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PubMed1976

The size of pulse-labeled fibroin messenger RNA.

A method has been developed for the isolation of fibroin gene transcripts from total RNA of the silkworm Bombyx mori. It is based on affinity chromatography using Sephadex-bound polynucleotides capable of selectively hybridizing with fibroin mRNA sequences. In vivo pulse labeling of the posterior silk gland for periods of 10-35 min produces labeled heterogeneous nuclear RNA of high molecular weight (greater 40S). Fibroin gene transcripts can be selected from the total hnRNA population by two consecutive passages through the affinity column. Analysis of the column-bound material in denaturing polyacrylamide-agarose gels reveals that the size of pulse-labeled fibroin mRNA is essentially the same (within 5%) as that of mature cytoplasmic mRNA. This holds true for pulses as short as 6 min, where even nascent mRNA can be observed. However, a small shoulder of material is present on the heavy side of the pulse-labeled mRNA, which could be indicative of an extremely short-lived precurosr species. The purified pulse-labeled mRNA (10 min incorporation) has been further analyzed by chromatography in oligo(dT)-cellulose. The data show that the mRNA is polyadenylated within a few minutes after synthesis.

Animals↗
PubMed2006

In-cell polymerase chain reaction: strategy and diagnostic applications.

In situ polymerase chain reaction (PCR) refers to the amplification of specific nucleic acid sequences and subsequent visualization of the PCR products in tissue sections. When PCR is performed in fixed cells in suspension the term in-cell PCR is normally applied instead. For example, in-cell PCR has been used for intracellular detection of specific viruses. Furthermore, in mixtures of cells in suspension with different genotypes, in-cell PCR may be used for intracellular detection of DNA or mRNA sequences specific for one of the genotypes/population of cells. An in-cell PCR method is described that makes it possible to genotype a specific gene of interest derived from one individual in a mixture of cells from two individuals. This new method is based on in-cell PCR and dependent upon the presence of a well characterized and specific DNA sequence or polymorphism, which has to be present only in the cells from the individual being genotyped for the gene sequence of interest. The in-cell PCR method might find diagnostic applications in detection of intracellular pathogenic sequences in subgroups of cells and in noninvasive prenatal genetic diagnoses with the use of the few fetal cells circulating in maternal blood.

Antigens, CD↗
PubMed1993

Synergism in replication and translation of messenger RNA in a cell-free system.

Combination of the Q beta replicase reaction with the Escherichia coli cell-free translation system markedly enhances replication of a recombinant RQ-DHFR RNA consisting of the dihydrofolate reductase (DHFR) mRNA sequence inserted into RQ135(-1) RNA, an efficient naturally occurring Q beta replicase template. The enhancement is associated with a replication asymmetry previously described for the replication of Q beta phage RNA in vivo; the sense (+)-strands are produced in large excess over the antisense (-)-strands. This, in turn, results in increased synthesis of the functionally active DHFR. These effects are not observed when DHFR mRNAs or RQ135(-1) RNAs are used as templates, if the translation system is not complete, or if it is inhibited by puromycin. The coupled replication-translation of nonviral mRNA recombinants can serve as a useful model for studying the fundamental aspects of virus amplification and can be implemented for large-scale protein synthesis in vitro.

Base Sequence↗
PubMed2001

Expression and complement d activity of porcine adipsin.

To learn how signals from adipocytes might be involved in regulation of energy intake and storage, we have begun to characterize the porcine complement protein, adipsin. Adipsin was originally identified as a protein that is produced rather specifically by adipocytes, is secreted, and is nearly absent in several obese rodent models. We now report that porcine adipsin mRNA sequence is 74% identical to rat and predicts a protein that has 82 and 68% identity to human and rat forms, respectively. Porcine adipsin has none of the asparagine glycosylation consensus sites which make recombinant expression of mouse adipsin in Escherichia coli impractical. We present a method for engineering the porcine cDNA to facilitate expression by E. coli and provide a protocol for refolding and purifying porcine adipsin protein and for immunoassay. We have found that in addition to adipose tissue, adipsin mRNA is present in gut tissues. Coupled with the fact that adipsin is required for processing of complement C3a-desArg, and that C3a-desArg is a potent stimulant of fatty acid acylation in adipocytes, the production of adipsin in the gut may be related to a mechanism for adipocyte removal of lipid from chylomicrons.

