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PubMed2003

Comparative promoter analysis and its application in analysis of PTH-regulated gene expression.

Taking advantage of the "working draft" of the human genome and the MIT shotgun assembly of the mouse genome, we performed a comparative promoter analysis of human RefSeq mRNA (sequences from GenBank's RefSeq database). By combining this analysis with a transcription factor (TF) binding site analysis using a TRANSFAC position weight matrix (PWM) search, 86% of non-specific TF sites were removed. Using a set of genes that are regulated by parathyroid hormone (PTH), a statistical analysis was performed on the conserved TF binding sites among a set of eight human and mouse genes. From among the eight genes tested, we obtained a set of 31 TFs, suggesting possible roles for associated genes in PTH-mediated pathways. All three known PTH-responsive TFs (AP1, RUNX2, CREB) were correctly predicted by this analysis as well as two other potential TFs (VDR and CEBP Delta). Additionally, a model was made to describe the TF site characteristic module of PTH-regulated genes. This model was then used to search all human RefSeq gene promoters with established human-mouse ortholog relationships to identify other PTH-regulated genes. This comparative approach combined with statistical analysis proved to be sufficiently specific to decipher critical TFs involved in PTH-regulated pathways.

Algorithms↗
PubMed1990

Processivity errors of gene expression in Escherichia coli.

Not all ribosomes that initiate translation of an mRNA sequence will successfully complete it and produce a full-length protein product. By comparing the amounts of lacZ monomer and lacZ dimer protein expressed from a plasmid in a strictly controlled assay, we calculate a dimer to monomer ratio of 0.76. We interpret this to mean that ribosomes have a 76% chance of completing the synthesis of a beta-galactosidase polypeptide. The remaining 24% of the initiated chains end in processivity accidents. For the wild-type, premature RNA polymerase termination is found to account for roughly one-third of the processivity accidents. For the hyperaccurate SmP mutant, we observe a processivity of 0.28, but the presence of streptomycin improves this to 0.50. Thus, the hyperaccuracy with respect to missense substitutions for this mutant is accompanied by a reduced processivity. Addition of streptomycin increase the first error class and reduces the second one. This finding is relevant to the optimization of ribosome function and the growth performance of ribosome mutants.

Base Sequence↗
PubMed1997

Immunohistochemical and genetic evidence of myeloperoxidase involvement in multiple sclerosis.

The myeloperoxidase enzyme (MPO) is expressed specifically in myeloid cells and catalyzes the formation of hypochlorous acid and other cytotoxic oxidants. We previously reported that two alleles of MPO exist which differ in promoter strength due to a base difference in an Alu-encoded hormone response element. The present study shows that the higher expressing MPO genotype is overrepresented in early onset multiple sclerosis in females, implicating MPO in this demyelinating disease. Contrary to the general conception that macrophages lack MPO, immunohistochemical analysis shows that MPO is present in microglia/macrophages in and around MS lesions as shown by colocalization with major histocompatibility antigens HLA-DR and phagocytized myelin. Also, MPO mRNA sequences are detected in cDNA derived from isolated human adult microglia. This is the first evidence that MPO is present in microglia/macrophages at MS lesions, that MPO gene expression occurs in microglia and that MPO plays a role in MS pathogenesis as shown by the allelic disequilibrium in early onset disease.

Adult↗
PubMed2002

Endoribonuclease activities of Trypanosoma brucei mitochondria.

RNA editing in kinetoplastids is a type of post-transcriptional processing that changes mitochondrial mRNA sequences by the addition or deletion of uridines. Multiple enzymatic activities, such as endoribonuclease and RNA ligase, are associated with this process and exist in a multienzyme complex. Endonuclease activities from Trypanosoma brucei mitochondrial extracts were fractionated by sequential ion exchange and gel filtration chromatography. The RNA editing specific endonuclease activity co-fractionated with in vitro editing while another endonuclease activity with a different substrate specificity, and the majority of mtRNase P activity fractionated away from the editing activity. The pH, salt, temperature, and Mg(2+) optima of all three endonucleases were determined. All three activities are sensitive to high temperature and protease digestion. In addition, treatment with micrococcal nuclease resulted in partial disruption of the editing complex and decreased pre-cleaved in vitro insertion editing activity, suggesting that both RNA(s) and protein(s) are necessary in the intact functional complex.

