Messenger RNA sequences in nuclear ribonucleoprotein particles are complexed with protein as shown by nuclease protection

The molecular mode of brain mRNA processing damage followed by the suppression of post-transcriptional poly(A) synthesis with cordycepin

Complete suppression of polyadenylation of nuclear precursors of rat brain mRNA by cordycepin leads to degradation of some translatable sequences of both poly(A)(+)- and poly(A)- pre-mRNA localized in 80S hnRNP-particles. This fact has been established by comparative analysis of the data of two-dimensional gel-electrophoretic mapping of translation products synthesized in reticulocytic cell-free system using the exogenous purified templates of rapidly labelling translatable 9-17S hn RNA (pre-mRNA) isolated from brain 80S hn RNP particles of experimental (4 hrs after cordycepin injection) and control (injection of physiological solution) adult healthy male rats. Long contact of brain cells with cordycepin (4 or more hrs) creates conditions for formation of hnRNP-particles devoid of poly(A)+ RNA and poly(A)-binding proteins. These particles differ from "normal" ones by the value of the RNA/protein ratio, and by considerably lower resistance to the action of exogenous ribonucleases and endogenous RNase. Cordycepin does not have a direct effect on biosynthesis of nuclear poly(A)-binding proteins within the duration of the experiment (8 hrs). The phenomena described are discussed.

Chemical modification as a tool for analysis of messenger RNA secondary structure in ribonucleoprotein particles

Chemical modification of unpaired bases is demonstrated in this study to be a reliable method for determining the conformation of nucleotides in mRNA. The modified nucleotides are identified by primer extension using reverse transcriptase. We have used this procedure to compare the structure of limited regions of SV40 T-antigen mRNA in solution, in nonpolysome-bound cytoplasmic messenger ribonucleoprotein particles, and in nuclear ribonucleoprotein complexes. The results indicate that SV40 T-antigen mRNA adopts a specific structure both in solution and when complexed with cellular proteins. The structures adopted by the mRNA in solution and in native cellular protein particles are very similar.

Nuclear polyadenylate-binding protein

Polyadenylate-binding activity can be detected in eluates from sodium dodecyl sulfate gels by a nitrocellulose filter-binding assay. Nuclear extracts from rat liver show a single peak of binding activity at 50 to 55 kilodaltons; cytoplasmic extracts show a single peak at 70 to 80 kilodaltons, corresponding to a 75-kilodalton protein previously described. Similar results are obtained with yeast and mouse fibroblasts, indicating a high degree of conservation of both nuclear and cytoplasmic polyadenylate-binding proteins. The activity from rat liver nuclei has been purified 125-fold on the basis of specific binding to polyadenylate and shows two main bands in sodium dodecyl sulfate gels at 53 and 55 kilodaltons.

Nuclear polyadenylate-binding protein

Polyadenylate-binding activity can be detected in eluates from sodium dodecyl sulfate gels by a nitrocellulose filter-binding assay. Nuclear extracts from rat liver show a single peak of binding activity at 50 to 55 kilodaltons; cytoplasmic extracts show a single peak at 70 to 80 kilodaltons, corresponding to a 75-kilodalton protein previously described. Similar results are obtained with yeast and mouse fibroblasts, indicating a high degree of conservation of both nuclear and cytoplasmic polyadenylate-binding proteins. The activity from rat liver nuclei has been purified 125-fold on the basis of specific binding to polyadenylate and shows two main bands in sodium dodecyl sulfate gels at 53 and 55 kilodaltons.

