On the structure of transcriptional unit in mammalian cells

Hybridization of mRNA and pre-mRNA with the sequences forming double-stranded structures in pre-mRNA

About 25% of the double-stranded sequences isolated from pre-mRNA are able to hybridize, after melting, with either mRNA or non-melted pre-mRNA. The retention of one branch of pre-mRNA hairpin in mRNA was suggested. It was also found that in addition to the hairpin-like structures comprising about 3% of the total sequences another 15% of the pre-mRNA sequences can form double-stranded structures upon annealing over a broad interval of Cot values.

Biosynthesis and cytoplasmic distribution of small poly(A)-containing B2 RNA

Previously, we described a small polyadenylated RNA predominantly located in cytoplasm and hybridizing with the ubiquitous B2 sequence of the mouse genome (Kramerov, D.A., Lekakh, I.V., Samarina, O.P. and Ryskov, A.P. (1982) Nucleic Acids Res. 10, 7477-7491). This 180-300 nucleotide long RNA was designated B2 RNA. Here, we demonstrate that B2 RNA is complementary to just one of the strands of cloned B2 sequence. The synthesis of B2 is rather resistant to ultraviolet irradiation of Ehrlich ascites carcinoma cells. The treatment of the cells with alpha-amanitin at a concentration completely blocking the formation of small nuclear RNAs U1, U2 and U3 does not interfere with the B2 RNA synthesis. These results suggest that B2 RNA formation is directly transcribed with the aid of RNA polymerase III, rather than being formed in the course of the processing of large RNA molecules which are known to contain a lot of B2 sequences. We also surprisingly found that the synthesis of up to 50% of long poly(A) +RNA in Ehrlich carcinoma cells is rather resistant to alpha-amanitin. The possible role of genetic elements including B2 sequences able to promote large RNA-polymerase III transcripts is discussed. B2 RNA in the cytoplasm is incorporated into the ribonucleoprotein particles, both small (12-18 S) and heavy. The latter probably correspond to informosomes. After deproteinization of heavy particles, a major part of B2 RNA still cosediments with mRNA and is split from it only after denaturation. We suggest that the B2 RNA of heavy ribonucleoproteins is associated with mRNA by short complementary stretches. About half of the B2 RNA is recovered in the cytoskeletal fraction. The possible role of B2 RNA in mRNA transport or in translation regulation is discussed.

Mouse ubiquitous B2 repeat in polysomal and cytoplasmic poly(A)+RNAs: uniderectional orientation and 3'-end localization

A cDNA library in pBR322 was prepared with cytoplasmic poly(A)+RNA from mouse liver cells. From 1 to 1.5% of clones hybridized to either B1 or B2 ubiquitous repetitive sequences. Several clones hybridizing to a B2 repeat were partially sequenced. The full-length B2 sequence was found at the 3'-end of abundant 20S poly(A)+RNA (designated as B2+mRNAx) within the non-coding part of it. B2+mRNAx is concentrated in mouse liver polysomes and absent from cytoplasm of Ehrlich carcinoma cells. The B2 sequence seems to be located at the 3'-end of some other mRNAs as well. To determine the orientation of the B2 sequence in different RNAs, its two strands were labeled, electrophoretically separated, and used for hybridization with Northern blotts containing nuclear, cytoplasmic and polysomal RNAs. In nuclear RNA, the B2 sequence is present in both orientations; in polysomal and cytoplasmic poly(A)+RNAs, only one ("canonical") strand of it can be detected. Low molecular weight poly(A)+B2+RNA [1] also contains the same strand of the B2 element. The conclusion has been drawn that only one its strand can survive the processing. This strand contains promoter-like sequences and AATAAA blocks. The latter can be used in some cases by the cell as mRNA polyadenylation signals.