Animals↗
PubMed2001

Proteomics: a technology-driven and technology-limited discovery science.

An emerging field for the analysis of biological systems is the study of the complete protein complement of the genome, the 'proteome'. There are several complementary tools available for proteome analysis including 2D protein electrophoresis and mass spectrometry. Emerging technologies for proteome analysis include spotted-array-based methods and microfluidic devices. Taken together, these technologies provide a wealth of information that is useful in discovery-based science. However, there are some key limitations of these approaches and new technology is required to be able to fully integrate proteomic information with information obtained about DNA sequence, mRNA profiles and metabolite concentrations into effective models of biological systems.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2002

Antisense transcripts in the human genome.

By a systematic search of vertebrate mRNA sequences, we have identified a surprisingly large number of human antisense transcripts. These data suggest that regulation of gene expression by antisense and double-stranded RNAs could be a common phenomenon in mammalian cells.

Algorithms↗
PubMed1997

Phosphorylation events mediated by protein kinase C alpha and epsilon participate in regulation of tau steady-state levels and generation of certain "Alzheimer-like" phospho-epitopes.

Hyperactivation of protein kinase C (PKC) in intact neuroblastoma cells by several methods increases site-specific tau phosphorylation as shown by increases in paired helical filament-I (PHF-I) and ALZ-50 but not AT-8 immunoreactivity. In the present study, the influence of PKC on tau metabolism was further examined by isoform-specific antisense oligonucleotide-mediated PKC downregulation in human SH-SY-5Y neuroblastoma cells and by generation of stably-transfected subclones expressing isoform-specific anti-PKC mRNA sequences. Downregulation of PKC epsilon by both of these methods reduced PHF-I and ALZ-50 immunoreactivity, suggesting that this PKC isoform, perhaps via downstream kinase cascades, regulated tau phosphorylation events that normally generate these epitopes. By contrast, downregulation of either PKC epsilon or PKC alpha reduced immunoreactivity towards the phosphate-independent anti-tau antibodies 5E2 and JM, suggesting that both of these isoforms participated in regulation of tau steady-state levels. Downregulation of PKC beta did not affect any of the above changes. The above roles were apparently unique for PKC epsilon and PKC alpha, since activation of multiple PKC isoforms by phorbol ester treatment and/or other calcium-dependent kinase(s) by ionophore-mediated calcium influx could not compensate for downregulation of PKC alpha or PKC epsilon in maintaining tau steady-state levels or PHF-I/ALZ-50 immunoreactivity, respectively. These findings suggest that hyperactivation of signal transduction pathways, including those regulated by PKC, could evoke changes in neuronal cells reminiscent of those seen in affected neurons in Alzheimer's disease.

Alzheimer Disease↗
PubMedDate not supplied

An attempt to correlate an idiotype with antibody structure.

The expression of different idiotypic families encountered in the anti-phosphorylcholine antibodies depends on the association of a heavy chain with one of the VL sub-families. Manipulation of the response by idiotypic suppression leads to formation of a T15cr family whose structural correlates are analysed by determination of the mRNA sequence of hybridoma heavy and light chains.

Animals↗
PubMed2003

Proteomic characterization of the human cortical neuronal cell line HCN-2.

Neuronal marker proteins are widely used for characterization and identification of normal and tumor tissue of the central nervous system, but the most commonly used neuronal markers have inherent methodological problems. We used a proteomic approach with two-dimensional (2-D) gel electrophoresis and subsequent MALDI identification to identify possible new marker proteins in the human cortical neuronal cell line HCN-2. We found 14 proteins that previously were predicted only on the basis of open reading frames from mRNA sequences or DNA. We could unambiguously identify the following proteins: Bab55091, BK65A6.2 (Novel Sushi Domain (Scr repeat), glucosidase II alpha subunit, glucosidase II precursor (KIAA0088 protein), HSPC108, hypothetical 35.8 kDa protein, hypothetical 40.7 KDA protein, hypothetical 49.4 kDa protein, leucine-zipper protein FKSG13, lysophospholipase homolog, mitofilin (fragment), P1.11659_4, reticulocabin precursor and one unknown protein for MGC:10432. We could prove the existence of these 14 proteins in the human neuron, extending the list of proteins with neuronal expression and identify possible new candidate marker proteins.

