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PubMed1994

Distribution and regulation of calmodulin mRNAs in rat brain.

Selective oligonucleotide probes were developed to determine the distribution and hormonal regulation of different calmodulin genes in rat brain and the relationship to calmodulin-dependent adenylate cyclase activity. (1) Probes directed against known CaMI, CaMII and CaMIII mRNA sequences selectively recognized molecular mRNA species of approximately 4.1 and 1.7 (CaMI mRNA), 1.4 (CaMII mRNA) and 2.0 and 1.0 kb (CaMIII mRNA) in rat brain. All three calmodulin genes appeared actively coexpressed at high levels in neuronal cell layers, as revealed by in situ hybridization and northern analysis. (2) Adrenalectomy selectively attenuated levels of CaMIII, but not CaMI or CaMII mRNA, in both cerebral cortex and hippocampus. (3) Adrenalectomy also decreased calmodulin dependent adenylate cyclase activity in hippocampal, but not cortical, cell membranes. (4) Corticosterone administration prevented adrenalectomy effects on hippocampal adenylate cyclase activity and calmodulin mRNA levels. However, steroid treatment also increased forskolin-stimulated enzyme activity in cerebral cortex, but not in hippocampus. These results suggest that hormonal factors regulate calmodulin gene expression in adult brain. Further evidence is required to establish the temporal interrelationships between steroid regulation of calmodulin and its target proteins.

Adenylyl Cyclases↗
PubMed2005

Construction of a bispecific antisense oligonucleotide containing multiple binding sites for the treatment of hormone insensitive prostate tumors.

Antisense oligonucleotides (oligos) have demonstrated efficacy for the treatment of various cancers, infectious diseases and metabolic disorders. While most studies have utilized single oligos either administered alone, or more recently in combination therapy with other drugs, some investigators have administered more than one oligo in a combined administration or have designed oligos which target multiple proteins (those which share mRNA sequence homology). Antisense oligos inhibit mRNA translation through complementary base pair binding, often about the AUG initiation codon. This inhibition is further enhanced through destruction of the mRNA:oligo hybrid by RNAse H. Construction of an oligo with multiple binding sites located about the respective mRNA initiation codons could simultaneously block translation of more than one protein, even those unrelated in sequence. Such binding could produce a complex mRNA:oligo hybrid more prone to degradation and clearance. Furthermore, such a formulation would increase oligo specific activity and cellular uptake, reduce toxicity, and stabilize at 1:1 the ratio between multiple oligo active sites which otherwise must be comparably delivered (in amount) and individually targeted. The activity of these newly constructed oligos could be tested in both in vitro and in vivo prostate tumor models, utilizing the hormone sensitive LNCaP and the hormone insensitive PC-3 lines. In vitro testing would evaluate oligos administered either alone or in combination with other chemotherapeutics. In vivo testing would administer the oligos to tumors carried in athymic nude mice by either intratumoral inoculation or by using a diffusion pump. Antisense oligos which target proteins associated with growth factors or their receptors, could have a role in the treatment of human prostate cancers when administered with hormone deprivation therapy, or against tumors which have already become hormone insensitive. In the later case, such treatment could form the basis of a second tier of therapy based upon growth factor deprivation.

Androgens↗
PubMed1998

Quantitative comparison of C-X-C chemokines produced by endotoxin-stimulated human alveolar macrophages.

