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Y T Yu

Publications and source records attributed to Y T Yu.

At least 37 records · Page 2Linked to original sources
PubMed1998

Heat-aggregated human IgG as immunosorbent for rheumatoid arthritis.

In order to selectively remove pathogenic rheumatoid factors (RF) from plasma of rheumatoid arthritis (RA) patients, a new immunosorbent was developed by immobilizing heat-aggregated human IgG (HAH IgG) on epichlorohydrin-activated agar gel. Different parameters influencing ligand coupling were studied, i.e., ligand concentration, reaction time, temperature and pH. The maximum amount of HAH IgG immobilized on the carrier was 2.7 mg/ml. Adsorption capacity was evaluated by ELISA technique. After incubation of 3.0 ml of RA plasma with 1.0 ml of the adsorbent, the RF IgM, IgG, and IgA were removed by 88%, 74%, and 50%, respectively. The decrease of total immunoglobulins and albumin were less than 7% and 9%. In vitro, perfusion of 10.0 ml plasma at 37 degrees C through 3.0 ml of adsorbent, at a flow rate of 5.0 ml/min for 60 min, resulted in the removal of 49% of RF IgM, 72% of RF IgG and 58% of RF IgA. No leakage of ligand and no decline in adsorption capacity and mechanical strength were observed after steam-sterilization.

Arthritis, Rheumatoid↗
PubMed1998

Malignant fibrous histocytoma of the heart presenting as right ventricular outflow tract obstruction: a case report.

Primary malignant fibrous histocytoma (MFH) of the heart is extremely rare. Herein, we report the case of a 17-year-old woman with a primary MFH in the right ventricular outflow tract, presenting with increasing dyspnea on exertion. Wide excision of the tumor, including part of the pulmonary artery and pulmonary valve, was performed under cardiopulmonary bypass. Her postoperative recovery was uneventful.

Adolescent↗
PubMed1997

Site-specific crosslinking of mammalian U11 and u6atac to the 5' splice site of an AT-AC intron.

A rare class of introns with AT-AC at their termini recently has been identified in metazoan genes. Splicing of these introns requires a different set of small nuclear ribonucleoprotein particles (snRNPs) (U11, U12, U5, and U4atac/U6atac) compared with the snRNPs (U1, U2, U5, and U4/U6) required for splicing the majority of pre-mRNA introns, but otherwise little is known regarding the excision of AT-AC introns. Here we use site-specific 4-thiouridine (4SU) crosslinking analysis to dissect the mechanism of 5' splice site recognition during in vitro splicing of the AT-AC intron from the P120 pre-mRNA. Upon irradiation with 365-nm UV light, three P120 substrates, each with a single 4SU substitution near the 5' splice site (at position +2, +4, or +7), produce two early ATP-independent crosslinks with similar kinetics. For one of the substrates, P120-4SU+2, a third ATP-requiring crosslink forms as the two early crosslinks diminish. RNase H digestion coupled with Northern blotting indicates that the two early crosslinks generated with P120-4SU+2 contain the U11 small nuclear RNA. Reverse transcription-PCR followed by cloning and sequencing demonstrates that the third crosslink involves U6atac. The dynamic appearance of the three crosslinks correlates with the kinetics of the splicing reaction and suggests that the 5' splice site is recognized first by U11 and then by U6atac. Our results argue that the splicing of AT-AC introns is mechanistically similar to the splicing of the major class of introns and that the U11 and U6atac snRNPs in the AT-AC spliceosome fulfill analogous roles to U1 and U6, respectively, in the major spliceosome.

Adenine↗
PubMed1997

A novel A/T-rich element mediates ANF gene expression during cardiac myocyte hypertrophy.

The induction of the atrial natriuretic factor (ANF) gene during alpha 1-adrenergic stimulation of neonatal rat ventricular myocytes has served as a model for gene expression during cardiac muscle cell hypertrophy. This study describes and identifies a single regulatory element that mediates expression of the ANF gene. Deletional mutations were generated in a 639-bp fragment of the ANF promoter that confers alpha 1-adrenergic inducibility to a luciferase reporter gene in transient transfection assays in ventricular myocytes. The results of gel mobility shift and diethylpyrocarbonate (DEPC) interference studies with nuclear cardiac cell extracts identified the nucleotide contract points for a novel A/T-rich element (ANF-AT) at positions -582/-575 that partially mediates alpha 1-adrenergic inducibility. Mutations in the ANF-AT element reduced alpha-adrenergic inducibility of an ANF-TK-luciferase fusion gene in cardiac cells by 35% but had no effect on expression in other muscle and non-muscle cells tested. Gel mobility supershift assays with antibodies directed against the MEF-2 protein, the homeobox protein MHox, or the zinc finger protein HF-1b, document that these factors are not major components of the endogenous ANF-AT binding activity in cardiac muscle cells. The current study provides evidence for a role for a novel A/T-rich element in the regulation of ANF gene expression in cardiac ventricular myocytes.

