Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “mRNA sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMed1976

Globin mRNA contains a sequence complementary to double-stranded region of nuclear pre-mRNA.

Melted ds RNA isolated from rabbit bone marrow pre-mRNA was hybridized with excess of globin mRNA which was prepared from rabbit reticulocytes. 7-9% of ds sequences became RNAase-stable and about 30% of the sequences could be bound to poly(U)-Sepharose through poly (A) of mRNA. The size of RNAase-stable hybrid is about 30 nucleotides, that is one fourth of the length of one strand of the ds RNA.

Animals↗
PubMed1997

A complex structure in the mRNA of Tf1 is recognized and cleaved to generate the primer of reverse transcription.

All retroviruses and LTR-containing retrotransposons are thought to require specific tRNA molecules to serve as primers of reverse transcription. An exception is the LTR-containing retrotransposon Tf1, isolated from Schizosaccharomyces pombe. Instead of requiring a tRNA, the reverse transcriptase of Tf1 uses the first 11 bases of the Tf1 transcript as the primer for reverse transcription. The primer is generated by a cleavage that occurs between bases 11 and 12 of the Tf1 mRNA. Sequence analysis of the 5' untranslated region of the Tf1 mRNA resulted in the identification of a region with the potential to form an RNA structure of 89 bases that included the primer binding site and the first 11 bases of the Tf1 mRNA. Systematic mutagenesis of this region revealed 34 single-point mutants in the structure that resulted in reduced transposition activity. The defects in transposition correlated with reduced level of Tf1 reverse transcripts as determined by DNA blot analysis. Evidence that the RNA structure did form in vivo included the result that strains with second site mutations that restored complementarity resulted in increased levels of reverse transcripts and Tf1 transposition. The majority of the mutants defective for reverse transcription were unable to cleave the Tf1 mRNA between bases 11 and 12. These data indicate that formation of an extensive RNA structure was required for the cleavage reaction that generated the primer for Tf1 reverse transcription.

Base Composition↗
PubMedDate not supplied

[Nuclear precursors for ceruloplasmin-coding messenger RNA from rat liver].

The distribution of the sequences coding for ceruloplasmin (CP) in rat liver heterogeneous nuclear RNA (hnRNA) was studied using highly specific CP cDNA as a hybridization probe. The content of CP-coding sequences in poly(A)-containing and poly(A)-free subfractions of hnRNA was shown to be respectively 1 and 27 equivalents of CP mRNA molecule per one hepatocyte. The gel electrophoresis of hnRNA under strongly denaturing conditions with the subsequent transfer of RNA to diazobenzyloxymethyl paper and hybridization with [32P]-cDNA probe showed that CP mRNA sequences were of multiple molecular weight distribution. In particular, 9.0, 6.6, 2.4 and 1.6 megadalton fractions of non-polyadenylate hnRNA carried CP-coding sequences while the only hand that hybridized to CP cDNA was detected in polyadenylated hnRNA. This band was of a molecular weight 1.1-1.2 megadaltons corresponding to that of cytoplasmic CP mRNA. The hybridization of high molecular weight hnRNA with full-length CP cDNA followed by the determination of the size of cDNA fragments protected against SI nuclease demonstrated that coding sequences of CP pre-mRNA are interrupted by intervening sequences.

Animals↗
PubMed2002

Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor.

Chemically synthesised 21-23 bp double-stranded short interfering RNAs (siRNA) can induce sequence-specific post-transcriptional gene silencing, in a process termed RNA interference (RNAi). In the present study, several siRNAs synthesised against different sites on the same target mRNA (human Tissue Factor) demonstrated striking differences in silencing efficiency. Only a few of the siRNAs resulted in a significant reduction in expression, suggesting that accessible siRNA target sites may be rare in some human mRNAs. Blocking of the 3'-OH with FITC did not reduce the effect on target mRNA. Mutations in the siRNAs relative to target mRNA sequence gradually reduced, but did not abolish mRNA depletion. Inactive siRNAs competed reversibly with active siRNAs in a sequence-independent manner. Several lines of evidence suggest the existence of a near equilibrium kinetic balance between mRNA production and siRNA-mediated mRNA depletion. The silencing effect was transient, with the level of mRNA recovering fully within 4-5 days, suggesting absence of a propagative system for RNAi in humans. Finally, we observed 3' mRNA cleavage fragments resulting from the action of the most effective siRNAs. The depletion rate-dependent appearance of these fragments argues for the existence of a two-step mRNA degradation mechanism.