Animals↗
PubMed1989

Structure of vaccinia virus late promoters.

Functional elements of vaccinia virus late promoters were characterized by mutagenesis. Synthetic oligonucleotides were inserted into a plasmid vector containing the lacZ gene of Escherichia coli flanked by sequences from the thymidine kinase (TK) gene of vaccinia virus. The lacZ gene, under control of the synthetic promoter, was introduced into the vaccinia virus genome at the TK locus by homologous recombination, and each of the 122 recombinants thus obtained was assayed for beta-galactosidase expression. The relative amounts and 5' ends of lacZ mRNAs specified by a subset of the recombinants were determined by primer extension. The analysis indicated that late promoters may be considered in terms of three regions; an upstream sequence of about 20 base-pairs, rich in T and A residues, separated by a spacer region of about six base-pairs from a highly conserved (-1)TAAAT(+4) element within which transcription initiates. All single nucleotide substitutions within the three A residues of the TAAAT, as well as the addition of a fourth A residue, caused drastic reductions in promoter strength. All substitutions of the T residues at -1 and +4 were also detrimental to promoter activity, to an extent that depended on the strength of the promoter as determined by the upstream sequence. mRNA synthesis appeared to initiate within the three A residues regardless of promoter strength. The 5'-poly(A) leader, which is a unique feature of poxvirus late mRNAs, was diminished in length when either of the T residues at -1 and +4 was mutated, was absent or limited to a few nucleotides when any of the three A residues was substituted, but was unaffected by changes outside the TAAAT sequence. The data are consistent with a model for the generation of the normal 5'-poly(A) leader by an RNA polymerase slippage mechanism requiring three consecutive A residues. Single nucleotide substitutions within the six base-pairs upstream and three base-pairs downstream from the TAAAT sequence had modest effects on promoter strength. The most and least favourable changes led to a fourfold increase and an eightfold decrease in activity, respectively. Sequences further upstream were essential for late promoter function; tracts of T or A residues enhanced expression up to 20-fold, the former conferring much greater activity. Highest expression was obtained with a tract of 18 or 20 T residues.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗
PubMedDate not supplied

Expression and cDNA sequence of matrix metalloproteinase-2 (MMP-2) in a mammalian model of human disease processes: Tupaia belangeri.

Matrix metalloproteinase-2 (MMP-2) is one of a family of proteolytic enzymes that are involved in the remodelling of tissue during normal growth processes and is capable of degrading structural components of the extracellular matrix. Increases in MMP-2 expression and activity have been reported in diseases that involve degradation of the extracellular matrix. Reported here for the first time are the relative levels of expression of MMP-2 in tissues of the tree shrew along with 2587 bases of the mRNA sequence. Translation of this sequence predicts a protein 660 amino acids in length, containing all of the features expected of mammalian MMP-2. The tree shrew is a species close to the primate line and is an emerging animal model for a variety of human diseases, including hepatitis and myopia that feature MMP-2 mediated remodelling of the extracellular matrix.

Amino Acid Sequence↗
PubMed2000

Complex regulation of calcium-binding protein D9k (calbindin-D(9k)) in the mouse uterus during early pregnancy and at the site of embryo implantation.

Establishment of receptive endometrium is essential for implantation. Our aim was to identify and characterize genes uniquely regulated at the sites of implantation in mouse uterus by RNA differential display polymerase chain reaction (DDPCR). One of the gene fragments identified was 86% homologous to rat calcium-binding protein D9k (calbindin-D(9k)); the mouse counterpart had not then been cloned, but subsequently an mRNA sequence of mouse calbindin-D(9k) became available in GenBank (accession number: AF028071). This sequence is 99% homologous to the DDPCR-derived gene tag but has a shorter 3' end. Reverse transcription-polymerase chain reaction (RT-PCR) was performed using the sequence of 3' end of the DDPCR product and the 5' end of AF028071, and a full cDNA was obtained. This gene was primarily up-regulated by progesterone, but not by estrogen. It was further increased by the combination of the two steroids. Expression of calbindin-D(9k) was overall increased in the uterus during early pregnancy, but the level was significantly lower in implantation compared to interimplantation sites on Days 4.5 and 5.5 of pregnancy, becoming barely detectable in both sites after Day 6.5. In situ hybridization localized this mRNA predominantly in the luminal epithelium of the pregnant uterus. The complex regulation of calbindin-D(9k) in mouse uterus suggests an important role for this protein during pregnancy.