Animals↗
PubMed1997

A new method for detecting sites of 2'-O-methylation in RNA molecules.

2'-O-methylation of eukaryotic ribosomal RNAs occurs in the cell nucleoli. At least 100 modification sites that are highly conserved among vertebrate rRNAs have been mapped. However, in part because of the insensitivity of current approaches, there are 2'-O-methylated sites that remain unidentified. We have developed an extremely sensitive method for detecting 2'-O-methylated residues that are predicted within a long RNA molecule. Utilizing RNase H cleavage directed by a 2'-O-methyl RNA-DNA chimeric oligonucleotide, this method has allowed identification of two methylated nucleotides, G1448 in Xenopus 18S rRNA and A394 in Xenopus 28S rRNA. The latter (A394 in 28S) had not been detected before. We have confirmed that the methylation at G1448 in 18S is dependent upon Xenopus U25 snoRNA and have demonstrated that the methylation at A394 in 28S requires U26 snoRNA. One advantage of this technique is that it can examine specific rRNA and precursor molecules. We show that about 30% of the 40S pre-rRNA has been methylated at these two sites and their methylation is complete at the stage of 20S (immediate precursor to 18S) and 32S (immediate precursor to 28S). We also show that methylation at these two sites is not essential for rRNA transport from the nucleus to the cytoplasm.

Animals↗
PubMed1997

A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule.

We describe a new protocol, which does not require (4S)UpG, for introducing (4S)U into specific sites in a pre-mRNA substrate. A 5'-half and a full-length RNA are first synthesized by phage RNA polymerase. p(4S)Up, which is derived from (4S)UpU and can therefore be 32P-labeled, is then ligated to the 3' end of the 5'-half RNA with T4 RNA ligase. The 3' phosphate of the ligated product is removed subsequently by CIP (calf intestinal alkaline phosphatase) to produce a 3'-OH group. The 3'-half RNA with a 5' phosphate is produced by site-specific RNase H cleavage of the full-length pre-mRNA directed by a 2'-O-methyl RNA-DNA chimera. The two half RNAs are then aligned with a bridging oligonucleotide and ligated with T4 DNA ligase. Our results show that 32P-p(4S)Up ligation to the 3' end of the 5'-half RNA is comparable to 32P-pCp ligation. Also, the efficiency of the bridging oligonucleotide-mediated two-piece ligation is quite high, approximately 30-50%. This strategy has been applied to the P120 pre-mRNA containing an AT-AC intron, but should be applicable to many other RNAs.

Affinity Labels↗
PubMed1996

More Sm snRNAs from vertebrate cells.

There are a number of low-abundance small nuclear RNAs (snRNAs) in eukaryotic cells. Many of them have been assigned functions in the biogenesis of cellular RNAs, such as splicing and 3' end processing. Here, we present the sequence of Xenopus U12 snRNA and compare the secondary structures of the low-abundance U11 and U12 with those of the high-abundance U1 and U2, respectively. The data suggest functional parallels between these two pairs of snRNAs in pre-mRNA splicing. Using a highly sensitive method, we have identified several new low-abundance snRNAs from HeLa cells. These include five U7 snRNA variants and six novel snRNAs. One of the six novel RNAs is an Sm snRNA, whereas the rest are not immunoprecipitable by either anti-Sm antibodies or anti-trimethylguanosine antibodies. The discovery of these new RNAs suggests that there may be yet more low-abundance snRNAs in the nuclei of eukaryotic cells.

Animals↗
PubMed1996

Distinct domains of myocyte enhancer binding factor-2A determining nuclear localization and cell type-specific transcriptional activity.

The myocyte enhancer binding factor 2 (MEF2) family of transcription factors plays an important role in the regulation of gene expression in multiple muscle cell types. Four mef2 genes (A, B, C, and D) have been identified in vertebrates. They share the conserved N-terminal MCM1-agamous-deficiens-serum response factor and MEF2 domains that determine DNA binding and dimerization functions. In this study, we have identified human MEF2A domains that control its nuclear localization and transcriptional activation function. Studies of subcellular localization of various truncated MEF2A proteins expressed in HeLa cells demonstrated that MEF2A contains a nuclear localization signal located at its C terminus within the peptide encompassing amino acids (aa) 472-507. Examination of MEF2A mutants with sequential C-terminal deletions indicates that the region encompassing aa 321-472 is essential for transcriptional activity. Analysis of the transcriptional activity of fusion proteins consisting of different domains of MEF2A fused to the DNA binding domain of yeast transcription factor GAL4 revealed a major transcriptional activation domain located between aa 274 and 373. Further studies demonstrated that this domain contains positive and negative regulatory subdomains that cooperate with one another to regulate the transcriptional activity of MEF2A in a cell-type discriminatory manner.

