Differential and coordinate regulation of the eukaryotic small molecular weight RNAs

Alu's dimeric consensus sequence destabilizes its transcripts

The effect that different regions of the Alu consensus sequence have upon the stability and accumulation of its RNA polymerase III (Pol III) directed transcripts was determined by transiently overexpressing Alu deletion and chimeric constructs in human 293 cells. Transcripts of the left Alu monomer are more stable than those of the full-length consensus sequence and any additional 3' sequence beyond the left monomer destabilizes the resulting transcript. Neither the middle A-rich region nor the 3' A-rich tail specifically affect the stability of Alu transcripts. However, the right monomer is inherently less stable than corresponding left monomer transcripts. Alu's dimeric structure and sequences peculiar to the right monomer each limit the stability and steady state accumulation of its transcripts. A host requirement to rapidly metabolize Alu RNA or restrict its abundance may have selected for these two features of the Alu consensus sequence.

Determination of degradation rates of transfer and ribosomal ribonucleic acids in cultured rat hepatocytes by measuring N6-threoninocarbonyladenosine, dihydrouridine, and pseudouridine in medium using high-performance liquid chromatography

Modified ribonucleic acid catabolites excreted into the medium by primary cultures of rat hepatocytes (2.3 +/- 0.42 x 10(6) cells/dish) during a 24-h cultivation period were quantified by reversed-phase high-performance liquid chromatography (fmol/10(3) cells): 613 +/- 81 dihydrouridine, 46 +/- 6 N6-threoninocarbonyladenosine, 1879 +/- 220 pseudouridine. On the basis of these excretion rates and the average frequency of occurrence of these modified ribonucleosides per cytoplasmic transfer ribonucleic acid (residues: 2.6 dihydrouridine, 0.22 N6-threoninocarbonyladenosine, 3 pseudouridine) as well as per cytoplasmic ribosomal ribonucleic acid (residues: 95 pseudouridine), the degradation rates of transfer and ribosomal ribonucleic acids were calculated. The degradation rate of transfer ribonucleic acid (fmol/10(3) cells/24 h) was 236 +/- 31 (via dihydrouridine) and 211 +/- 28 (via N6-threoninocarbonyladenosine) and that of ribosomal ribonucleic acid (fmol/10(3) cells/24 h) was 13.1 +/- 1.7 (via pseudouridine and N6-threoninocarbonyladenosine).

Total contractile protein contents and gene expression in skeletal muscle in response to chronic ethanol consumption in the rat

An investigation was carried out to determine changes in the contents of skeletal muscle myofibrillary proteins (i.e., the contractile fraction composed principally of actin and myosin) and gene expression in skeletal muscle in response to ethanol feeding. Male Wistar rats were fed a nutritionally complete liquid diet, which contained 35% of total calories as ethanol. Controls were pair-fed isocaloric amounts of the same diet, in which ethanol was replaced by isocaloric glucose. Total mixed and contractile protein contents of the gastrocnemius in ethanol-fed rats were rapidly reduced by ethanol feeding: a response was discernible as early as 1 week after the commencement of the ethanol feeding regimen (approx. -10%, p < 0.025 and p = 0.05 for mixed and myofibrillary proteins, respectively). At 2, 4, and 6 weeks, mixed and myofibrillary protein contents were further reduced in alcohol-fed rats, by between 12% and 22%, compared to pair-fed controls. Similar changes occurred in the soluble (i.e., sarcoplasmic) protein fractions of skeletal muscle. At 2 weeks the composition of total messenger RNA and individual messenger RNA species was measured. Total messenger RNA content per muscle was reduced by 35% (p < 0.05). Messenger RNA levels for alpha-actin, beta-myosin heavy chain, and carbonic anhydrase III were not significantly altered. In conclusion, skeletal muscle protein contents are rapidly reduced by ethanol feeding, compared to pair-fed controls, though mRNA species encoding specific isoforms of myosin and actin are not affected. It is possible that chronic ethanol feeding may significantly alter the stability of mRNAs encoding other contractile proteins, or alternatively, defects in translation may predominate.

Protein synthesis in the heart in vivo, its measurement and patho-physiological alterations

Changes in cardiac protein composition occur in a variety of patho-physiological situations and are usually accompanied by modifications in protein synthesis. Although adjustments in protein synthesis during starvation may be adaptive, the alterations in protein synthesis seen in response to ethanol ingestion may be pathological and an important step in the genesis of alcoholic heart muscle disease. The alterations in heart muscle in hypertension are initially adaptive but in the long term they are deleterious, and involve both transcription and translation. While adequate methods exist for quantifying the amount of mRNA for contractile and non-contractile proteins, such studies of gene-expression provide no dynamic information on the rate at which tissue proteins are lost or accrued. This can only be determined by measuring the rate of protein turnover, i.e. either protein synthesis or protein breakdown. Techniques for directly determining the rates of protein breakdown are limited or involve surgical procedures. Methods for measuring the rate of protein synthesis are described, and are illustrated by their application to the investigation of starvation and ethanol toxicity. In particular, attention is focused on the fact that reliable rates of protein synthesis are obtained only if the specific radioactivity of the precursor at the site of protein synthesis (aminoacyl-tRNA) is assessed.