Human beta-globin pre-mRNA synthesized in vitro is accurately spliced in Xenopus oocyte nuclei

To study the mechanisms of RNA splicing we have synthesized beta-globin mRNA precursors by in vitro transcription using a plasmid in which a human beta-globin gene is fused to an efficient bacteriophage promoter. The structural requirements for accurate splicing of the in vitro synthesized pre-mRNAs were investigated by injection into Xenopus oocyte nuclei. We detect splicing only if the pre-mRNA is capped in vitro prior to injection; uncapped RNA is rapidly degraded. In addition, we find that in vitro synthesized pre-mRNAs that are not polyadenylated or lack a normal 3' end are spliced following injection into oocytes. The observation that a purified pre-mRNA can be spliced in oocytes indicates that transcription and splicing are not obligatorily coupled. When an in vitro synthesized beta-globin pre-mRNA containing a splice junction mutation is microinjected, the affected junction is not spliced, indicating that sequences necessary for accurate splicing in human cells are also necessary for splicing in oocytes.

Assembly of nuclear ribonucleoprotein particles during in vitro transcription

The assembly of heterogeneous nuclear RNA (hnRNA) into ribonucleoprotein (RNP) particles has been investigated during in vitro transcription in isolated nuclei. Approximately 80% of the in vitro transcription observed in mouse Friend erythroleukemia cell nuclei is attributable to the activity of RNA polymerase II. In vitro hnRNA transcripts are assembled into particles having the same properties as the nuclear ribonucleoprotein (hnRNP) particles in which hnRNA is found in vivo. Direct contact of hnRNP proteins with newly transcribed hnRNA was demonstrated by nuclease protection experiments and by the covalent transfer of 32P-labeled nucleotides from [alpha-32P]UTP-labeled hnRNA transcripts to specific proteins by RNA--protein crosslinking followed by nuclease digestion and electrophoresis of the nucleotide-bearing proteins. The availability of an in vitro system for hnRNP assembly opens a new route for investigating the functional relationship between nuclear structure and mRNA processing.

Structure of nuclear ribonucleoprotein: identification of proteins in contact with poly(A)+ heterogeneous nuclear RNA in living HeLa cells

The processing of heterogeneous nuclear RNA into messenger RNA takes place in special nuclear ribonucleoprotein particles known as hnRNP. We report here the identification of proteins tightly complexed with poly(A)+ hnRNA in intact HeLa cells, as revealed by a novel in situ RNA-protein cross-linking technique. The set of cross-linked proteins includes the A, B, and C "core" hnRNP proteins, as well as the greater than 42,000 mol wt species previously identified in noncross-linked hnRNP. These proteins are shown to be cross-linked by virtue of remaining bound to the poly(A)+ hnRNA in the presence of 0.5% sodium dodecyl sulfate, 0.5 M NaCl, and 60% formamide, during subsequent oligo(dT)-cellulose chromatography, and in isopycnic banding in Cs2SO4 density gradients. These results establish that poly(A)+ hnRNA is in direct contact with a moderately complex set of nuclear proteins in vivo. This not only eliminates earlier models of hnRNP structure that were based upon the concept of a single protein component but also suggests that these proteins actively participate in modulating hnRNA structure and processing in the cell.

Nuclear ribonucleoprotein particles probed in living cells

Contacts between heterogeneous nuclear RNA (hnRNA) and protein in nuclear ribonucleoprotein particles have been photochemically crosslinked in intact HeLa or Friend erythroleukemia cell by irradiation with 254-nm light at doses of 10(1) to 10(5) ergs/mm2 (1 to 10(4) microJ/mm2). The resulting crosslinked particles were isolated and compared with conventional hnRNA . protein (hnRNP) preparations. By the criteria of nuclear fractionation behavior, sedimentation coefficients, nuclease digestion profiles, and RNA-to-protein ratio measured by banding in Cs2SO4 density gradients, the hnRNP particles crosslinked in vivo are identical to nonirradiated particles. Gel blot hybridization of RNA from Friend cell hnRNP crosslinked in vivo reveals that beta-globin RNA sequences remain both intact and hybridizable after the irradiation procedure. The crosslinked hnRNA--protein bonds are stable in 8 M urea/0.5% sodium dodecyl sulfate and withstand centrifugation in Cs2SO4 gradients of initial density 1.50 g/cm3. These results establish that hnRNA is tightly complexed with nuclear proteins in vivo and that hnRNP particles isolated by nuclear fractionation represent native structures.