Amino Acid Sequence↗
PubMed1996

Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs.

Most nuclear pre-mRNAs in nematodes are processed by both cis- and trans-splicing. In trans-splicing, the 5' terminal exon, the spliced leader sequence (SL), is derived from a trans-splicing specific Sm snRNP, the SL RNP. Because U snRNPs are required cofactors for trans-splicing, and because this processing reaction proceeds via a two-step reaction pathway identical to that of cis-splicing, it has long been assumed that trans-splicing is catalyzed in a complex analogous to the cis-spliceosome. However, similarities or differences between cis- and trans-spliceosomes have not been established. In particular, the role of U5 snRNP in trans-splicing has been unclear. Here, we have used affinity selection to analyze the U snRNA constituents of nematode cis- and trans-spliceosomes. We find that U5 snRNP is an integral component of the trans-spliceosome and, using site-specific crosslinking, we show that U5 snRNP establishes specific Interactions with the SL RNA exon. We also identify two novel Sm snRNPs that are enriched in both cis- and trans-spliceosomes. Finally, we provide evidence that a SL RNP-containing multi-snRNP (SL, U4, U5, and U6 RNPs) may be a functional precursor in trans-spliceosome assembly.

Animals↗
PubMed1996

Multiple requirements for nematode spliced leader RNP function in trans-splicing.

The 5' exon donor in nematode trans-splicing, the SL RNA, is a small (approximately 100 nt) RNA that resembles cis-spliceosomal U snRNAs. Extensive analyses of the RNA sequence requirements for SL RNA function have revealed four essential elements, the core Sm binding site, three nucleotides immediately downstream of this site, a region of Stem-loop II, and a 5' splice site. Although these elements are necessary and sufficient for SL RNA function in vitro, their respective roles in promoting SL RNA activity have not been elucidated. Furthermore, although it has been shown that assembly of the SL RNA into an Sm RNP is a prerequisite for function, the protein composition of the SL RNP has not been determined. Here, we have used oligoribonucleotide affinity to purify the SL RNP and find that it contains core Sm proteins as well as four specific proteins (175, 40, 30, and 28 kDa). Using in vitro assembly assays; we show that association of the 175- and 30-kDa SL-specific proteins correlates with SL RNP function in trans-splicing. Binding of these proteins depends upon the sequence of the core Sm binding site; SL RNAs containing the U1 snRNA Sm binding site assemble into Sm RNPs that contain core, but not SL-specific proteins. Furthermore, mutational and thiophosphate interference approaches reveal that both the primary nucleotide sequence and a specific phosphate oxygen within a segment of Stemloop II of the SL RNA are required for function. Finally, mutational activation of an unusual cryptic 5' splice site within the SL sequence itself suggests that U5 snRNA may play a primary role in selecting and specifying the 5' splice site in SL addition trans-splicing.

Animals↗
PubMed1995

Clinical trials of immunoadsorbent in systemic lupus erythematosus therapy.

Five patients with systemic lupus erythematosus (SLE) were perfused through an extracorporeal shunt filled with DNA-immunoadsorbent (DNA immobilized on carbonized resin beads). High concentrations of anti-DNA antibodies (36.4-67.0%) (binding percentage with 125I-DNA) in the serum of SLE patients were reduced to 13.8-53.0%, respectively. The highest removal percentage was 62.1%. Although the decline levels varied, the symptoms of patients, i.e., long-term severe joint pain, severe edema, hydropericardium, and ascites were all relieved considerably. The immunoadsorbent showed satisfactory blood compatibility.

Antibodies, Antinuclear↗
PubMed1995

Synergistic interactions between heterologous upstream activation elements and specific TATA sequences in a muscle-specific promoter.

Previous investigations have defined three upstream activation elements--CCAC, A/T, and TATA sequences--necessary for muscle-specific transcription of the myoglobin gene. In the present study, we demonstrate that these three sequences elements, prepared as synthetic oligonucleotide cassettes, function synergistically to constitute a cell-type-specific transcription unit. Previously, cognate binding factors that recognize the CCAC and TATA elements were identified. In this study we determine that the A/T element binds two nuclear factors, including myocyte enhancer factor-2 (MEF-2) and an apparently unknown factor we provisionally termed ATF35 (A/T-binding factor, 35 kDa). Mutations that alter in vitro binding of either MEF-2 or ATF35 to this site diminish promoter function in vivo. Functional synergism between factors binding the CCAC and A/T elements is sensitive to subtle mutations in the TATA sequence, recapitulating the unusual preference for specific TATA variants exhibited by the native myoglobin promoter. These results provide new insights into mechanisms that underlie the distinctive pattern of myoglobin gene regulation in mammalian muscle development and lay a foundation for further studies to elucidate general principles of transcriptional control of complex mammalian promoters through combinatorial actions of heterologous transcriptional factors.