The C-X-C chemokines are a structurally related and functionally redundant family of proteins with neutrophil chemotactic activity. Many of the C-X-C chemokines are produced by endotoxin-stimulated alveolar macrophages (AMs), but knowledge of their relative quantities and their relative contributions to the total chemotactic activity released from these cells is incomplete. Human AMs were stimulated with or without Escherichia coli endotoxin for 2, 4, 8, and 24 h. The mRNA sequences of interleukin (IL)-8, the 78-amino acid epithelial cell-derived neutrophil activator (ENA-78), growth-related protein (GRO) alpha, GRObeta, and GROgamma were cloned by PCR and identified by sequence analysis. The relative mRNA quantities were compared by Northern analysis, and IL-8 was found to predominate. Similarly, IL-8 protein concentrations in the cell supernatants were consistently higher than either the ENA-78 or GRO concentration, and by 24 h, IL-8 concentrations were 10-fold higher than those of the other C-X-C chemokines. Blocking polyclonal antibodies to IL-8 substantially reduced the chemotactic activity in the AM supernatants, whereas antibodies to ENA-78 and GRO had little or no effect. We conclude that IL-8 is the predominant C-X-C chemokine and the dominant neutrophil chemoattractant accumulating in 24-h supernatants of lipopolysaccharide-stimulated human AMs. These studies provide insight into potentially effective strategies of interrupting AM-derived inflammatory signals in the lungs.

Amino Acid Sequence↗
PubMed1983

Analysis of antibody diversity: V-D-J mRNA nucleotide sequence of four anti-GAT monoclonal antibodies. A paucigene system using alternate D-J recombinations to generate functionally similar hypervariable regions.

The nucleotide sequence of four anti-(Glu60-Ala30-Tyr10)n (GAT) monoclonal gamma 1 heavy chain mRNAs was determined from codon 10 to 120. This sequence overlaps with the NH2-terminal amino acid sequence, allowing elucidation of the complete protein sequence encompassing regions VH, D and JH. These sequences, which are highly conserved, indicate that anti-GAT antibodies expressing the same public idiotypic specificities represent a paucigene system, which uses at least two D-J combinations leading to functionally similar hypervariable regions involved in the recognition of the dominant Glu-Tyr determinant. D regions are encoded by D genes which are closely related either to the D-SP2 or the D.FL16 germ line gene cores.

Amino Acid Sequence↗
PubMed1993

Flow cytometric quantitation of sequence-specific mRNA in hemopoietic cell suspensions by primer-induced in situ (PRINS) fluorescent nucleotide labeling.

We modified a technique of RNA detection based upon primed in situ labeling of RNA (PRINS) to quantitate poly(A) and histone mRNA in HL60 cell suspensions by flow cytometry. The direct PRINS technique was used to label poly(A) mRNA, based upon the incorporation of fluoresceinated nucleotides into cDNA chains generated by reverse transcription from the site of oligo(dT) primer-specific annealing on the poly(A) template. By this method, poly(A) fluorescent signals of up to 20-fold above background were obtained when primer concentrations were saturating. Nonspecific binding of the fluorochrome-conjugated nucleotide proved to be the greatest source of background fluorescence in cell suspensions. This was considerably reduced by preincubation of the cells in lysine and an excess of cold nucleotides prior to the PRINS reaction. The application of indirectly fluoresceinated antibodies to the FITC moiety of the conjugated nucleotide (indirect PRINS) enhanced detection of a fluorescent signal generated from cells by the direct PRINS technique after stringent histone priming. Cell cycle analysis, based upon DNA histograms obtained after PRINS labeling, showed the histone fluorescence to be primarily in S-phase cells of an exponentially growing population. Confocal laser scanning microscopy revealed good retention of cellular architecture, with cytoplasmic localization of poly(A) and histone mRNA fluorescence and heterogeneous mRNA expression among cells. Our modified PRINS labeling of RNA represents a useful advance in the precise quantitation of RNA species in cell suspension by flow cytometry.

Flow Cytometry↗
PubMed2004

Polarization of immunity induced by direct injection of naked sequence-stabilized mRNA vaccines.