Animals↗
PubMed1984

Complete nucleotide sequence of the mRNA coding for the N protein of vesicular stomatitis virus (New Jersey serotype).

The nucleotide sequence of the mRNA encoding the nucleocapsid protein of the New Jersey serotype (Ogden strain) of vesicular stomatitis virus (VSV) was determined from two overlapping cDNA clones spanning almost entirely the coding region of the mRNA. The 5'-terminal noncoding sequence present in the mRNA but not in the cDNA clones was determined from a primer extended to the 5' terminus of the mRNA. The mRNA is 1329 nucleotides long (excluding polyadenylic acid) and encodes a protein of 422 amino acids. The nucleotide sequence was compared with the previously determined nucleotide sequence of the nucleocapsid protein of the Indiana serotype. An overall identity of 67.7% was found between the two serotypes. The only place where insertions and/or deletions have occurred during the evolution of the two viral genes from their presumed common ancestor is in the untranslated region. The nonidentical nucleotides are distributed throughout the length of the mRNA although not in an entirely random manner. The predicted amino acid sequence demonstrates that both proteins are initiated from the initiator codon located at the same distance from the 5' end (nucleotides 14 to 16) and contain the same number of amino acids. An overall identity of more than 80% of the amino acid sequence was observed between the two proteins when conservative replacements of amino acids were considered.

Amino Acid Sequence↗
PubMed1996

PDGF induction of alpha 2 integrin gene expression is mediated by protein kinase C-zeta.

Platelet-derived growth factor (PDGF) stimulates fibroblasts to move over collagen and contract three-dimensional collagen gels, processes important in wound repair and fibrocontractive diseases. These processes depend on alpha 2 beta 1 integrin ligation of collagen and PDGF induces the expression of this integrin. Several lines of evidence presented here suggest that PKC-zeta plays a role in alpha 2 integrin gene expression. The induction was blocked by chemical inhibitors for protein tyrosine kinases (PTK), genistein, and protein kinase C (PKC), chelerythrine, and bisindolylmaleimide GF 109203X. Cells depleted of phorbol 12-myristate 13-acetate (PMA)-inducible PKCs by chronic treatment with PMA still demonstrated an alpha 2 response to PDGF indicating that a non-PMA-sensitive PKC isoform was required. PDGF induced kinase activity in PKC-zeta immunoprecipitates. Antisense oligonucleotides complementary to 5' end of PKC-zeta mRNA sequences blocked the PDGF-induced increase of alpha 2 mRNA levels up to 70%, indicating PKC-zeta, a non-PMA-sensitive PKC isoform, is a component of the PDGF stimulatory pathway for alpha 2 mRNA synthesis. A 961-base pair (bp) upstream region of alpha 2 gene/CAT construct transfected into human dermal fibroblasts was positively regulated by PDGF as judged by CAT enzymatic levels. Both PTK and PKC inhibitors blocked PDGF-stimulation of the alpha 2 promoter fragment/CAT construct, indicating that the phosphorylation requirement occurred at alpha 2 promoter-directed transcription level. Therefore, we propose that PDGF-stimulatory pathway of alpha 2 integrin gene expression involves multiple cellular protein kinases, one of which is PKC-zeta.

Adult↗
PubMed1982

Isolation and characterization of the rat tryptophan oxygenase gene.