2,5-Hexanedione-induced intermediate filament aggregates contain ubiquitin-protein conjugate immunoreactivity and resemble Rosenthal fibres

A number of chronic degenerative disorders including cerebellar astrocytomas and Parkinson's disease are characterized by the presence of cytosolic inclusions which contain intermediate filament (IF) aggregates and ubiquitin-protein conjugate immunoreactivity. In cerebellar astrocytomas these inclusions are known as Rosenthal fibres. 2,5-hexanedione (HD) treatment is known to induce IF aggregates in cells in culture. HD-induced aggregates have therefore been studied as a potential model for the clinical inclusions. Exposure of astrocyte cultures to 2 mM HD for 2 or 4 weeks led to the formation of aggregates of the IFs (glial fibrillary acidic protein and vimentin). The aggregates contained ubiquitin-protein conjugates, which, on electron microscopy appeared to be localized in a peripheral shell. In addition, ubiquitin mRNA levels were found to be elevated approximately threefold by HD treatment. HD-induced inclusions and Rosenthal fibres were found to share a number of features. HD administration, therefore, appears to be a suitable model for the production of pathological inclusions.

Ubiquitin gene expression in brain and spinal cord in motor neurone disease

A restriction fragment of the coding region of a human ubiquitin gene has been used in Northern analyses of RNA prepared from human motor cortex and anterior horn region of cervical spinal cord. The analyses show that there is a substantial increase (approximately two-fold) in the expression of a polyubiquitin gene in motor cortex and spinal cord from patients with motor neurone disease compared to these tissues from control cases. Polyubiquitin gene expression in other organisms is associated with physical or chemical cell stresses. The data indicate that the primary stresses which result in the generation of ubiquitinated filamentous inclusion bodies in neurones in motor neurone disease also result in increased transcription of a gene coding for a polyprotein of ubiquitin.

Serum-induced stimulation of snRNA synthesis in mouse 3T3 fibroblasts

Small nuclear RNAs (snRNAs) from quiescent and serum-stimulated 3T3 cultures, labeled with [3H]uridine [( 3H]U), were electrophoresed in polyacrylamide-urea slab gels and revealed by staining with ethidium bromide and by fluorography. Judged by labeling with [3H]U, synthesis of 7S and U1-U6 RNAs was very low or absent in quiescent cultures. The serum-induced transition of 3T3 cells from a resting to a growing state was accompanied by an early, apparently sequential stimulation of snRNA synthesis; stimulated synthesis of 7S, U1, U2, U3, U4 and U6 RNAs coincided in time with serum-induced stimulation of 45S pre-ribosomal RNA (pre-rRNA) and heterogeneous nuclear RNA (hnRNA) synthesis.

DNA sequences complementary to human 7 SK RNA show structural similarities to the short mobile elements of the mammalian genome

A complementary DNA clone of 7 SK RNA from HeLa cells was used to study the genomic organization of 7 SK sequences in the human genome. Genomic hybridizations and genomic clones show that 7 SK is homologous to a family of disperse repeated sequences most of which lack the 3' end of the 7 SK RNA sequence. Only few of the genomic K sequences are homologous to both 3' and 5' 7 SK probes and presumably include the gene(s) for 7 SK RNA. The sequence of four genomic 7 SK clones confirms that they are in most cases pseudogenes. Although Alu sequences are frequently found near the 3' and 5' end of K DNA, the sequences immediately flanking the pseudogenes are different in all clones studied. However, direct repeats were found flanking directly the K DNA or the K-Alu unit, suggesting that the K sequences alone or in conjunction with Alu DNA might constitute a mobile element.

Isolation and characterization of hnRNA-snRNA-protein complexes from Morris hepatoma cells

Of the RNA labelled after incubation of hepatoma cells with radioactive precursors for 20 and 150 min. 35% and 70%, respectively, can be isolated from nuclei by two consecutive extractions with 0.14 M NaCl at pH 8. The isolated RNA is complexed with nuclear proteins forming structures with sedimentation coefficients of less than 30 S to greater than 100 S. Similar complexes from rat liver isolated under the same experimental conditions show coefficients of 30-40 S. The RNA-associated proteins are similar, on the basis of sodium dodecyl sulphate/polyacrylamide gel electrophoresis, to the respective proteins of other cell types. The presence on these RNP complexes of six discrete small nuclear RNAs (snRNA) has been established. Experiments with a reversible inhibitor of RNA synthesis, D-galactosamine, demonstrated, differences in the turnover of hnRNA and snRNA. The half-lives of the six snRNA species has been determined, varying from 32 h for snRNA species a, b and d, to 22 h for snRNA species e and f and to 13 h for snRNA species c. Treatment of the nuclear extracts with 0.7 M and 1 M NaCl results in dissociation of hnRNA from the 'core' and other polypeptides, whereas snRNA remains complexed with polypeptides of Mr 54 000-59 000. Incubation of the nuclear extracts at 0 C with low doses of pancreatic R Nase (up to 1.5 micrograms/ml), which renders approximately 80% of the hnRNA acid-soluble and cleaves most of the snRNA, results in conversion of the high-molecular-weight hnRNPs to 30-S structures, without disrupting the 30-S RNP. Treatment of the nuclear extracts with higher doses of RNase (3 micrograms/ml) leads to disruption of the 30-S RNP and release of the hnRNA-associated proteins, underlining the importance of hnRNA-protein interaction for the retainment of the hnRNP structures.

Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence

We have cloned and sequenced a cDNA copy of in vitro-polyadenylated 7SL RNA of HeLa cells. The cloned fragment is 303 bp long and has a composite structure. A central block of 140 bp is homologous to a new set of human middle-repetitive sequences. This block appears to be inserted in an Alu consensus sequence, 100 bp from the 5' end and 40 bp from the 3' end of the Alu monomer. Two 6 bp direct repeats are found at the junction between the Alu flanking sequences and the central element. The analysis of several clones shows the existence of sequence microheterogeneity in the 5' portion of the molecule. The 7L DNA probably represents a subset of the Alu family of DNA, highly conserved in evolution.