In the context of developing a safe genetic vaccination strategy we tested and studied globin-stabilized mRNA-based vaccination in mice. This vaccination strategy has the advantages of genetic vaccination (easy production, adaptability to any disease and inexpensive storage when lyophilized), but not the drawbacks of DNA vaccination (long-term uncontrolled expression of a transgene, possibility of integration into the host genome and possible induction of anti-DNA antibodies). We report here that injection of naked beta-globin untranslated region (UTR)-stabilized mRNA coding for beta-galactosidase is followed by detectable translation in vivo. In addition, we show that such a vaccination strategy primes a T helper 2 (Th2) type of response which can be enhanced and shifted to a Th1-type immune response by application of recombinant granulocyte/macrophage colony-stimulating factor 1 day after mRNA injection. Our data demonstrate that the administration of globin UTR-stabilized mRNA is a versatile vaccination strategy that can be manipulated to fit the requirement of antiviral, antibacterial or antitumor immunity.

Animals↗
PubMed1985

Regions of complementarity between the messenger RNAs for epidermal growth factor, transferrin, interleukin-2 and their respective receptors.

Messenger (m)RNA sequences complementary to the mRNA sequences for the receptors to epidermal growth factor (EGF), interleukin-2 (IL-2) and transferrin (TF) were written out and compared for homologies with their ligands (EGF, IL-2 and TF, respectively). Highly significant amino acid and nucleotide homologies between the ligands and their appropriate receptor complements were detected in each case. For example, EGF and its receptor complement contained two homologous segments, each being six amino acids in length. When these segments were screened for matches against a protein sequence bank (3060 proteins and 616,748 test segments), only EGF contained either sequence. Similar results were obtained with IL-2 and TF. In each case, the homologous segments corresponded to complementary regions in the ligand binding portion of the receptor.

Amino Acid Sequence↗
PubMed1985

The preferential translation of Drosophila hsp70 mRNA requires sequences in the untranslated leader.

When Drosophila cells are heat shocked, the translation of normal cellular mRNAs is repressed, while mRNAs encoding the heat-shock proteins are translated at high rates. We have found that the hsp70 message is not translated at high temperatures when its leader sequence is deleted. This message is translated when the cells are allowed to recover at 25 degrees C, but the translation ceases when the cells are given a second heat shock. A message with an extra 39 bases added onto the 5' end of the leader behaves in the same way. However, if either of two conserved sequence elements in the leader is deleted, the message is still translated during heat shock. Although the specific feature responsible for the preferential translation of heat-shock messages is not yet identified, we conclude that it must reside in the 5' untranslated leader.

Amino Acid Sequence↗
PubMed1993

Molecular and biochemical analyses of combining sites of monoclonal anti-morphine antibodies.

V region nucleotide sequences were determined by mRNA sequencing for 11 monoclonal anti-morphine antibodies with slightly different specificities for morphine-related opiates. The VH region nucleotide sequences of the antibodies MOR8, MOR33, MOR35, MOR44, MOR83, and MOR76 were classified into the VH-5 (7183) family, while the antibodies MOR39, MOR115, MOR131, MOR158 and MOR180 used VH-1 (J558) family genes. MOR39, MOR115 and MOR131 used the V lambda-1 gene for their L chain V region. MOR158 and MOR180 used the Vk-10 gene. MOR8, MOR33, OR35, MOR44, MOR76 and MOR83 used VK-21D. The antibody sets MOR158 and MOR180; MOR39 and MOR131; and MOR8, MOR33, MOR35, MOR44, MOR76 and MOR83 appeared to be somatic mutants derived from the same clones since they showed the same VH/VL usage and V(D)J recombination pattern. The pH-reactivity profiles for these antibodies revealed that the binding of morphine to the antibodies is highly dependent on the pH value of the assay solution, suggesting the importance of the electrostatic interaction between the positive charge of morphine and the negative charges at or near the combining sites. Direct UV-photoaffinity labeling with 3H-morphine was carried out in order to estimate the orientation of morphine in the combining sites. The H chains were preferentially labeled in MOR8, MOR33, MOR35, MOR76, and MOR83, whereas most of the crosslinked hapten was found in the L chains in MOR39, MOR115, MOR131, MOR158 and MOR180. Thus, these 11 antibodies were classified into two types in terms of reactivity in the photoaffinity labeling.

