HeLa cell cytoplasmic mRNA contains three classes of sequences: predominantly poly(A)-free, predominantly poly(A)-containing and bimorphic

Capping of Viral RNA in Cultured Spodoptera frugiperda Cells Infected with Autographa californica Nuclear Polyhedrosis Virus

Viral RNA from fall armyworm (Spodoptera frugiperda) cells infected with Autographa californica nuclear polyhedrosis virus contains cap structures. Most of the cap labeled in vivo with [(3)H]methionine or (32)P(i) cochromatographed on DEAE-cellulose with the -5 charge marker; a minor component appeared at -4 net charge. The former is probably a cap 1 structure (m(7)GpppX(m) (p)Yp), and the latter is probably a cap 0 (m(7)GpppXp). On the basis of relative labeling of the two caps with [(3)H]adenosine and [(3)H]guanosine, we concluded that each cap contained at least one adenosine residue in addition to guanosine and, therefore, that cap 0 contained m(7)GpppAp. Cleavage of [(3)H]methionine-labeled viral RNA with tobacco acid pyrophosphatase released a labeled component that cochromatographed on polyethyleneimine-cellulose with m(7)Gp, confirming the m(7)GpppX linkage in the cap. These results were also seen with host polyadenylated RNA. The caps appeared in nearly equal abundance in viral polyadenylated and non-polyadenylated RNAs. The ratio of (32)P(i) incorporated into the cap to that incorporated into mononucleotides suggested average lengths for the polyadenylated and non-polyadenylated RNAs of 1,800 and 1,200 nucleotides, respectively.

Cloning of DNA corresponding to rare transcripts of rat brain: evidence of transcriptional and post-transcriptional control and of the existence of nonpolyadenylated transcripts

To examine the expression of genes encoding rare transcripts in the rat brain, we have characterized genomic DNA clones corresponding to this class. In brain cells, as in all cell types, rare transcripts constitute the majority of different sequences transcribed. Moreover, when compared with other tissues or cultured cells, brain tissue may be expected to have an even larger set of rare transcripts, some of which could be restricted to subpopulations of neural cells. We have identified seven clones whose transcripts are nonabundant, averaging less than three copies per cell. Clone rg13 (rat genomic 13) RNA was detected only in the brain, whereas RNA of a second clone, rg40, was also detected in the brain and in a melanoma. Transcripts of rg13 were found in cerebellum, cerebral cortex, and regions underlying the cortex, whereas rg40 transcripts were not detected in the cerebellum. Transcripts of both rg13 and rg40 were found in pelleted polysomal RNA. RNA of another clone, rg34, was found in the brain, liver, and kidney but was found in pelleted polysomal RNA only in the brain, suggesting that its expression may be post-transcriptionally controlled. The remaining four clones represent rare transcripts that are common to the brain, liver, and kidney; rg18 RNA is restricted to the nucleus, whereas rg3, rg26, and rg36 transcripts are found in the cytoplasm of all three tissues. Transcripts of the brain-specific clone, rg13, and the commonly expressed clone, rg3, are nonpolyadenylated, presumably belonging to the high-complexity, nonpolyadenylated class of transcripts in the mammalian brain.

The poly(A)(+)RNA sequence complexity is also represented in poly(A)(-)RNA in sea-urchin embryos

The extent to which the poly(A)(+)RNA sequence complexity from sea-urchin embryos is also represented in poly(A)(-)RNA was determined by cDNA cross-hybridization. Eighty percent or more of both the cytoplasmic poly(A)(+)RNA and polysomal poly(A)(+)RNA sequences appeared in a poly(A)(-) form. In both cases, the cellular concentrations of the poly(A)(-)RNA molecules that reacted with the cDNA were similar to the concentrations of the homologous poly(A)(+) sequences. Additionally, few, if any, abundant poly(A)(+)mRNA molecules were quantitatively discriminated by polyadenylation, since the abundant poly(A)(+)sequences were also abundant in poly(A)(-)RNA. Neither degradation nor inefficient binding to oligo (dT)-cellulose can account for the observed cross-reactivity. These data indicate that, in sea-urchin embryos, the poly(A) does not regulate the utilization of mRNA by demarcating an mRNA subset that is specifically and completely polyadenylated.