Amino Acid Sequence↗
PubMed1995

Detection of BCR-ABL transcripts from the Philadelphia translocation by hybridization in microtiter wells and time-resolved immunofluorometry.

Two hybridization assays have been developed to detect BCR-ABL mRNA transcripts arising from the Philadelphia translocation. Both assays use time-resolved immunofluorometric detection of polymerase chain reaction-amplified BCR-ABL mRNA sequences hybridized to specific probes. In configuration I, biotinylated amplified target is immobilized onto streptavidin-coated wells and hybridized to a probe labeled with the hapten digoxigenin. Hybrids are detected via an alkaline phosphatase-labeled antibody and fluorosalicylylphosphate as substrate. The fluorosalicylate produced forms highly fluorescent complexes with Tb(3+)-EDTA. In configuration II, biotinylated probe is immobilized onto streptavidin-coated wells. PCR, performed in the presence of hapten-labeled deoxyribonucleotide, generates labeled product, which is hybridized to immobilized probe and quantified as above. BCR-ABL transcripts from one leukemic cell amidst mRNA from 500,000 normal granulocytes are detectable with signal/background ratios as high as 36.4 and 24.6 for configurations I and II, respectively. The respective CVs for the assays were 6.6-9.0% and 5.1-12.5%.

Base Sequence↗
PubMed2005

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

We describe here the results of the first genome-wide survey of candidate exon repetition events in expressed sequences from human, mouse, rat, chicken, zebrafish and fly. Exon repetition is a rare event, reported in <10 genes, in which one or more exons is tandemly duplicated in mRNA but not in the gene. To identify candidates, we analysed database sequences for mRNA transcripts in which the order of the spliced exons does not follow the linear genomic order of the individual gene [events we term rearrangements or repetition in exon order (RREO)]. Using a computational approach, we have identified 245 genes in mammals that produce RREO events. RREO in mRNA occurs predominantly in the coding regions of genes. However, exon 1 is never involved. Analysis of the open reading frames suggests that this process may increase protein diversity and regulate protein expression via nonsense-mediated RNA decay. The sizes of the exons and introns involved around these events suggest a gene model structure that may facilitate non-linear splicing. These findings imply that RREO affects a significant subset of genes within a genome and suggests that non-linear information encoded within the genomes of complex organisms could contribute to phenotypic variation.

Alternative Splicing↗
PubMed2004

Interaction between 3' untranslated region of calcitonin receptor messenger ribonucleic acid (RNA) and adenylate/uridylate (AU)-rich element binding proteins (AU-rich RNA-binding factor 1 and Hu antigen R).