Affinity Labels↗
PubMed1994

Only cytidines 5' of the apolipoprotein B mRNA mooring sequence are edited.

A 22 nucleotide 'cassette' containing three distinct sequence elements is required for efficient apolipoprotein B (apoB) RNA editing. One of the elements, the mooring sequence, has been proposed as the apoB RNA-recognition element in binding 66 and 44 kDa proteins during editosome assembly. We show here that editing can only take place on cytidines 5' of the mooring sequence; thereby providing further proof for the proposed orientation-specific assembly of editing factors at the editing site. We also provide direct evidence for the existence of a cryptic mooring sequence immediately downstream of the wild-type editing site (between nucleotides 6688-6710). When a cytidine is introduced 5' of this site (at nucleotide 6687), editing occurs at wild-type (nucleotide 6666) and cryptic sites. The cytidine to be edited is not involved in 66 and 44 kDa protein binding, and therefore, the data suggest that the cryptic mooring sequence binds these factors, and may facilitate factor recruitment to the wild-type editing site. These data may also explain why wild-type levels of editing on chimeric, RNA editing substrates can only be achieved when the 22 nucleotide editing cassette is flanked 3' by apoB RNA sequence.

Apolipoproteins B↗
PubMed1980

The nucleotide sequence of the transforming early region E1 of adenovirus type 5 DNA.

The sequence of the leftmost 11.3% of the non-oncogenic human adenovirus type 5 (Ad5) DNA has been determined. This segment contains the entire early region E1 of the Ad5 genome which has been shown to be involved in in vitro transformation of non-permissive rodent cells (Van der Eb et al., 1980). From the DNA sequence, and from the mRNA sequence data obtained by Perricaudet et al, (1979, 1980) for the E1 mRNAs from the closely related adenovirus type 2 (Ad2), it is possible to predict the primary structure of the polypeptides encoded by this region. The function of these proteins in cell transformation is discussed. From the positions of mapped restriction endonuclease sites and termini of RNA segments in the nucleotide sequence the length of the Ad5 DNA is estimated to be 36.6 kb.

Adenoviruses, Human↗
PubMed1990

Complexity charts can be used to map functional domains in DNA.

We measured local compositional complexity (LCC) of DNA sequences by calculating Shannon information content over mononucleotide frequencies. Eukaryotic DNA appeared to be "simpler" than bacterial DNA even at the level of short oligonucleotides. Moreover, different DNA functional domains displayed different compositional complexity in a systematic manner. In particular, the complexity of exon sequences was systematically higher than the complexity of corresponding introns. We therefore present examples of complexity charts (plots of complexity versus position in sequence) for pre-mRNA sequences from higher eukaryotes. By taking a window width of 100 nucleotides and a window step of 1 nucleotide, introns can be distinguished from exons in the majority of cases studied. Complexity charts of immunoglobulin variable regions allowed correct mapping of exons and introns in these sequences as well, a task that was impossible with commercial programs available to date.

Acanthamoeba↗
PubMed2000

Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos.

BACKGROUND: RNA interference (RNAi) is a phenomenon in which introduced double-stranded RNAs (dsRNAs) silence gene expression through specific degradation of their cognate mRNAs. Recent analyses in vitro suggest that dsRNAs may be copied, or converted, into 21-23 nucleotide (nt) guide RNAs that direct the nucleases responsible for RNAi to their homologous mRNA targets. Such small RNAs are also associated with gene silencing in plants. RESULTS: We developed a quantitative single-embryo assay to examine the mechanism of RNAi in vivo. We found that dsRNA rapidly induced mRNA degradation. A fraction of dsRNAs were converted into 21-23 nt RNAs, and their time of appearance and persistence correlated precisely with inhibition of expression. The strength of RNAi increased disproportionately with increasing dsRNA length, but an 80bp dsRNA was capable of effective gene silencing. RNAi was saturated at low dsRNA concentration and inhibited by excess unrelated dsRNA. The antisense strand of the dsRNA determined target specificity, and excess complementary sense or antisense single-stranded RNAs (ssRNAs) competed with the RNAi reaction. CONCLUSIONS: Processed dsRNAs can act directly to mediate RNAi, with the antisense strand determining mRNA target specificity. The involvement of 21-23 nt RNAs is supported by the kinetics of the processing reaction and the observed size dependence. RNAi depends on a limiting factor, possibly the nuclease that generates the 21-23 mer species. The active moiety appears to contain both sense and antisense RNA strands.