Cloning of DNA corresponding to rare transcripts of rat brain: evidence of transcriptional and post-transcriptional control and of the existence of nonpolyadenylated transcripts

To examine the expression of genes encoding rare transcripts in the rat brain, we have characterized genomic DNA clones corresponding to this class. In brain cells, as in all cell types, rare transcripts constitute the majority of different sequences transcribed. Moreover, when compared with other tissues or cultured cells, brain tissue may be expected to have an even larger set of rare transcripts, some of which could be restricted to subpopulations of neural cells. We have identified seven clones whose transcripts are nonabundant, averaging less than three copies per cell. Clone rg13 (rat genomic 13) RNA was detected only in the brain, whereas RNA of a second clone, rg40, was also detected in the brain and in a melanoma. Transcripts of rg13 were found in cerebellum, cerebral cortex, and regions underlying the cortex, whereas rg40 transcripts were not detected in the cerebellum. Transcripts of both rg13 and rg40 were found in pelleted polysomal RNA. RNA of another clone, rg34, was found in the brain, liver, and kidney but was found in pelleted polysomal RNA only in the brain, suggesting that its expression may be post-transcriptionally controlled. The remaining four clones represent rare transcripts that are common to the brain, liver, and kidney; rg18 RNA is restricted to the nucleus, whereas rg3, rg26, and rg36 transcripts are found in the cytoplasm of all three tissues. Transcripts of the brain-specific clone, rg13, and the commonly expressed clone, rg3, are nonpolyadenylated, presumably belonging to the high-complexity, nonpolyadenylated class of transcripts in the mammalian brain.

Genetic expression in the developing brain

The adult mouse brain contains complex populations of polyadenylated [poly(A)+] and nonpolyadenylated [poly(A)-] messenger RNA's (mRNA's). These mRNA's are separate sequence populations, similar in complexity, and in combination are equivalent to approximately 150,000 different mRNA sequences, of average length. Essentially all of the "adult" poly(A)+ mRNA's are present in the brain at birth. In contrast, most of the poly(A)- mRNA's are absent. Brain poly(A)- mRNA's begin to appear soon after birth, but the full adult complement is not reached until young adulthood. This suggests that these poly(A)- mRNA's specify proteins required for the biological capabilities of the brain that emerge during the course of postnatal development.

Association of poly(adenylate)-deficient messenger ribonucleic acid with membranes in mouse kidney

To describe further the metabolism of messenger ribonucleic acid (mRNA) in mouse kidney, we examined newly synthesized mRNA deficient in poly(adenylate) [poly(A)]. Approximately 50% of renal polysomal mRNA that labeled selectively in the presence of the pyrimidine analogue 5-fluoroorotic acid lacks or is deficient in poly(A) as defined by its ability to bind to poly(A) affinity columns. Nearly one-half of this poly(A)-deficient mRNA is associated uniquely with a cellular membrane fraction detected by sedimentation of renal cytoplasm in sucrose density gradients containing EDTA and nonionic detergents. Poly(A+) mRNA and poly(A)-deficient mRNA [poly(A-) mRNA] have similar modal sedimentation coefficients (20-22 S) and similar cytoplasmic distribution. Although 95% of newly synthesized poly(A+) mRNA is released in 10 mM EDTA as 20-90 S ribonucleoproteins from polysomes greater than 80 S, only 55% of poly(A)-deficient mRNA is released under the same conditions. Poly(A)-deficient mRNA recovered from greater than 80 S ribonucleoproteins resistant to EDTA treatment lacks ribosomal RNA, is similar in size to poly(A+) mRNA, and is associated with membranous structures, since 70% of poly(A)-deficient mRNA in EDTA-resistant ribonucleoproteins is released into the 20-80 S region by solubilizing membranes with 1% Triton X-100. These membrane-associated renal poly(A-) mRNAs could have unique coding or regulatory functions.

Isolation and characterisation of a non-polyadenylated mRNA species with an affinity for poly(adenylic acid) from Friend leukaemia cells

Utilizing the technique of poly(A)-Sepharose affinity chromatography, it is possible to isolate a novel class of RNA molecules from polysomes of Friend leukaemia cells. These RNA species display messenger RNA-like behaviour. They are released from polysomes on treatment with EDTA and are able to direct polypeptide synthesis in a cell-free protein synthesising system. They appear to be distinct from the polyadenylated mRNAs, as judged by their lack of a 3'-terminal poly(A) tract, by their different size distribution, by their unusual base composition, by the presence of a possible 'uridylate rich' region towards their 3'-end, by their low sequence homology to polyadenylated mRNAs and by the difference in at least some of their translation products.

A modified nucleotide in the poly(A) tract of maize RNA

poly(A)+ RNA was isolated from maize by affinity chromatography on columns of oligo(dT)-cellulose. A modified nucleotide ('X') was detected in ribonuclease T2 digests of the RNA as part of a resistant dinucleotide. The dinucleotide was detected by means of the polynucleotide kinase-mediated transfer of a radioactive phosphate atom from adenosine triphosphate to the 5'-OH position of the dinucleotide. Intact poly(A) tracts were released from poly(A)+ RNA by digestion with ribonuclease T1 and A in a high salt buffer and were isolated by oligo(dT)-cellulose chromatography. The poly(A) preparation was found to consist of a series of polyadenylate fragments which varied in chain length from approximately 17 to greater than 70. The modified nucleotide was shown to occupy an internal position in these poly(A) tracts.