Tryptophan oxygenase (TO, EC 1.13.1.12) from rat liver is subject to glucocorticoid and developmental control. To study the mechanism of regulation, TO mRNA sequences and the chromosomal TO gene were cloned. From a cDNA library prepared from rat liver poly(A)+ RNA enriched for TO mRNA, a recombinant plasmid containing TO cDNA sequences was identified by translation of hybrid-selected RNA and immunoprecipitation with antibodies directed against TO. This cDNA clone hybridizes to a mRNA 2000 bases long that is inducible by dexamethasone. With this clone as probe we isolated from a bacteriophage lambda rat DNA library genomic clones which together span a region of 32 kilobase pairs (kb). Heteroduplex analysis revealed that the gene extends over 19 kb and is interrupted by at least 11 introns. To characterize the presumptive control region the DNA sequence around the 5' end of the TO gene was determined. S1 nuclease protection experiments revealed two separate start sites for TO mRNA transcription within this region.

Animals↗
PubMed1975

Characterization of the mRNA of influenza virus.

The kinetics of the appearance of influenza mRNA, the distribution of mRNA between free and membrane-associated polyribosomes, its poly(A) content, and the extent to which the genome was transcribed into mRNA early in infection were determined. Polyribosomes were prepared from influenza virus-infected cells labeled for 30-min periods at various times after infection with [3H]uridine. Most of the 3H-labeled RNA extracted from these polyribosomes sedimented as a heterogeneous 8S to 20S peak in sucrose gradients, and it was largely complementary to virion RNA. By the following criteria, the complementary RNA had properties normally ascribed to mRNA: (i) it labeled rapidly with [3H]uridine; (ii) after glutaraldelyde treatment, it banded with polyribosomes in CsCl density gradients; and (iii) it contained poly(A). In chick cells at 37 C, virus mRNA was first detectable at 45 min postinfection and reached its maximal rate of appearance at 2 to 2.5 h postinfection. The free and membrane-bound polyribosomes of infected cells were separated and were found to contain the same classes of mRNA. There was no absolute segregation of mRNA sequences into either polyribosome class although each probably contained distinct ratios of the different mRNA's. From 45 min postinfection onwards, both membrane-bound and free polysomal poly(A)-containing RNA contained sequences complementary to at least 80% of the genome RNA, whereas poly(A)-minus RNA contained sequences complementary to 90 to 100% of the genome. There was no evidence for the temporal control of transcription of influenza mRNA. At 31 C, when virus development was slowed relative to 37 C,complementary RNA first appeared at 1 h postinfection. At this time, total polysomal RNA contained sequences complementary to the whole genome.

Base Sequence↗
PubMed2003

Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene.

PURPOSE: To determine the full-length sequence of a gene with similarity to RP1 and to screen for mutations in this newly characterized gene, named retinitis pigmentosa 1-like 1(RP1L1). Since mutations in the RP1 gene cause autosomal dominant retinitis pigmentosa, it is possible that mutations in RP1's most sequence similar relative, RP1L1, may also be a cause of inherited retinal degeneration. METHODS: A combination of cDNA clone sequencing, RACE, and database analysis were used to determine the RP1L1 mRNA sequence and its genomic organization. PCR analysis, semi-quantitative RT PCR, and in situ hybridization were used to determine the expression pattern of RP1L1. Single-strand conformational analysis and automated sequencing were used to screen probands from 60 adRP families for potential disease-causing mutations in RP1L1. RESULTS: The human RP1L1 gene is encoded in 4 exons, which span 50 kb on chromosome 8p. The length of the RP1L1 mRNA is large, over 7 kb, but its exact length is variable between individuals due to the presence of several length polymorphisms, including a 48 bp repeat. RP1L1 encodes a protein with a minimal length of 2,400 amino acids and a predicted weight of 252 kDa. Expression of RP1L1 is limited to the retina and appears to be specific to photoreceptors. Mutational analysis of 60 autosomal dominant retinitis pigmentosa probands revealed the presence of 38 sequence substitutions in RP1L1. Over half of these substitutions result in alteration of the RP1L1 protein, but none of these substitutions appear to be pathogenic. CONCLUSIONS: The RP1L1 gene encodes a large, highly polymorphic, retinal-specific protein. No RP1L1 disease-causing mutations were identified in any of the samples tested, making it unlikely that mutations in RP1L1 are a frequent cause of autosomal dominant retinitis pigmentosa. Additional experiments will be needed to determine if mutations in RP1L1 cause other forms of inherited retinal degeneration.

