcloned and sequenced in M13 phage. Although the coding region was 96.5% homologous to rat U1a RNA, there is no direct evidence that this clone is a true gene. 3' and 5' flanking sequences of this as well as other published clones have been searched for homologies and the results of this search are discussed.

Animals↗
PubMed1982

Relationship between snRNA species contained in nuclear antigens recognized by autoantibodies and the clinical profile in systemic rheumatic diseases.

Antibodies to extractable nuclear antigens (ENA) are generally used in the diagnosis of connective tissue diseases. Using a rapid, very sensitive method we have shown that extractable nuclear antigens, which are now well-characterized at the molecular level, differ by their RNA content. The method was applied to the sera of 17 patients suffering from different connective tissue diseases. The results show that mixed connective tissue disease (MCTD) and other mild connective tissue diseases are characterized by the presence in the antigen of U1 small nuclear RNA (U1 snRNA) only. On the other hand, antibodies from 6 out of 8 patients tested with Systemic Lupus Erythematosus (SLE) recognize antigens exhibiting a more complex RNA pattern. Three of them precipitated all five snRNAs U2, U1, U4, U5, U6 whereas some snRNAs were lacking or quantitatively less important in precipitates obtained with the three others.

Antibodies, Antinuclear↗
PubMed1981

Primary structure identification of snRNAs present in highly purified snRNPs from HeLa cells.

Extensive purification of snRNPs as a subset of hnRNP from HeLa cells has been previously reported (Brunel et al. (1981), Nucleic Acids Research, 9, 815). These snRNPs were shown to contain discrete RNA species comigrating in gel electrophoresis with authentic U1, U2, U4, U5 and U6 species. We now report sequence analysis data of about 50 nucleotides from the 3'-end which serve to positively establish the identity of snRNAs present in these purified snRNPs. Sequence heterogeneity was found at the 3'-end of U4 species. A minor species identical to U1 at its 3'-end but slightly shorter was identified as the U1 described by Lerner et al. (Nature (1980) 283, 220-224) through sequencing of the 5'-end. When unfixed hnRNP are centrifuged in a CsCl gradient containing 4M guanidinium chloride instead of 0.5% sarkosyl as above, a band containing only one RNA species was observed. T1 RNAse fingerprinting and sequence analysis of the oligonucleotides produced allowed identification of this RNA as U5 snRNA.

Base Sequence↗
PubMed1980

Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man.

The methods of enzymatic and chemical treatment of end-labeled RNA were applied to the determination of the nucleotide sequence of chicken and man U1A RNA and to the reexamination of that of rat U1A RNA. The chemical method allowed the easy demonstration of the cap structure. All three RNA were 165 nucleotide long. Two hitherto non described modified pyrimidines were detected close to the 5' end. Only 9 base substitutions were observed from chicken to man indicating high degree of conservation of U1A RNA through evolution.

Animals↗