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At least 307 records · Page 17Linked to original sources
PubMed1983

Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing.

Sequence comparison of the introns of two yeast genes (rp51A and rp51B) coding for the same ribosomal protein shows homology only in the last 50 bases of the intron. This region of the intron contains an internal conserved sequence (ICS) present near the 3' end of all sequenced yeast nuclear mRNA introns. Removal of a 29 bp sequence containing the ICS prevents splicing of an intron-containing hybrid gene. In cells containing the wild-type gene, we have detected RNA molecules that we suggest are normal splicing intermediates, generated by an endonucleolytic cut in the primary transcript at the ICS. The homology of the ICS with a sequence near the 5' end of U1 snRNA suggests a model in which an interaction in cis between the ICS and the 5' splice junction in yeast is the counterpart of the interaction in trans between U1 and 5' splice junctions in higher eucaryotes.

Base Sequence↗
PubMed1983

Biphasic regulation by dibutyryl cyclic AMP of tubulin and actin mRNA levels in neuroblastoma cells.

Blot hybridization analysis that used labeled tubulin cDNA probes revealed that N6,O2'-dibutyryladenosine 3',5'-cyclic monophosphate [dibutyryl cyclic AMP (Bt2cAMP)] initially increases and later decreases the level of tubulin mRNA in a neuroblastoma-glioma hybrid cell line as well as in the parent cells. A significant increase in tubulin mRNA sequences is already evident 1 hr after the addition of Bt2cAMP to the neuroblastoma cells, and a maximal induction of 2-fold is seen after 12 hr. Continued treatment with Bt2cAMP for 4 days results in a down-regulation of the initial tubulin mRNA level independently of cell density. In the glioma cells Bt2cAMP also rapidly increases the level of tubulin mRNA sequences, reaching a maximum within 6 hr. However, in these cells the subsequent decrease in tubulin mRNA content depends on the culture's phase of growth: cells at the logarithmic growth phase do not down-regulate the tubulin mRNA content even after prolonged treatment with Bt2cAMP, whereas confluent cells do. The hybrid cell line manifests intermediate characteristics in Bt2cAMP regulation of tubulin mRNA level. The time course of induction and down-regulation of tubulin mRNA content observed in the hybrid cells is similar to that of the parent neuroblastoma, whereas the sensitivity to induction is glioma-like and is 8-fold over the initial level. Blot hybridization with labeled actin cDNA probes showed a similar but not identical induction of actin mRNA synthesis with the hybrid and glioma cells, whereas no significant change was observed with the neuroblastoma cells. Moreover, prolonged treatment with Bt2cAMP of all these cell lines did not result in down-regulation of actin mRNA sequences below the initial control value. It was also observed that the level of tubulin sequences in mRNA isolated from 12-day-old rat brain was higher than that in the newborn brain. However, at an age of 30 days, the level of tubulin sequences decreases to about 75% of the newborn level.

Actins↗
PubMed1980

Sizes, locations, and directions of transcription of two genes on a cloned maize chloroplast DNA sequence.

mRNA for the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] of Zea mays is complementary to an uninterrupted 1600-base-pair-long chloroplast DNA sequence that has been mapped precisely within the 4350-base-pair-long chloroplast DNA fragment Bam 9 to which it had been traced earlier [Bedbrook, J. R., Coen, D. M., Beaton, A. R., Bogorad, L. & Rich, A. (1979) J. Biol. Chem. 254, 905-910]. An additional 1400-base-pair-long uninterrupted region that is colinear with a chloroplast RNA has been detected on Bam 9. The transcript from this region is part of a 2200-nucleotide-long RNA. The remainder of the DNA sequence for the 2200-base-pair RNA maps outside Bam 9. The 1600-base-pair LS gene and the gene for the 2200-nucleotide transcript are close to one another. They are separated by an untranscribed intercistronic "gap" about 330 base pairs long. These two closely packed genes are inverted on the chromosome-i.e., their 3' termini are at opposite ends of the untranscribed gap and they map on opposite strands.