Our previous results in mouse osteoclasts suggested that calcitonin (CT) alters CT receptor (CTR) mRNA stability. The CTR mRNA transcript contains several adenylate/uridylate (AU)-rich destabilizing elements in the 3' untranslated region (3'UTR). When the 3'UTR of mouse CTR mRNA was labeled by [alpha-(32)P]-uridine 5-triphosphate, interactions were observed between the transcript and several cell extracts, including those from the osteoclast progenitor monocyte/macrophage cell line, RAW 264.7. The molecular masses of the interacting proteins ranged from approximately 35 to 50 kDa, similar to AU-rich RNA-binding factor 1 (AUF1) and Hu antigen R (HuR). Radiolabeled 3'UTR transcripts bound with a 40-kDa protein, which could be extracted from cells transfected with AUF1 p40. To confirm the binding specificity, a pSG5 vector construct, containing the AUF1 p40 with an hemagglutinin tag, was transiently transfected into NIH3T3 cells. The extracts were incubated with poly(A)-added CTR3'UTR. The reaction mixture was immunoprecipitated using an antihemagglutinin antibody and precipitated mRNA species were extracted and reverse transcribed using oligo-dT primers. It was found that PCR primers specific for the 3'UTR of CTR mRNA sequence generated a PCR signal. No signal was observed when mutated AUF1 p40 was transfected. In a manner similar to the AUF1 binding, HuR was also found to bind to the 3'UTR. Specific binding of AUF1 p40 and HuR was also found with RNA extracted from mouse osteoclasts. Treatment of osteoclasts with CT did not significantly affect the expression of AUF1 but decreased the levels of HuR and its mRNA. The role of CTR3'UTR in mRNA stability was further tested by expressing luciferase reporter constructs that did, or did not, contain the CTR3'UTR, under the control of the tetracycline-regulatory system. The results showed that the addition of 3'UTR considerably shortened the mRNA half-life of the luciferase reporter gene. These results suggest that AUF1 p40, HuR, and the 3'UTR of the CTR mRNA transcript could be involved in posttranscriptional regulation of CTR mRNA expression.

3' Untranslated Regions↗
PubMed2005

Analysis of progressively overexpressed genes in tumorigenesis of colorectal cancers using cDNA microarray.

The identification of differentially expressed genes has important implications in understanding the biology of colorectal tumorigenesis and progression, as well as developing new diagnostic and therapeutic strategies. In this study, cDNA microarray technology was used to identify colorectal tumor-related functional genes, which are overexpressed continuously from colorectal adenoma to adenocarcinoma. A set of 23 genes with progressive overexpression in the development of colorectal cancer (CRC) was identified by cDNA microarray, then analyzed by sequencing and Northern blot analysis. Validation of our array results was simultaneously performed by exploring the SAGEmap database. Furthermore, the gradually over-expressed genes from adenoma to adenocarcinoma were validated by Northern blot analysis with additional samples from three patients with synchronous colorectal adenocarcinoma and adenoma and four patients with CRC. Of these 23 genes, one was a function-unknown gene, designated as Homo sapiens chromosome 21q22.1 anonymous mRNA sequence (Genbank accession no. AF003738), and 22 were function-known genes. Searching through the Gene Ontology Browser at the Cancer Genome Analysis Project website revealed that the biological roles of these 22 function-known genes are involved in cell motility, cell adhesion, chemokine activity, signal transduction, cytoskeleton organization, proteolysis, apoptosis, and cell proliferation. The genes identified in the present study offer valuable information on colorectal carcinogenesis and metastasis, and represent a potential source of novel targets for new strategies for CRC diagnosis and therapy.

Blotting, Northern↗
PubMed1981

The construction, identification and partial characterization of plasmids containing guinea-pig milk protein complementary DNA sequences.

A complementary DNA (cDNA) plasmid library has been constructed in the plasmid pAT153, using poly(A)-containing RNA isolated from the lactating guinea-pig mammary gland as the starting material. Double stranded cDNA was inserted into the EcoRI site of the plasmid using poly(dA . dT) tails, then transformed into Escherichia coli HB101. From the resulting colonies we have selected and partially characterized plasmids containing cDNA copies of the mRNAs for casein A, casein B, casein C and alpha-lactalbumin. However, the proportion containing casein C cDNA was exceptionally low, and these contained at best 60% of the mRNA sequence.

Animals↗
PubMed2005

Type 1 Stickler syndrome: a histological and ultrastructural study of an untreated globe.