Biomarkers↗
PubMed2002

Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding.

The ribosome is a molecular machine that converts genetic information in the form of RNA, into protein. Recent structural studies reveal a complex set of interactions between the ribosome and its ligands, mRNA and tRNA, that indicate ways in which the ribosome could avoid costly translational errors. Ribosomes must decode each successive codon accurately, and structural data provide a clear indication of how ribosomes limit recruitment of the wrong tRNA (sense errors). In a triplet-based genetic code there are three potential forward reading frames, only one of which encodes the correct protein. Errors in which the ribosome reads a codon out of the normal reading frame (frameshift errors) occur less frequently than sense errors, although it is not clear from structural data how these errors are avoided. Some mRNA sequences, termed programmed-frameshift sites, cause the ribosome to change reading frame. Based on recent work on these sites, this article proposes that the ribosome uses the structure of the codon-anticodon complex formed by the peptidyl-tRNA, especially its wobble interaction, to constrain the incoming aminoacyl-tRNA to the correct reading frame.

Protein Biosynthesis↗
PubMed2002

Structure of the mammalian kinin receptor gene locus.

The genes encoding the two kinin receptors, B1 and B2, are closely linked on the same chromosome in human, mouse, and rat. In this article, we present the organisation of the B B2 locus in these mammals. This organisation was obtained by comparing the kinin receptor mRNA sequences of man and mouse with the sequence of chromosomes 14 and 12, respectively. We found that the two genes are located in tandem orientation, separated by only 7.8 kb in mice and 12 kb in humans. The distance of the two genes on rat chromosome 6 was determined by long-range PCR to be 9.5 kb. The organisation of the two genes encoding the kinin receptors is similar in the three species, except that the human B1 gene harbors an additional exon, which may originate from the insertion of an Alu repetitive sequence during evolution. Moreover, the human and rat, but not the murine, B2 genes carry an alternatively spliced exon between exons 2 and 3, termed exon 2b.

Animals↗
PubMed2002

Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression.

Translating ribosomes can shift reading frame at specific sites with high efficiency for gene expression purposes. The most common type of shift to the -1 frame involves a tandem realignment of two anticodons from pairing with mRNA sequence of the form X XXY YYZ to XXX YYY Z where the spaces indicate the reading frame. The predominant -1 shift site of this type in eubacteria is A AAA AAG. The present work shows that in Escherichia coli the identity of the 6 nt 3' of this sequence can be responsible for a 14-fold variation in frameshift frequency. The first 3' nucleotide has the primary effect, with, in order of decreasing efficiency, U > C > A > G. This effect is independent of other stimulators of frameshifting. It is detected with other X XXA AAG sequences, but not with several other heptameric -1 shift sites. Pairing of E. coli tRNALYS with AAG is especially weak at the third codon position. We propose that strong stacking of purines 3' of AAG stabilizes pairing of tRNALys, diminishing the chance of codon:anticodon dissociation that is a prerequisite for the realignment involved in frameshifting.

Anticodon↗
PubMed1999

A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons.