Journal Article↗
PubMed2003

The Drosophila synaptotagmin-like protein bitesize is required for growth and has mRNA localization sequences within its open reading frame.

The vertebrate synaptotagmin-like protein granuphilin binds to the vesicle-trafficking proteins Rab27a and Munc18 and can modulate exocytosis of insulin-containing secretory granules in pancreatic beta cell lines. Here, we report the molecular and genetic characterization of bitesize, a granuphilin homolog and the only Drosophila synaptotagmin-like protein. Mutations that affect bitesize have reduced cell size and number, resulting in smaller animals that develop slowly. We also show that at least two classes of bitesize transcripts are localized to the apical plasma membrane in polarized epithelial cells. Whereas most cis-acting mRNA localization sequences map to 3' untranslated regions, bitesize contains a 2.2-kb sequence within its ORF that is necessary and sufficient for apical localization. Thus, we have found that bitesize is a metazoan example of a transcript for which all identifiable mRNA localization sequences are contained within the protein-coding region.

3' Untranslated Regions↗
PubMed1978

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells.

Nuclei were isolated from synchronized HeLa S3 cells and transcribed utilizing their endogenous RNA polymerases. Our data suggest that S phase nuclei are capable of synthesizing histone mRNA sequences while nuclei from G1 phase cells are not. Transcription of histone mRNA sequences by S phase nuclei can be abolished completely by low levels of alpha-amanitin (1.0 microgram/ml, a concentration which completely inhibits RNA polymerase II). From these results it appears that transcription of the histone mRNA sequences occurs during the S phase but not during the G1 phase of the cell cycle and that RNA polymerase II is responsible for histone gene readout.

Amanitins↗
PubMed1982

Rat pancreatic ribonuclease messenger RNA. The nucleotide sequence of the entire mRNA and the derived amino acid sequence of the pre-enzyme.

We have cloned via recombinant DNA technology the mRNA sequence of rat pancreatic ribonuclease, and have determined the entire nucleotide sequence of the mature message. Clones bearing RNase sequences within a double-stranded complementary DNA library of rat pancreatic mRNA were initially detected by hybridization with size-fractionated rat pancreatic polyadenylated RNA that included mRNA 0.85 to 1.0 kilobase in length. Recombinant plasmids bearing RNase mRNA sequences were conclusively identified by comparison of the amino acid sequence of the encoded protein with the known amino acid sequence of rat RNase. RNase mRNA is 783 nucleotides in length, plus a poly(a) tail with an average length of 140 nucleotides, and contains long 5' and 3' noncoding regions relative to other pancreatic mRNAs. It encodes a secretory preRNase of 152 amino acid residues including a signal peptide of 25 amino acids.

Amino Acid Sequence↗
PubMed1973

Demonstration of globin messenger sequences in giant nuclear precursors of messenger RNA of avian erythroblasts.

Highly purified globin mRNA from ducks was copied with RNA-directed DNA polymerase from avian myeloblastosis virus into anti-messenger DNA. With excess RNA, more than 90% of this DNA annealed back to its template with a C(o)t/2 value of 7.5 x 10(-4) mol.sec. liter(-1); the melting temperature of the hybrid was 86 degrees . Giant nuclear RNA fractions with sedimentation coefficients of more than 50 S formed hybrids of almost equal stability at C(o)t/2 values of 0.05-0.42 mol.sec. liter(-1), indicating amRNA content of 0.3-1.5%. 12S RNA from the same polyribosomes and nuclear giant RNA from HeLa cells did not cross-hybridize. Although a large part of the giant RNA broke down in 99% dimethylsulfoxide gradients, RNA fractions sedimenting faster than 28S rRNA still were found to consist of up to 0.03% globin mRNA sequences. Thus, the mRNA sequences are contained in the covalent structure of giant nuclear precursors, which are termed precursor-mRNA.

Animals↗
PubMed1986

Sodium regulation of angiotensinogen mRNA expression in rat kidney cortex and medulla.

