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PubMed1986

Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements.

U1 and U2 snRNAs are thought to be transcribed by RNA polymerase II. A conserved sequence known as the 3' box is located just downstream from the snRNA coding region and directs formation of the 3' end of pre-U1 and pre-U2 snRNA. We show here that a U1 or U2 promoter containing an intact snRNA enhancer is required for the U1 3' box to function efficiently. Promoters for genes encoding mRNAs cannot substitute for the snRNA promoter. Thus snRNAs must be transcribed by a specialized transcription complex that differs from transcription complexes synthesizing mRNAs. Moreover, in contrast to polyadenylated and nonpolyadenylated mRNAs, the 3' ends of pre-snRNAs must be generated either by termination of transcription, or by an RNA processing event intimately coupled to transcription.

Chromosome Deletion↗
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↗
PubMed1993

Nonlinear ribosome migration on cauliflower mosaic virus 35S RNA.

Cauliflower mosaic virus 35S RNA contains a 600 nt leader with several small open reading frames that by themselves inhibit translation of downstream coding regions. In the context of the whole leader and in certain plant cells, however, translation of downstream coding regions is allowed. This translation is dependent on the RNA 5' terminus and other elements of the leader. However, its central portion is dispensable or can be modified by insertion of an energy-rich stem-loop structure or long coding region with many internal AUG codons. We conclude that this region can be by-passed (shunted) by the scanning complex. Shunting was also observed in trans between two separate RNA molecules.

Base Sequence↗
PubMed1995

Degradation of mRNA in eukaryotes.

Based on the above mechanisms of mRNA degradation, an integrated model of mRNA turnover can be proposed (Figure 1). In this model, all polyadenylated mRNAs would be degraded by the deadenylation-dependent pathway at some rate. In addition to this default pathway, another layer of complexity would come from degradation mechanisms specific to individual mRNAs or to classes of mRNAs. Such mRNA-specific mechanisms would include sequence-specific endonuclease cleavage and deadenylation-independent decapping. Thus, the overall decay rate of an individual transcript will be a function of its susceptibility to these turnover pathways. In addition, cis-acting sequences that specify mRNA decay rate, as well as regulatory inputs that control mRNA turnover, are likely to affect all the steps of these decay pathways. One important goal in future work will be to identify the gene products that are responsible for the nucleolytic events in these pathways and to delineate how specific mRNA features act to affect the function of these degradative activities. The identification of distinct mRNA decay pathways should allow, genetic and biochemical approaches that can be designed to identify these gene products. A second important goal is to understand the nature of the interaction between the 5' and 3' termini, which may also be critical for efficient translation.

Adenosine Monophosphate↗
PubMed1991

The spliced leader gene of Angiostrongylus cantonensis.

A 5' leader sequence has been identified on mRNAs of the parasitic nematode Angiostrongylus cantonensis. A 720-bp XhoI restriction fragment containing the gene encoding the leader sequence has been cloned and sequenced. It contains a 22-nt sequence identical to that of the leader sequence of Caenorhabditis elegans, a consensus splice site and a putative Sm antigen binding site. The gene is present as a tandem repeating unit of approximately 60 copies, and unlike C. elegans it is not associated with the 5S ribosomal RNA gene. The SL-RNA is 110 nt long and the sequence and primer extension studies suggest that it is transcribed from the tandemly repeating SL gene. It is precipitable from cell-free extracts of adult nematodes by anti-Sm anti-sera, and from RNA by anti-TMG anti-sera, thus suggesting its inclusion with small nuclear ribonucleoproteins in RNA splicing.

Amino Acid Sequence↗
PubMed1986

Synthesis of epidermal growth factor (EGF) receptor in vitro using SP6 RNA polymerase-transcribed template mRNA.

The epidermal growth factor (EGF) receptor plays a key role in the control cellular proliferation, and its homology to the avian erythroblastosis virus erb B oncogene implicates its involvement in cellular transformation. The establishment of a correlation between the various structural domains of the EGF receptor and their functional counterparts would greatly advance our understanding of these processes. To this end, we have constructed an expression vector containing the SP6 viral promoter and an adjacent cDNA fragment encoding the full-length EGF receptor. Upon addition of SP6 RNA polymerase, this DNA is capable of generating large amounts of EGF receptor mRNA; this RNA can then be translated in vitro into immunoprecipitable EGF receptor protein. The translational efficiency of this EGF receptor RNA was found to be relatively low: approx. 100-fold lower than globin RNA synthesized using SP6 RNA polymerase. Use of these tools should now permit the synthesis and analysis of mutated EGF receptor protein in an effort to clarify the role of this receptor in growth control.

Cell-Free System↗
PubMed1995

The methyltransferase inhibitor Neplanocin A interferes with influenza virus replication by a mechanism different from that of 3-deazaadenosine.

Neplanocin A (NeplA) and 3-deazaadenosine (3DA-Ado) are both inhibitors of methyltransferases, and both interfere with influenza virus replication. Their modes of action, however, are different. In chicken embryo cells NeplA inhibits only in media depleted of or low in methionine, while 3DA-Ado acts independently of the concentration of methionine. While homocysteine partially reverses the effect of NeplA, it strongly potentiates the effect of 3DA-Ado. While NeplA inhibits the synthesis of all viral proteins to nearly the same extent, 3DA-Ado interferes only with the production of late proteins (Fischer et al. (1990) Virology 177, 523-531). In NeplA-pretreated cells there is an extreme accumulation of S-adenosylhomocysteine, independent of the concentration of methionine in the medium, although NeplA inhibits influenza virus replication only in methionine-depleted medium. Therefore an accumulation of this intermediate by NeplA cannot account for the inhibitory effect, as has been implicated in the inhibition of the replication of other viruses. Our results indicate that at least two different methyltransferases are involved in influenza virus replication.