We have prepared a novel optical fiber evanescent wave DNA biosensor using a newly developed molecular beacon DNA probe. The molecular beacons (MB) are oligonucleotide probes that become fluorescent upon hybridization with target DNA/RNA molecules. Biotinylated MBs have been designed and immobilized on an optical fiber core surface via biotin-avidin or biotin-streptavidin interactions. The DNA sensor based on a MB does not need labeled analyte or intercalation reagents. It can be used to directly detect, in real-time, target DNA/RNA molecules without using competitive assays. The sensor is rapid, stable, highly selective, and reproducible. We have studied the hybridization kinetics of the immobilized MB by changing the ionic strength of the hybridization solution and target DNA concentration. Our result shows divalent cations play a more important role than monovalent cations in stabilizing the MB stem hybrids and in accelerating the hybridization reaction with target DNA/RNA molecules. The concentration detection limit of the MB evanescent wave biosensor is 1.1 nM. The MB DNA biosensor has been applied to the analysis of specific gamma-actin mRNA sequences amplified by polymerase chain reaction.

Actins↗
PubMedDate not supplied

3'-End conjugates of minimally phosphorothioate-protected oligonucleotides with 1-O-hexadecylglycerol: synthesis and anti-ras activity in radiation-resistant cells.

Activation of the ras oncogene has been implicated in many types of human tumors. It has been shown that downmodulation of ras expression can lead to the reversion of the transformed phenotype of these tumor cells. Antisense oligodeoxyribonucleotides (ODNs) can inhibit gene expression by hybridization to complementary mRNA sequences. To minimize toxicity associated with all-phosphorothioated ODNs and improve cellular uptake, we used partially phosphorothioate (PPS)-modified ODNs having an additional hydrophobic tail at the 3'-end (PPS-C(16)). The PPS ODNs are protected against degradation by PS internucleotide linkages at both the 3'- and 5'-ends and additionally stabilized at internal pyrimidine sites, which are the major sites of endonuclease cleavage. Here we show that anti-ras PPS-C(16) ODN retains the high sequence-specificity of PPS ODNs and provides maximal inhibition of Ras p21 synthesis with minimal toxicity even without the use of a cellular uptake enhancer. Moreover, treatment of T24, a radiation-resistant human tumor cell line that carries a mutant ras gene, with anti-ras PPS-C(16) ODN resulted in a reduction in the radiation resistance of the cells in vitro. We also demonstrate that the growth of RS504 (a human c-Ha-ras transformed NIH/3T3 cell line) mouse tumors was significantly inhibited by the combination of intratumoral injection of anti-ras PPS-C(16) ODN and radiation treatment. These findings indicate the potential of this combination of antisense and conventional radiation therapy as a highly effective cancer treatment modality.

3' Untranslated Regions↗
PubMed1986

Glucocorticoids decrease the synthesis of type I procollagen mRNAs.

Glucocorticoids selectively decrease procollagen synthesis in animal and human skin fibroblasts. beta-Actin content and beta-actin mRNA are not affected by glucocorticoid treatment of chick skin fibroblasts. The inhibitory effect of glucocorticoids on procollagen synthesis is associated with a decrease in total cellular type I procollagen mRNAs in chick skin fibroblasts. These effects of dexamethasone are receptor mediated as determined by pretreatment with the glucocorticoid antagonists progesterone and RU-486 and with the agonist beta-dihydrocortisol. Dexamethasone has a small but significant inhibitory effect on cell growth of chick skin fibroblasts. The ability of this corticosteroid to decrease the steady-state levels of type I procollagen mRNAs in nuclei, cytoplasm, and polysomes varies. The largest decrease of type I procollagen mRNAs is observed in the nuclear and cytoplasmic subcellular fractions 24 h after dexamethasone treatment. Type I procollagen hnRNAs are also decreased as determined by Northern blot analysis of total nuclear RNA. The synthesis of total cellular type I procollagen mRNAs is reversibly decreased by dexamethasone treatment. In addition the synthesis of total nuclear type I procollagen mRNA sequences is decreased at 2, 4, and 24 h following the addition of radioactive nucleoside and dexamethasone to cell cultures. Although the synthesis of pro alpha 1(I) and pro alpha 2(I) mRNAs is decreased in dexamethasone-treated chick skin fibroblasts, the degradation of the total cellular procollagen mRNAs is not altered while the degradation of total cellular RNA is stabilized. These data indicate that the dexamethasone-mediated decrease of procollagen synthesis in embryonic chick skin fibroblasts results from the regulation of procollagen gene expression.

Actins↗
PubMed1980

Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter.