Rat liver angiotensinogen cDNA (pRang 3) and mouse renin cDNA (pDD-1D2) were used to identify angiotensinogen and renin mRNA sequences in rat kidney cortex and medulla in rats on high and low salt diet. Angiotensinogen mRNA sequences were present in renal cortex and medulla in apparently equal proportions, whereas renin mRNA sequences were found primarily in renal cortex. Average relative signal of rat liver to whole kidney angiotensinogen mRNA was 100:3. Densitometric analysis of Northern blots demonstrated that renal cortical angiotensinogen mRNA concentrations increased 3.5-fold (P less than 0.001) and medulla, 1.5-fold (P less than 0.005) on low sodium compared with high sodium diet, whereas renal cortex renin mRNA levels increased 6.8-fold (P less than 0.0005). Dietary sodium did not significantly influence liver angiotensinogen mRNA levels. These findings provide evidence for sodium regulation of renal renin and angiotensinogen mRNA expressions, which supports potential existence of an intrarenally regulated RAS and suggest that different factors regulate renal and hepatic angiotensinogen.

Angiotensinogen↗
PubMed1979

The synthesis and processing of a nuclear RNA precursor to rat pregrowth hormone messenger RNA.

A recombinant DNA plasmid, pBR322-GH1, which contains about 80% of the sequences of rat pregrowth hormone (pGH) mRNA, allowed an analysis of nuclear RNA from GH3 cells for possible precursors of cytoplasmic pGH mRNA. A single 20-22S RNA SPECIES ABOUT 2-3 TIMes larger than pGH mRNA was detected in nuclear RNA from GH3 cells labeled for 5 min. with 3H-uridine. After longer label times a 12S RNA indistinguishable in size from cytoplasmic 12S pGH mRNA became the predominant labeled RNA complementary to the plasmid pBR322-GH1. Both of these nuclear RNA species contained poly (A). Kinetic analysis of the labeling of nuclear and cytoplasmic pGH mRNA sequences showed that the 20S and 12S nuclear RNA molecules were labeled before significant labeling of cytoplasmic pGH mRNA was detected, and also indicated that there is complete conservation of nuclear pGH mRNA sequences in the production of cytoplasmic pGH mRNA. These results indicate that cytoplasmic pGH mRNA is generated by nuclear processing of a larger nuclear RNA molecule.

Animals↗
PubMed1996

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.

A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome.

Amino Acid Sequence↗
PubMed1982

No evidence for post-transcriptional control of albumin and alpha-fetoprotein gene expression in developing rat liver neoplasia.

Rot analysis of hybridization data using highly labeled alpha-fetoprotein (AFP) and albumin (32P)cDNA probes has been used to quantitate AFP and albumin mRNA sequences in RNA preparations from different subcellular fractions of developing rat liver and Morris hepatoma 7777. In addition, size analysis of these mRNA sequences has been carried out by electrophoretic fractionation on agarose gels containing methylmercury hydroxyde and hybridization to radioactive cloned albumin and AFP cDNA probes. In all the tissues examined (fetal, newborn and adult rat liver, and hepatoma 7777) most of the albumin and AFP mRNA sequences were found associated with the polysomes as mature mRNA molecules; less than 2% of these sequences were present in the nuclear or the non polysomal cytoplasmic compartments. The number of AFP mRNA molecules was found to decrease in parallel in all the cellular compartments during rat liver development. In Morris hepatoma 7777 the content of albumin mRNA was considerably decreased in all the cellular fractions as compared to normal liver. These results demonstrate that post-transcriptional control mechanisms leading to an accumulation of non-functional mRNA molecules are not implicated in the changes of expression of albumin and AFP genes during rat liver development and neoplasia.

Animals↗
PubMed1981

Further evidence for translational regulation of tyrosine aminotransferase synthesis by dibutyryl cyclic AMP in Reuber H35 hepatoma cells.