Adenosine↗
PubMed1990

Expression of RNA transcripts of potato virus X full-length and subgenomic cDNAs.

Translation of synthetic potato virus X (PVX) RNAs was examined in Krebs II ascite cell extracts and rabbit reticulocyte lysates. Either full-length or subgenomic RNAs produced by in vitro transcription of cDNAs cloned in the T7 promoter vectors were used. Full-length PVX RNA-transcript directed the synthesis of a large polypeptide which was indistinguishable from the translation product (165 kDa) of authentic viral genomic RNA on SDS-PAGE. Translation of the full-length and 3'-truncated RNA species was stimulated by addition of m7GpppG to the T7 transcription system. Subgenomic cDNA transcripts corresponding to the 3'-proximal part of PVX RNA were efficiently translated into the PVX coat protein and 2 as yet unidentified small hydrophobic proteins.

Animals↗
PubMed1996

Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure.

Nucleoli contain complex populations of small nucleolar RNAs (snoRNAs) likely to be involved in pre-rRNA processing and ribosome biogenesis. A growing family of snoRNAs which interacts with nucleolar protein fibrillarin is structurally related by the presence of long complementarities to rRNA (12 to 21 nucleotides) and of a pair of common sequence motifs, termed boxes C and D. All are encoded in introns and produced by processing of intronic RNA. We have analysed the mechanism of processing of one of these snoRNAs, U20, by transfection in mouse cells. We show here that the cis-acting signals for its processing are restricted to a minor portion of the mature snoRNA sequence. A terminal structure in which the two box motifs are brought in close vicinity by the pairing of the 5' and 3' terminal nucleotides is sufficient to direct faithful processing. Particularly, the key role of the terminal stem shared by most snoRNAs of this family is demonstrated by the effect of compensatory mutations. Our results also indicate that faithful processing at both ends of the snoRNA can be uncoupled and that it is not strictly dependent on pre-mRNA splicing. Finally, our data point to the exclusive involvement of 5'-->3' and 3'-->5' exonucleolytic activities in the processing of intronic snoRNAs of this family.

Animals↗
PubMed1994

Analysis of transcriptional initiation and translatability of brain-derived neurotrophic factor mRNAs in the rat brain.

The rat brain-derived neurotrophic factor (BDNF) gene consists of four 5' exons linked to separate promoters and one 3' exon encoding the prepro-BDNF protein. In the present study, using RNase protection analysis, we show that the same major transcription initiation sites are used for each BDNF exon mRNA in different brain regions and that in addition to hippocampus and cerebral cortex, kainate differentially induces the expression of BDNF exon mRNAs in thalamus, cerebellum and striatum. The 4.2 kb transcripts, are less enriched in the polysomal fraction of rat brain than the shorter 1.6 kb transcripts suggesting their translational discrimination.

Animals↗
PubMed1982

Nucleotide sequence of the transcription initiation region of a rat ribosomal RNA gene.

We cloned the part of the rDNA containing the transcription initiation region, and determined the exact site of initiation of the 45S RNA transcription. The nucleotide sequence of the region surround the initiation site was determined. Comparison of the mouse and rat genes revealed extensive homology between the initiation regions of the two species. Notably, upstream the transcription initiation site had higher homology (77%) than downstream (51%), suggesting functional significance of this region.

Animals↗
PubMed1985

A cloned human immunoglobulin heavy chain gene with a novel direct-repeat sequence in 5' flanking region.

A rearranged human immunoglobulin gamma 1 heavy-chain gene (HIG1) was cloned from a human plasma cell leukemia cell line, ARH-77. The cloned gene possessed a unique direct repeat sequence of 84 bp in the 5' flanking region as well as an enhancer-like element in the JH-C gamma 1 intron. The latter sequence is located 1 kb downstream of 3' end of the J6 exon. The direct-repeat sequence in the 5'-flanking region contained a core-like sequence resembling that of viral enhancer elements. It is located in the intron between two leader exons. P1 nuclease mapping and exonuclease VII digestion experiments showed that most of the direct repeats are noncoding regions and spliced out from the transcript. These data suggested that HIG1 gene might have two kinds of enhancer-like elements at both sides of the V region gene. HIG1 gene has been introduced by the protoplast fusion into mouse myeloma cells (NSI and J558L cells) and mouse fibroblasts. A pSV2gpt vector containing HIG1 gene (pSV2-HIG1) was used to transform the cells. The amounts of mRNA synthesized in the transformed cells were at least 50 to 100 times larger than those in ARH-77 cells, although about one copy of HIG1 gene was present in DNA of a transformed cell. HIG1 gene was not expressed in fibroblasts, indicating that the enhancer of HIG1 gene acts in a tissue-specific manner but not in a species-specific one. The role of two kinds of enhancer-like elements in HIG1 gene is discussed in connection with the high-level expression of this gene in mouse myeloma cells.

Animals↗