Amino Acid Sequence↗
PubMed1990

Organization of minicircle genes for guide RNAs in Trypanosoma brucei.

We have identified four T. brucei minicircle sequences that are complementary to cytochrome oxidase III (COIII) edited mRNA sequence and have shown the existence of transcripts from three of these minicircle sequences. These minicircle transcripts potentially serve as guide RNAs (gRNAs) for RNA editing of the COIII transcript. These gRNAs range in size from 55 to 70 nucleotides, are heterogeneous in sequence, and have a 5' terminal triphosphate. The genes for these gRNAs are flanked by imperfect 18 bp repeats separated by approximately 110 bp. Transcription initiates at the first purine within a conserved sequence, 5'-RYA-YA-3', 31 or 32 bp from the upstream inverted repeat. We propose that these 18 bp inverted repeats are important for minicircle gRNA expression in T. brucei.

Animals↗
PubMed1981

Sequence divergence of nucleus-confined polyadenylated ribonucleic acids in Friend erythroleukemic cells.

For determination of whether any potential protein-coding RNA sequences are confined to the nucleus in Friend cells, a comparison has been made of the sequence divergence of polyadenylated RNA molecules which are either nucleus confined or transported to the cytoplasm. Both unique DNA and cDNA probes enriched in such sequences were reacted with a large excess of mouse or rat DNA. The extent of hybridization and the thermal stability of hybrids formed under various stringency conditions were used as a measure of the amount of sequence divergence which had taken place. The results confirmed that messenger sequences are relatively conserved during evolution. Furthermore, experiments involving both unique DNA probes representative of the full length of nucleus-confined RNA molecules and cDNA probes complementary to their poly(A)-adjacent fragments indicated that the polyadenylated nucleus-confined sequences have, on average, diverged during evolution much more than mRNA sequences. The vast majority of these sequences therefore probably do not represent potential mRNAs which are confined to the nucleus and subject to posttranscriptional control in a manner similar to those which have been demonstrated in sea urchins [Wold, B., Klein, W. H., Hough-Evans, B. R., Britten, R. J., & Davidson, E. H. (1978) Cell (Cambridge, Mass.) 14, 941-950].

Animals↗
PubMed1985

Sea urchin metallothionein sequence: key to an evolutionary diversity.

The metallothioneins (MTs) constitute a diverse family of proteins, which are enriched in cysteines and bind heavy metals. The amino acid sequence of sea urchin MT has been obtained from its mRNA sequence and compared with MT sequences of various sources. A largely conserved sequence of 10 amino acids, the "central segment," is located near the center of the MT molecules of Neurospora, yeast, and Drosophila and the center of putative domains in mammalian and sea urchin MTs. The sea urchin carboxyl-terminal-half MT resembles the mammalian 9-cysteine amino-terminal MT domain I, both in the presence of this central segment and in the relative placement of cysteine residues. Conversely, the sea urchin amino-terminal-half MT, containing 11 cysteines, resembles the mammalian carboxyl-terminal MT domain II in its exclusive enrichment in vicinal cysteines. The reversed order of these sea urchin and mammalian MT halves appears to be just one aspect of a diversity based on the elaboration of structures containing the central segment. Still another variation in this diversity is the duplication of the central segment, apparent in Drosophila and crab MTs.

Amino Acid Sequence↗
PubMed1982

Further evidence that the majority of primary nuclear RNA transcripts in mammalian cells do not contribute to mRNA.