Relative distribution of post-nuclear poly(A)-containing RNA abundance groups within the nuclear and post-nuclear polyadenylated and non-polyadenylated RNA populations of the lactating guinea-pig mammary gland

1. RNA isolated from the post-nuclear supernatant of the lactating guinea-pig mammary gland was fractionated with oligo(dT)-cellulose into three populations; those that bound at ;low salt' [long poly(A) tracts, 78-32 nucleotides]; those that bound at ;high salt' [shorter poly(A) tracts, 48-21 nucleotides]; and those that did not bind [no poly(A) or short poly(A) tracts, <20 nucleotides]. Nuclear RNA was fractionated into two populations, those that bound in ;low salt' and those that did not bind. All the post-nuclear RNA fractions directed the synthesis of milk proteins in a Krebs II ascites cell-free system. 2. (3)H-labelled DNA complementary to the post-nuclear poly-(A)-containing RNA population (low-salt fraction) was fractionated into abundant (milk-protein mRNA), moderately abundant and scarce sequences. This complementary DNA was then used to investigate the distribution of the mRNA sequences in the different RNA populations. This showed that all sequences were present in polyadenylated and non-polyadenylated fractions, but that major quantitative differences were apparent. The abundant milk-protein mRNA sequences predominated in the ;low-salt' post-nuclear poly(A)-containing RNA fraction, whereas the moderately abundant sequences predominated in the non-polyadenylated post-nuclear RNA fraction. In total cellular RNA, those sequences deemed initially to be moderately abundant within the ;low-salt' poly(A)-containing RNA population were present at a concentration very similar to those of the abundant milk-protein mRNA (approx. 6x10(5) copies of each sequence/cell). Similarly, analysis of the nuclear RNA populations showed that the ;abundant' and so-called ;moderately abundant' sequences were present in essentially identical concentrations (2x10(3) copies of each sequence/cell). The majority of these (90-95%) were non-polyadenylated. 3. The results are discussed in terms of the post-transcriptional mechanisms involved in the regulation of gene expression in the lactating guinea-pig mammary gland.

Light-induced appearance of polysomal poly(A)-rich messenger RNA during greening of barley plants

Changes in polysomal poly(A)-rich mRNA during greening of etiolated barley plants were studied by the technique of cDNA-mRNa hybridization. Hybridizaiton data of the homologous reactions reveal that in etiolated as well as in greened shoots a complexity of 5 X 10(7) nucleotides or about 33000 different average-sized mRNAs are present. These are organized in different abundancy classes with 94% of the total complexicity present in each of the slowest reacting class representing rare messengers. Heterologous hybridizations indicate that 92% of all polysomal poly(A)-rich mRNAs in etiolated shoots are complementary to those of greened and 82% of 'green' poly(A)-rich mRNAs are complementary to white ones. It is shown that the abundant mRNA clases are essentially responsible for these differences. The prevalent classes making up 15% ('white') and 31% ('green') of the poly(A)-rich mRNA mass but comprising only a complexity of 1.8 X 10(4) and 2.1 X 10(4) nucleotides are identical to 50% with each other. Hybridization of isolated prevalent 'green' cDNA with whole 'white' poly(A)-rich mRNA indicates that the additionally appearing 50% prevalent green messengers must be regarded as green-specific, only present in polysomal poly(A)-rich mRNA after illumination. This conclusion is underlined by the hybridization of the 'green' cDNA with total polysomal RNa of etiolated shoots. Evidently appearance of these prevalent messengers in functional polysomes is not caused by a shift from poly(A)-free mRNA to poly(A)-rich mRNA. The results clearly demonstrate that light induces greening by turning on genes or influencing post-transcriptional processing to produce mature green-specific poly(A)-rich mRNA.

Cell cycle regulation of dihydrofolate reductase mRNA metabolism in mouse fibroblasts

We have used the technique of DNA-excess filter hybridization to measure directly the content and metabolism of the mRNA for dihydrofolate reductase (DHFR; 5,6,7,8-tetrahydrofolate:NADP+ oxidoreductase, EC 1.5.1.3). The studies were conducted with a methotrexate-resistant derivative of mouse 3T6 fibroblasts (M50L3) that overproduces the enzyme and its mRNA by a factor of 300 but regulates the level of the enzyme during the cell cycle in the same manner as normal 3T6 cells. We found that, when resting (G0) M50L3 cells were serum-stimulated to reenter the cell cycle, the 10-fold increase in the rate of synthesis of DHFR that occurs at the beginning of S phase was the result of a corresponding increase in DHFR mRNA content. In pulse-labeling experiments, we found that there was a similar increase in the rate of production of the mRNA just prior to S phase. However, the half-life of the mRNA was the same (7.5 hr) in resting and exponentially growing cells. Therefore, the increase in DHFR mRNA content was due to an increase in the rate of production rather than an increase in the stability of the message. The delay between addition of [3H]-uridine to the culture medium and the emergence of DHFR mRNA from the nucleus was 15-20 min for both resting and growing M50L3 cells. A similar delay was observed for total mRNA. Therefore, the time required for the processing of newly synthesized DHFR heterogeneous nuclear RNA into DHFR mRNA is about the same as that for the average mRNA.