AIMS: To present a histological and ultrastructural study of an untreated globe in a patient with genetically confirmed type 1 Stickler syndrome. METHODS: Histological and electron microscopic examinations were performed on the enucleated globe from the proband of a pedigree with type 1 Stickler syndrome. Linkage analysis was carried out using polymorphic markers flanking the COL2A1 gene and the mutation was identified by direct sequencing. RESULTS: The significant retinal abnormality was incarceration of vitreous collagen within glial strands on the inner surface of an atrophic and gliotic detached retina. The incarcerated collagenous layers contained glial cells and extended from the retina to form strands, some of which contributed to a retrolental membrane. Mutation screening detected a C to T mutation in exon 47 that inserted a premature termination codon into the reading frame of the mRNA. Sequence analysis of three of the four affected children confirmed that they were also heterozygous for the base change. The youngest child's DNA was not analysed. CONCLUSIONS: The study represents the first evidence of abnormal interactions between pathological vitreous collagen and the inner retina in a patient with type 1 Stickler syndrome with a confirmed mutation in the COL2A1 gene.

Adult↗
PubMed1995

Sulfated glycoprotein-1 (SGP-1) expression in ovine endometrium during the oestrous cycle and early pregnancy.

This study determined effects of day of oestrous cycle and early pregnancy on sulfated glycoprotein-1 (SGP-1) expression in ovine endometrium. A 364-bp clone of the ovine SGP-1 mRNA was amplified from reverse transcribed Day-15 cyclic endometrial mRNA using the polymerase chain reaction (PCR) and primers specific for the rat SGP-1 mRNA sequence. Nucleotide sequence of the ovine SGP-1 cDNA shared significant identity with rat SGP-1 and human prosaposin. Ewes (n = 40) were hysterectomized on either Day 1, 6, 11, 13 or 15 of the oestrous cycle or on Day 11, 13, 15, 17 or 25 of early pregnancy. Total cellular RNA was isolated from endometrium and subjected to Northern and slot blot hybridization analyses using an antisense cRNA probe transcribed from the ovine SGP-1 cDNA clone. A single 2.6-kb mRNA transcript was detected by Northern hybridization analyses. Slot blot hybridization analyses indicated that steady-state levels of endometrial SGP-1 mRNA varied during the oestrous cycle (cubic, P < 0.02) and increased between Day 11 and Day 25 of early pregnancy (linear, P < 0.01). On Days 11, 13 and 15, endometrial SGP-1 mRNA levels were greater in pregnant ewes than in cyclic ewes (day x pregnancy status, P < 0.01). Immunohistochemical localization of SGP-1 in uterine tissues with rabbit anti-rat SGP-1 antibody revealed intense immunoreactivity associated primarily with the endometrial epithelium. These results indicate that the ovine endometrium expresses SGP-1, a prosaposin, and that SGP-1 expression varies during the oestrous cycle and is enhanced by the conceptus. The presence of SGP-1 in the endometrium suggests intracellular and extracellular roles for this protein in glycosphingolipid metabolism or transport in the uterine environment.

Animals↗
PubMed1996

Naturally occurring nucleosome positioning signals in human exons and introns.

We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity of roughly ten nucleotides. The periodic pattern is also present in intron sequences, although the strength per nucleotide is weaker. Using two independent profile methods based on triplet bendability parameters from DNase I experiments and nucleosome positioning data, we show that the pattern in multiple alignments of internal exon and intron sequences corresponds to a periodic "in phase" bending potential towards the major groove of the DNA. The nucleosome positioning data show that the consensus triplets (and their complements) have a preference for locations on a bent double helix where the major groove faces inward and is compressed. The in-phase triplets are located adjacent to GCC/GGC triplets known to have the strongest bias in their positioning on the nuclesome. Analysis of mRNA sequences encoding proteins with known tertiary structure exclude the possibility that the pattern is a consequence of the previously well-known periodicity caused by the encoding of alpha-helices in proteins. Finally, we discuss the relation between the bending potential of coding and non-coding regions and its impact on the translational positioning of nucleosomes and the recognition of genes by the transcriptional machinery.

Base Sequence↗
PubMed1986

Effect of dichloroacetic acid on rat hepatic messenger RNA activity profiles.