Cellular Moloney murine sarcoma (c-mos) sequences are hypermethylated and transcriptionally silent in normal and transformed rodent cells

Moloney murine sarcoma virus carries an oncogenic sequence (v-mos) which is homologous to a single copy gene (c-mos) present in the normal cells of several vertebrate species. Because of the possible significance of c-mos sequences in normal development and malignant transformation induced by physical or chemical agents, we have examined the state of integration, methylation, and transcriptional activity of c-mos sequences in a variety of normal rodent tissues, normal cell lines, or cell lines transformed by radiation or chemical carcinogens. DNA-DNA hybridization, utilizing the Southern blotting technique and a plasmid-derived DNA probe representing the v-mos sequence, gave no evidence for rearrangements of the c-mos sequence in the DNAs obtained from these diverse cell types. Parallel studies employing the restriction enzyme isoschizomers HpaII and MspI indicated that in all of these cell types the c-mos sequences were heavily methylated. In addition, analysis of cellular RNAs by blot hybridization with the v-mos probe failed to detect evidence of transcription of the c-mos sequences in any of these cell types. This was in contrast to a Moloney sarcoma virus-transformed cell line in which we found that the integrated v-mos sequence was both undermethylated and extensively transcribed. Thus, it would appear that c-mos sequences do not play a role in the transformation of rodent cells by chemical or physical agents, although the possible role of other endogenous onc sequences remains to be determined.

A cloned unique gene of Drosophila melanogaster contains a repetitive 3' exon whose sequence is present at the 3' ends of many different mRNAs

We have started a cloned genomic DNA fragment approximately 7 kb long (denoted as H55) from the 7B3-4 region in the X chromosome of Drosophila melanogaster. The major part of the fragment is a single-copy sequence. It directs the synthesis of mRNA that makes up approximately 0.1% of the cytoplasmic poly(A)+ RNA from Drosophila embryos. The H55 gene is split by an intervening sequence, yielding a large single-copy exon and a small repetitive 3' exon represented by hundreds of copies in the genome. This repetitive sequence ("suffix") is also present at the 3' ends of approximately 2% of all cytoplasmic poly(A) chains.

Cellular Moloney murine sarcoma (c-mos) sequences are hypermethylated and transcriptionally silent in normal and transformed rodent cells

Moloney murine sarcoma virus carries an oncogenic sequence (v-mos) which is homologous to a single copy gene (c-mos) present in the normal cells of several vertebrate species. Because of the possible significance of c-mos sequences in normal development and malignant transformation induced by physical or chemical agents, we have examined the state of integration, methylation, and transcriptional activity of c-mos sequences in a variety of normal rodent tissues, normal cell lines, or cell lines transformed by radiation or chemical carcinogens. DNA-DNA hybridization, utilizing the Southern blotting technique and a plasmid-derived DNA probe representing the v-mos sequence, gave no evidence for rearrangements of the c-mos sequence in the DNAs obtained from these diverse cell types. Parallel studies employing the restriction enzyme isoschizomers HpaII and MspI indicated that in all of these cell types the c-mos sequences were heavily methylated. In addition, analysis of cellular RNAs by blot hybridization with the v-mos probe failed to detect evidence of transcription of the c-mos sequences in any of these cell types. This was in contrast to a Moloney sarcoma virus-transformed cell line in which we found that the integrated v-mos sequence was both undermethylated and extensively transcribed. Thus, it would appear that c-mos sequences do not play a role in the transformation of rodent cells by chemical or physical agents, although the possible role of other endogenous onc sequences remains to be determined.

Studies on dissociation and reconstitution of nuclear 30-S ribonucleoprotein particles containing pre-mRNA

Treatment of nuclear 30-S ribonucleoprotein (RNP) particles containing pre-mRNA (precursor of mRNA) with 2 M NaCl leads to dissociation of RNA and protein. The protein component is present either as an aggregate with a sedimentation coefficient close to 30 S (a free informofer) or as a slowly sedimenting material (monomers or oligomers of informatin). Most of the informofers and slowly sedimenting material are in the equilibrium state. Iodination or aging of the 30-S particles stabilizes informofers. Lowering of NaCl concentration in the mixture of RNA with informofers or informatin subunits leads to reconstitution of RNP particles. In both cases, the particles formed have a sedimentation coefficient of about 30 S and a buoyant density equal to 1.4-1.41 g/cm3 but their response to pancreatic RNAase (EC 3.1.27.5) and high salt treatment is very different. Both the particles reconstituted from RNA and informofers and the original particles are very sensitive to pancreatic RNAase and after high salt treatment free informofers are formed. In contrast, the RNA of the particles reconstituted from slowly sedimenting material is much more protected against pancreatic RNAase action. These particles are also rather stable to high salt treatment. Thus, only if a protein in the form of an informofer aggregate is used, faithful reconstitution takes place. The data obtained are discussed in terms of the structure of the nuclear ribonucleoprotein particles containing precursor of messenger RNA.