High-resolution gel electrophoresis has been used to detect and quantitate promoter-specific oligonucleotides produced during initiation of transcription in vitro at the lactose operon (lac) UV5 promoter. The resolved products are RNA species of various lengths which correspond to the initial lac mRNA sequence. Quantitation shows that many oligonucleotides can be formed per preinitiation complex, including species as long as hexanucleotide. Synthesis occurs without dissociation of the enzyme, as evidenced by levels of synthesis in the presence of heparin, a selective inhibitor of free RNA polymerase. Thus, RNA polymerase cycles at this promoter in vitro producing oligonucleotides reiteratively. In general, the yield of oligonucleotides decreases when the total concentration of all four substrates is increased or when a missing nucleoside triphosphate substrate is added. Nevertheless, oligonucleotide synthesis persists under all conditions tested. Strikingly, the dinucleotide always represents 50% of the total of all oligonucleotides, even when conditions are manipulated to cause a 100-fold variation in this total. This shows that, after formation of the first phosphodiester bond at the lac UV5 promoter, dissociation of the dinucleotide is as likely as formation of the second phosphodiester bond. As discussed above, after release of a small RNA, RNA polymerase may then begin another RNA chain, which is again subject to premature release. These considerations lead to a model in which RNA polymerase cycles to produce oligonucleotides during initiation of transcription at the lac UV5 promoter in vitro. Production of a long RNA transcript is then essentially an escape from this cycling reaction. The drug rifampicin, which drastically inhibits escape to produce RNA, limits, but dose not prevent, the cycling reaction.

DNA-Directed RNA Polymerases↗
PubMed1980

Productive and abortive initiation of transcription in vitro at the lac UV5 promoter.

The rates of productive and abortive initiation of transcription in vitro at the lac UV5 promoter have been determined and compared to values determined for phage lambda and T7 promoters. The rate constants for productive initiation of lac transcript are consistently lower over a range of low to moderate concentration of initiating nucleoside triphosphate (ATP). Abortive initiation of lac dinucleoside tetraphosphate is also slower at low to moderate concentrations of ATP. These data demonstrate the existence of significant differences in initiation rate among promoters. We suggest that these differences may be a consequence of the initial mRNA sequences and extents of RNA polymerase cycling during initiation of promoter-specific transcription.

Adenosine Triphosphate↗
PubMed1976

Activation of in vitro histone gene transcription from Hela S3 chromatin by S-phase nonhistone chromosomal proteins.

Using a 3H-labeled single-stranded complementary DNA probe for detection of histone mRNA sequences (Thrall, CL., Park, WD., Rashba, HW., Stein, JL.,Mans, RJ., and Stein, GS.(1974), biochem. Biophys. Res. Commun. 61,1443) we have found that histone genes are transcribed in vitro from chromatin isolated from S-phase HeLa cells but not from chromatin isolated from G1-phase cells (Stein, G., Park W., Thrall, C., Mans, R., and Stein, J. (1975a), Nature (London) 2578 764; Stein, G., Park, W., Thrall, C., Mans, R., Steins, J.(1975b), Biochem. Biophys. Res. Commun. 63, 945). Utilizing the technique of chromatin reconstitution, we have recently demonstrated that it is the nonhistone chromosomal protein portion of the genome that is responsible for this difference in in vitro histone gene expression (Stein et al., 1975a). In order to determine whether this is attributable to some component of the S-phase chromosomal proteins that promotes the transcriptin of histone genes, a component of the G1 phase chromosomal proteins that inhibits histone gene transcription, or both, in the present study chromatin from both G1 and S-phase cells was dissociated and then reconstituted in the presence of various chromosomal proteins. The results of this study confirm that it is the nonhistone chromosomal proteins that are responsible for the cell cycle stage specific differences in in vitro histone gene expression and further show that these differences can be accounted for by a component or components of the S-phase nonhistone chromosomal proteins that has the capacity, when reconstituted in the presences of G1 phase chromatin, to render the histone genes transcribable in a dose-dependent fashion.

Cell Division↗