Cyclic AMP derivatives increase the rate of synthesis of tyrosine aminotransferase in Reuber H35 hepatoma cells. Various studies lend support to the hypothesis that cyclic AMP increases the synthesis of tyrosine aminotransferase by acting at a posttranscriptional site. The presence of a limited non-translatable pool of tyrosine aminotransferase mRNA prior to the formation of the translatable tyrosine aminotransferase mRNA implicates a possible site of action of cyclic AMP. We compared the capacity of N6,O2'-dibutyryl cyclic AMP to induce tyrosine aminotransferase synthesis when untranslatable tyrosine aminotransferase mRNA sequences are present or absent. The transition of a condition in which non-translatable tyrosine aminotransferase mRNA sequences were present to a condition in which they were absent was established by preinduction of Reuber H35 cells with dexamethasone, followed by addition of actinomycin D. In the time period thereafter, the amount of non-translatable mRNA decreased and 1.5-2 h after addition of actinomycin D, only translatable tyrosine aminotransferase mRNA was present. It can be seen that the induction of tyrosine aminotransferase synthesis by dibutyryl cyclic AMP follows the normal decrease of tyrosine aminotransferase mRNA. We present evidence that dibutyryl cyclic AMP in Reuber H35 hepatoma cells regulates tyrosine aminotransferase synthesis at a posttranscriptional site independent of the pool of non-translatable tyrosine aminotransferase mRNA sequences, but influencing the efficiency of translation of active tyrosine aminotransferase mRNA.

Animals↗
PubMed1978

Effect of a short term fast on the distribution of cytoplasmic albumin messenger ribonucleic acid in rat liver. Evidence for formation of free albumin messenger ribonucleoprotein particles.

Recently, using molecular hybridization techniques with albumin [3H]cDNA, we have determined that in normally fed rats 98% of total liver polyribosomal albumin mRNA sequences are found in membrane-bound polyribosomes (Yap, S. H., Strair, R. K., and Shafritz, D. A. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 5397-5401). We now observe that a 24- to 30-h withdrawal of food leads to major changes in the amount and subcellular distribution of albumin mRNA molecules. The total amount of cytoplasmic albumin mRNA per liver and concentration of albumin mRNA per unit of membrane-bound polyribosomal RNA are decreased. However, the proportion of albumin mRNA present in the postribosomal supernatant fraction increases dramatically in a short term fast, so that it now represent 60% of total cytoplasmic albumin mRNA sequences. Most of the albumin mRNA sequences in the postribosomal supernatant fraction sediment between 30 S and 50 S. These findings suggest that albumin mRNA is probably stored in the messenger ribonucleoprotein fraction during the fasting state.

Albumins↗
PubMed2003

Quantitative assays for maedi-visna virus genetic sequences and mRNA's based on RT-PCR with real-time FRET measurements.

We developed robust, ultrasensitive, and accurate quantitative assays for maedi-visna virus (MVV) RNA and DNA genomic sequences and mRNA's expressed at various stages of lentiviral replication. Assay design was based on PCR with real-time fluorescence resonance energy transfer measurements. Specific assays were developed for gag-pol (genomic), tat, rev, env, and vif transcripts. Assay linearity ranged from 60 to 6 x 10(7) copies of target DNA. All assays were able to detect and measure corresponding mRNA's in MVV-infected FOS cells, whereas no signal was detected in mock-treated cells. In addition, RT-PCR based on amplification of gag sequences could be used to quantify RNA genomic sequences in supernatants from infected cells. These quantitative assays can be used to study the role of genetic elements in MVV infection and pathogenesis. They also allow rapid testing of lentiviral vectors and packaging systems based on MVV.

Animals↗
PubMed1989

Quantification analysis of 5'-splice signal sequences in mRNA precursors. Mutations in rabbit beta-globin gene.