Nuclear RNA from Chinese hamster ovary cells was effectively separated into polyadenylic acid [poly(A)]-containing [poly (A)+] and non-poly(A)-containing [poly(A)-] fractions so that -90% of the poly(A) was present in the (A)+ fraction. Only 25% of the 5'-terminal caps of the large nuclear molecules were present in the (A)+ class, but about 70% of the specific mRNA sequences (assayed with cDNA clones) were in the (A)+ class. It appears that many long capped heterogeneous nuclear RNA molecules are of a different sequence category from those molecules that are successfully processed into mRNA.

Animals↗
PubMed1990

Frame shift mutations as a novel mechanism for the generation of neutralization resistant mutants of human respiratory syncytial virus.

The genetic characterization of four previously reported mutants of human respiratory syncytial (RS) virus resistant to monoclonal antibody 63G is described. Sequences of the G protein genes were obtained from: (i) mRNA derived cDNA recombinants, (ii) direct mRNA sequencing and (iii) amplified vRNA derived cDNAs. The results obtained indicate that the original escape mutants, recovered from individual plaques, contained heterogeneous viral populations. This heterogeneity affected the number of adenosine residues present after nucleotides 588 or 623 of the G protein gene. Mutant viruses recovered after a second plaque purification step generated homogeneous sequences but contained single adenosine insertions or deletions at those two sites compared with the Long sequence. These genetic alterations introduced frameshift changes which are reflected in both the antigenic and structural properties of the mutant G proteins. The origin and importance of frameshift mutations in the RS virus G protein gene are discussed.

Amino Acid Sequence↗
PubMed1985

Transcriptional regulation of the thyrotropin subunit genes by thyroid hormone.

Thyrotropin (TSH), a pituitary glycoprotein, consists of two subunits (alpha and beta), and regulates thyroid hormone production by the thyroid gland. The thyroid hormones, in turn, feedback negatively on TSH production. We have investigated the effect of triiodothyronine (T3) on the transcription of the TSH subunit genes. Hypothyroid LAF1 mice bearing TtT 97 thyrotropic tumors were injected daily with T3 (5 micrograms/100 g of body weight, intraperitoneal) and killed after 0, 0.5, 1, 4, or 120 h. Nuclei were isolated from the tumors and allowed to continue RNA synthesis in the presence of [alpha-32P]UTP. Newly synthesized mRNA sequences were quantitated by hybridization to immobilized cloned cDNA containing sequences specific for either alpha subunit or TSH-beta mRNA. Basal levels of mRNA synthesis were similar for alpha subunit and TSH-beta. After only 30 min of T3 treatment in vivo, mRNA synthesis was decreased for both alpha subunit (by 28%) and TSH-beta (by 61%). These decreases were maximum after 4 h, (75% for alpha subunit, greater than 95% for TSH-beta mRNA synthesis), and were maintained for the 5 days of T3 treatment. Decreases in mRNA synthesis precede decreases in tissue mRNA concentrations. Our studies suggest that T3 rapidly decreases the transcription of both the alpha subunit and TSH-beta genes, and that the transcription of the TSH-beta gene is affected to a greater extent than the alpha subunit gene.

Animals↗
PubMed2001

Identification of the gene encoding Brain Cell Membrane Protein 1 (BCMP1), a putative four-transmembrane protein distantly related to the Peripheral Myelin Protein 22 / Epithelial Membrane Proteins and the Claudins.