We have previously suggested that the ability of glucose to induce rat hepatic lipogenic enzymes is mediated by the mitochondrial oxidation of pyruvate. In part, this hypothesis is supported by the finding that an activator of pyruvate dehydrogenase, dichloroacetic acid (DCA), is capable of inducing malic enzyme in hepatocyte cultures. In order to further test this hypothesis, we compared the mRNA responses induced by carbohydrate feeding in vivo and by glucose administration to hepatocytes in culture with those mRNA responses induced in DCA both in vivo and in culture. DCA administration to rats resulted in a significant increase in liver:body weight ratio. It was, in addition, a potent inducer of malic enzyme. Hepatic mRNA activity profiles were examined by two-dimensional gel electrophoretic analysis of in vitro translation products. Six of the seven mRNAs altered by carbohydrate feeding were similarly altered by DCA feeding in vivo. In cultured hepatocytes 10 mmol/L DCA significantly increased four of six glucose-induced mRNAs. The mRNA for malic enzyme was among those mRNA sequences induced both in vivo and in culture. Increasing glucose concentrations in the culture medium resulted in an expected rise in pyruvate levels, whereas DCA caused a significant decrease in the concentration of this intermediate. It is likely, therefore, that augmentation of the flux of pyruvate through pyruvate dehydrogenase rather than alterations in pyruvate levels per se, is a proximal event leading to the induction of multiple mRNAs. The marked overlap in mRNA response to both carbohydrate and DCA indicates that the signal regulating the content of the carbohydrate responsive mRNAs is derived from mitochondrial pyruvate oxidation.

Acetates↗
PubMed2006

Automatic generation of gene finders for eukaryotic species.

BACKGROUND: The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically generate species-specific gene finders and to re-train them as the quantity and quality of reliable gene annotation grows. RESULTS: We present a procedure, Agene, that automatically generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome. We apply a Hidden Markov model (HMM) that implements explicit length distribution modelling for all gene structure blocks using acyclic discrete phase type distributions. The state structure of the each HMM is generated dynamically from an array of sub-models to include only gene features represented in the training set. CONCLUSION: Acyclic discrete phase type distributions are well suited to model sequence length distributions. The performance of each individual gene predictor on each individual genome is comparable to the best of the manually optimised species-specific gene finders. It is shown that species-specific gene finders are superior to gene finders trained on other species.

Algorithms↗
PubMed1988

Multiple abnormal beta-hexosaminidase alpha chain mRNAs in a compound-heterozygous Ashkenazi Jewish patient with Tay-Sachs disease.

Abnormal beta-hexosaminidase alpha chain cDNA clones were isolated from fibroblasts of an Ashkenazi Jewish patient with Tay-Sachs disease. Four abnormal cDNA clones were sequenced in their entirety. We showed previously that three of these mRNAs retained intron 12 with a mutation from G to C at the 5' donor site and that the patient was heterozygous with respect to this splicing defect (Ohno, K., and Suzuki, K., (1988) Biochem. Biophys. Res. Commun. 153, 463-469). One clone retained, in addition to intron 12, intron 13, which was truncated and polyadenylated due to a polyadenylation signal within intron 13. The fourth clone did not contain intron 12 and was missing exon 12. Some of these abnormal mRNAs were also missing one or more of upstream exons. The regions of exon 12-intron 12 and of upstream exons were evaluated in a total of 30 clones, including those completely sequenced, by restriction mapping and Southern analysis with appropriate probes. Of the 25 cDNA clones that included the exon 12-intron 12 region, 11 contained the exon 12-intron 12 sequence with the junctional transversion, and 11 were missing both exon 12 and intron 12. Among the 12 clones that included the region of exon 3-exon 9, 7 were missing one or more of upstream exons. Three clones gave results expected of normal cDNA in the region of exons 12 and 13. One of the three, furthermore, was 3.6-kilobases long and contained the completely normal beta-hexosaminidase alpha chain mRNA sequence on the 3' side and an abnormal 1.7-kilobase segment at the 5' end. These findings suggest that the splicing defect results in either retention of intron 12 or skipping of exon 12 in approximately equal proportions and that remote upstream exons are also frequently excised out. The three clones that were normal in the exon 12-intron 12 region could have derived from the other yet-to-be-characterized mutant allele. However, we were unable to obtain firm evidence that the abnormal upstream sequence is directly related to Tay-Sachs disease.

Base Sequence↗