Animals↗
PubMed1987

A gene for rabbit synovial cell collagenase: member of a family of metalloproteinases that degrade the connective tissue matrix.

We have determined the nucleotide sequence of a collagenase mRNA from rabbit synovial cells from which the primary structure of the encoded protein was deduced. This proteinase is 51% homologous to the enzyme that activates it from the zymogen form, rabbit synovial cell activator/stromelysin. Rabbit collagenase and activator/stromelysin thus share comembership in a gene family that includes human skin collagenase; the human and rabbit metalloproteinase, activator/stromelysin; and an oncogene-induced proteinase from rat named transin. The mRNA sequence of collagenase enabled us to completely map the structure of its gene, which is 9.1 kilobases and is composed of 10 exons and 9 introns. This is the first report of the structure of a collagenase gene. We show that it has striking similarity to additional members of this metalloproteinase gene family, transin genes I and II of rat. We have further sequenced genomic DNA flanking the collagenase gene and have identified nucleic acid elements of possible importance in gene regulation.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequences for the gene junctions of human respiratory syncytial virus reveal distinctive features of intergenic structure and gene order.

Complete sequences for the intergenic regions of the genome of human respiratory syncytial virus were obtained by dideoxynucleotide sequencing using synthetic oligonucleotides. These experiments established that the 10 respiratory syncytial viral genes are arranged, without additional intervening genes, in the order 3' 1C-1B-N-P-M-1A-G-F-22K-L 5'. For the first nine genes, the exact gene boundaries were identified by comparison of the genomic sequences with previously determined mRNA sequences. The intergenic regions varied in length from 1 to 52 nucleotides and lacked any obvious conserved features of primary or secondary structure except that each sequence ended (3' to 5') with an adenosine residue. The exact start site of the 10th gene, the L gene, was not determined. However, RNA blot hybridization using a synthetic oligonucleotide designed from the genomic sequence mapped the L gene to within 54 nucleotides of the end of the penultimate 22K gene. The lack of conservation of chain length and nucleotide sequence for the respiratory syncytial viral intergenic regions, together with the complexity of the genetic map, contrasts with previous observations for other nonsegmented negative-strand viruses.

Base Sequence↗
PubMed2003

Presence of multiple mRNA cycling sequence element-binding proteins in Crithidia fasciculata.

A consensus sequence present in the 5'- or 3'-untranslated regions of several Crithidia fasciculata messenger RNAs encoding proteins involved in DNA metabolism has been shown to be necessary for the periodic accumulation of these mRNAs during the cell cycle. A protein complex termed cycling sequence-binding protein (CSBP) has two subunits, CSBPA and CSBPB, and binds the consensus sequence with high specificity. The binding activity of CSBP was shown to vary during the cell cycle in parallel with the levels of putative target mRNAs. Although disruption of the CSBPA gene resulted in loss of both CSBPA and CSBPB, the putative target message levels still continued to vary during the cell cycle. The presence of an additional and distinct binding activity was revealed in these CSBPA null mutant cells. This activity, termed CSBP II, was also expressed in wild-type Crithidia cells. CSBP II has higher binding specificity for the cycling sequence element than the earlier described CSBP complex. Three polypeptides associated with purified CSBP II show specific binding to the cycling sequence. These proteins may represent a family of sequence-specific RNA-binding proteins involved in post-transcriptional regulation.

Animals↗