BACKGROUND: A partial cDNA clone from dog thyroid presenting a very significant similarity with an uncharacterized mouse EST sequence was isolated fortuitously. We report here the identification of the complete mRNA and of the gene, the product of which was termed "brain cell membrane protein 1" (BCMP1). RESULTS: The 4 kb-long mRNA sequence exhibited an open-reading frame of only 543 b followed by a 3.2 kb-long 3' untranslated region containing several AUUUA instability motifs. Analysis of the encoded protein sequence identified the presence of four putative transmembrane domains. Similarity searches in protein domain databases identified partial sequence conservations with peripheral myelin protein 22 (PMP22)/ epithelial membrane proteins (EMPs) and Claudins, defining the encoded protein as representative of the existence of a novel subclass in this protein family.Northern-blot analysis of the expression of the corresponding mRNA in adult dog tissues revealed the presence of a huge amount of the 4 kb transcript in the brain. An EGFP-BCMP1 fusion protein expressed in transfected COS-7 cells exhibited a membranous localization as expected. The sequences encoding BCMP1 were assigned to chromosome X in dog, man and rat using radiation hybrid panels and were partly localized in the currently available human genome sequence. CONCLUSIONS: We have identified the existence in several mammalian species of a gene encoding a putative four-transmembrane protein, BCMP1, wich defines a novel subclass in this family of proteins. In dog at least, the corresponding mRNA is highly present in brain cells. The chromosomal localization of the gene in man makes of it a likely candidate gene for X-linked mental retardation.

Journal Article↗
PubMed1989

RNA editing in wheat mitochondria results in the conservation of protein sequences.

RNA editing is a process that results in the production of a messenger RNA with nucleotide sequences that differ from those of the template DNA, and provides another mechanism for modulating gene expression. The phenomenon was initially described in the mitochondria of protozoa. Here we report that RNA editing is also required for the correct expression of plant mitochondrial genes. It has previously been proposed that in plant mitochondria there is a departure from the universal genetic code, with CGG specifying tryptophan instead of arginine. This was because CGG codons are often found in plant mitochondrial genes at positions corresponding to those encoding conserved tryptophans in other organisms. We have now found, however, wheat mitochondrial gene sequences containing C residues that are edited to U residues in the corresponding mRNA sequences. In this way, CGG codons can be changed to UGG codons in the mRNA so that tryptophan may be encoded according to the universal genetic code. Furthermore, for each codon modification resulting from a C----U conversion that we studied, we found a corresponding change in the amino acid that was encoded. RNA editing in wheat mitochondria can thus maintain genetic information at the RNA level and as a result contribute to the conservation of mitochondrial protein sequences among plants.

Amino Acid Sequence↗
PubMed1992

Regulation by thyrotropin-releasing hormone (TRH) of TRH receptor mRNA degradation in rat pituitary GH3 cells.

In rat pituitary GH3 cells, thyrotropin-releasing hormone (TRH) down-regulates TRH receptor (TRH-R) mRNA (Fujimoto, J., Straub, R.E., and Gershengorn, M.C. (1991) Mol. Endocrinol. 5, 1527-1532), at least in part, by stimulating its degradation (Fujimoto, J., Narayanan, C.S., Benjamin, J.E., Heinflink, M., and Gershengorn, M.C. (1992) Endocrinology 130, 1879-1884). Here we show that TRH regulates RNase activity in GH3 cells and that specific mRNA sequences are needed for in vivo regulation of TRH-R mRNA by TRH. TRH affected RNase activity in a biphasic manner with rapid stimulation (by 10 min) followed by a decrease to a rate slower than in control lysates within 6 h. This time course paralleled the effects of TRH on degradation of TRH-R mRNA in vivo. The regulated RNase activity was in a polysome-free fraction of the lysates and was not specific for TRH-R RNA. A truncated form of TRH-R RNA that was missing the entire 3'-untranslated region (TRHR-R5) was more stable than full-length TRH-R RNA (TRHR-WT). In contrast to TRHR-WT mRNA, TRHR-R5 mRNA and TRHR-D9 mRNA, which was missing the 143 nucleotides 5' of the poly(A) tail, were not down-regulated by TRH in stably transfected GH3 cells as their rates of degradation were not increased. These data show that TRH regulates RNase activity in GH3 cells, that the 3'-untranslated region bestows decreased stability on TRH-R mRNA and that the 3' end of the mRNA is necessary for regulation by TRH of TRH-R mRNA degradation. We present an hypothesis that explains specific regulation of TRH-R mRNA degradation by TRH in GH3 pituitary cells.

Animals↗