Animals↗
PubMed1995

Serum induction of MEF2/RSRF expression in vascular myocytes is mediated at the level of translation.

Vascular smooth muscle cells (VSMCs) reversibly coordinate the expression of VSMC-specific genes and the genes required for cell cycle progression. Here we demonstrate that isoforms of the MEF2/RSRF transcription factor are expressed in VSMCs and in vascular tissue. The MEF2A DNA-binding activity was upregulated when quiescent VSMCs were stimulated to proliferate with serum mitogens. The serum-induction of MEF2A DNA-binding activity occurred approximately 4 h following serum activation, and this correlated with an increase in the level of MEF2A protein without changes in the level of MEF2A mRNA or protein stability. These results indicate that MEF2A induction by serum is regulated at the level of translation.

Animals↗
PubMed1995

U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone.

U6 snRNA is essential for and may participate in the catalysis of pre-mRNA splicing. Extensive mutational analyses in several systems have identified nucleotides essential for U6 function in splicing; however, relatively little is known regarding the role of the U6 phosphate backbone. We previously described a mutation in a nematode U6 snRNA that causes it to be used as a splicing substrate within the spliceosome. This unusual reaction has made it possible to apply modification interference analysis to U6 function. Here, we have used phosphorothioate substitution to identify pro-R oxygens throughout the U6 backbone that are necessary for the first and/or second catalytic steps of splicing. Four pro-R oxygens are important for the first step; of these only two appear to be required. One additional pro-R oxygen is uniquely required for the second step. The two pro-R oxygens critical for the first step of splicing are in the helix 1b U2/U6 interaction region and the intramolecular stem-loop of U6, respectively. A comparison of the positions of these two pro-R oxygens with those found to be critical for autocatalytic excision of a group II intron suggests a possible functional similarity between U6 snRNA and domain V of group II introns.

Animals↗
PubMed1994

Translation elongation factor Tu cleaved by a phage-exclusion system.

Bacteriophage T4 multiples poorly in Escherichia coli strains carrying the defective prophage, e14; the e14 prophage contains the lit gene for late inhibitor of T4 in E. coli. The exclusion is caused by the interaction of the e14-encoded protein, Lit, with a short RNA or polypeptide sequence encoded by gol from within the major head protein gene of T4. The interaction between Lit and the gol product causes a severe inhibition of all translation and prevents the transcription of genes downstream of the gol site in the same transcription unit. However, it does not inhibit most transcription, nor does it inhibit replication or affect intracellular levels of ATP. Here we show that the interaction of gol with Lit causes the cleavage of translation elongation factor Tu (EF-Tu) in a region highly conserved from bacteria to humans. The depletion of EF-Tu is at least partly responsible for the inhibition of translation and the phage exclusion. The only other phage-exclusion system to be understood in any detail also attacks a highly conserved cellular component, suggesting that phage-exclusion systems may yield important reagents for studying cellular processes.

Amino Acid Sequence↗
PubMed1993

Functional reconstitution of U6 snRNA in nematode cis- and trans-splicing: U6 can serve as both a branch acceptor and a 5' exon.

Maturation of nuclear pre-mRNAs in nematodes requires both cis- and trans-splicing. Both processing pathways involve analogous two-step phosphotransfer reactions and both are dependent upon the integrity of U6 snRNA. We have developed a functional reconstitution assay to assess the U6 snRNA sequence requirements for cis- and trans-splicing. Branch formation between the splicing substrates and U6 snRNA was observed. The frequency of this event was greatly enhanced when a highly conserved sequence in U6 snRNA was altered by mutation. In cis- and trans-splicing reactions reconstituted with this mutant U6 snRNA the liberated exon of U6 proceeded through the second step of splicing using the appropriate splice acceptor sites. These results demonstrate covalent interactions between a U snRNA required for splicing and a splicing substrate, and they provide evidence for an unexpected degree of catalytic flexibility within the spliceosome.

Animals↗
PubMed1993

MEF2C, a MADS/MEF2-family transcription factor expressed in a laminar distribution in cerebral cortex.

We have cloned cDNA encoding a human transcription factor that belongs to the MEF2 (myocyte-specific enhancer-binding factor 2) subfamily of the MADS (MCM1-agamous-deficiens-serum response factor) gene family. This factor, which we have named MEF2C, binds specifically to the MEF2 element and activates transcription via this element. Specific isoforms of this factor are found exclusively in brain and are robustly expressed by neurons in cerebral cortex. In situ hybridization indicates that the factor is expressed preferentially in certain neuronal layers of cortex and that expression declines during postnatal development. The unusual pattern of expression in brain suggests that this transcription factor may be important in the development of cortical architecture.

Amino Acid Sequence↗