Concerning the signals which direct excision of introns from mRNA precursors in genes of higher eukaryotes, a consensus sequence composed of nine nucleotides, CAAG/GTAGAGT, has been proposed for the 5'-splice site, but actual 5'-splice site sequences differ from it to a greater or lesser degree. In the present paper, the 5'-splice site sequence of the rabbit beta-globin gene was analyzed using a quantification method (categorical discriminant analysis). In this method, each 9-nucleotide sequence in the pre-mRNA was characterized by its sample score, which shows the extent to which the sequence contains the signal. This approach could explain not only the location of the 5'-splice site, but also the experimental results of various point mutations in the 5'-splice region, as reported by Aebi et al. Our method further predicted the positions of cryptic 5'-splice sites, which are activated when the authentic 5'-splice site is abolished.

Animals↗
PubMed1989

RNA editing: the creation of nucleotide sequences in mRNA--a minireview.

RNA editing changes the nucleotide sequence of mRNAs that are encoded in genes which contain the sequences in an abbreviated form. Editing adds uridines that are not encoded in the gene to the transcripts and less frequently removes encoded uridines. The process appears to be posttranscriptional and to proceed in the 3'-to-5' direction. Some sites may undergo multiple editings until the final sequence is produced; in some cases uridines may be added and subsequently removed. A general hypothesis is proposed that predicts a series of reactions that may occur in association with a macromolecular complex, the editosome, which interacts with a multinucleotide region.

Animals↗
PubMed1996

Strength of translation initiation signal sequence of mRNA as studied by quantification method: effect of nucleotide substitutions upon translation efficiency in rat preproinsulin mRNA.

Concerning the translation initiation signals in vertebrate mRNAs, both the ATG initiation codon and the sequences flanking the initiation codon are required to direct the position of initiation. A consensus sequence for the signal, (GCC)GCC(A or G)CCATGG, has been proposed, but actual initiation sequences differ from it to a greater or lesser degree. In the present report, the translation initiation signal sequences of rat preproinsulin and its mutant mRNAs were analyzed using a quantification method proposed previously. In this method, each 16 nt sequence in the mRNA was characterized by its sample score, which shows strength of the signal. So far, Kozak has constructed a number of preproinsulin mutant mRNAs in which nucleotides flanking the ATG codon are systematically varied, and measured the translation initiation efficiency in terms of the proinsulin product. Her experimental results were well understood on the basis of the strength of the translation initiation signal sequence.

Animals↗
PubMed1985

The envelope-associated 22K protein of human respiratory syncytial virus: nucleotide sequence of the mRNA and a related polytranscript.

We recently determined that respiratory syncytial virus (strain A2) encodes a fourth unique envelope-associated virion protein that has molecular weight of approximately 24,000, as estimated by gel electrophoresis. The nucleotide sequence of the mRNA encoding this novel protein has now been determined from five cDNA clones, including three that contain the complete mRNA sequence. The complete mRNA sequence is 957 nucleotides, exclusive of polyadenylate, and contains two partially overlapping open reading frames. The 5'-proximal open reading frame is favored for utilization by the criteria of the location and sequence of its translational start site. Furthermore, the calculated molecular weight of the encoded protein, 22,153, is in agreement with the previous estimate of 24,000 for the authentic protein identified by hybrid selection and in vitro translation. The sequence of the predicted protein, now designated the 22K protein, contains 194 amino acids, is relatively hydrophilic, and appears to be the most basic of the respiratory syncytial virus proteins. The mRNA also contains a second, internal open reading frame which would encode a protein of 90 amino acids. However, no evidence for this translation product is known. The first nine nucleotides in the mRNA sequence, 5'-GGGGCAAAU, are identical to the conserved sequence identified previously at the 5' termini of seven other respiratory syncytial viral mRNAs; the sequence at the 3' end of the 22K mRNA, 5'. . . AGUUAUUU-polyadenylate, contains the elements of the previously identified 3'-terminal consensus sequence for respiratory syncytial virus mRNAs, AGUUAA(N)1-4-polyadenylate (P. L. Collins, Y. T. Huang, and G. W. Wertz, Proc. Natl. Acad. Sci. U.S.A. 81:7683-7687). In addition, we present and describe the intergenic sequence of a dicistronic RNA derived from readthrough of the F and 22K protein genes.

Amino Acid Sequence↗