Sequences hybridizing to mRNA, oligo(dT) and dsRNA from pre-mRNA are contiguous in the cloned mouse DNA fragments

Fragments from the DNA of mouse embryos produced by restriction endonucleases HindIII were cloned in pBR322 plasmid and examined for the ability to hybridize in situ with [32P] labeled cDNA synthesized from the polysomal poly(A)+mRNA template. Several of the selected clones were examined for the presence of specific sequences inside the cloned mouse DNA fragments by the blotting procedure of southern [1]. The data obtained indicate that the majority of the cloned mouse DNA fragments contained sequences hybridizing with cDNA, oligo(dT) and double-stranded regions from pre-mRNA. The results of hybridization experiments and double digestion with HindIII+HaeIII endonucleases provide evidence that these sequences could be contiguous in the given restriction DNA fragments.

On the activity of RNA polymerase B in lysates from Ehrlich ascites cells

Transcription by endogenous RNA polymerase B in lysates of Ehrlich ascites cells was investigated. The enzyme exhibits two salt optima at 0.025 M and at 0.3 M (NH4)2SO4 respectively. Preincubation of the cells with the nucleoside analogue 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole results in an inactivation of the polymerase molecules active under condition of low salt. This indicates two functional states of the enzyme in vivo. Initiations of RNA chains by polymerase B do not occur in vitro as judged by the incorporation of [beta-32P]GTP. Thus the two functional states seem to be both elongating polymerase molecules. Polymerase B does not occur in the lysates in a state ready to initiate on an exogenous template, in contrast to polymerase A and C which do occur in free form. Pretreatment with dichlororibofuranosylbenzimidazole in vivo does not result in an accumulation of free polymerase B.

The relationship between hnRNA+-poly(A) and mRNA+-poly (A) in non-dividing human lymphocytes. Evidence for distinct synthetic pathways for mRNA precursor- and nonprecursor-hnRNA

The processing of hnRNA+-poly(A) to mRNA+-poly(A) has been studied in resting lymphocytes from human peripheral blood. In pulse-chase experiments, two types of hnRNA+-poly(A) have been distinguished: the first is labeled predominantly with exogenous radioactive precursors supplied during the pulse, and the second incorporates primarily scavenged labeled precursors made available during a chase incubation. When the disappearance of both types of hnRNA+-poly(A) was quantitatively compared with the appearance of stable and labile mRNA+-poly(A), only 10% of the anticipated cytoplasmic material was actually obtained. Statistically, 90% of the poly(A)-bearing hnRNA molecules processed were degraded. The two types of hnRNA+-poly(A) were found to be functionally different. Pulse-labeled material was processed to poly(A)-bearing mRNA; "chase-labeled" molecules did not leave the nucleus and never served as precursors for cytoplasmic mRNA. The data fit a model in which there are distinct pathways for mRNA precursor- and nonprecursor-hnRNA+-poly(A).

The structural organization of nuclear pre-mRNA. II. Very long double-stranded structures in nuclear pre-mRNA

High molecular weight nuclear pre-messenger RNA (pre-mRNA or hnRNA) isolated from Ehrlich ascites carcinoma cells contains besides moderately long (100--200 base pairs) snap-back double-stranded structures, also longer double-stranded structure containing at least 300--800 base pairs. Their double-stranded nature was proved by Cs2SO4 gradient centrifugation. Very long double-stranded sequences are not able to snap-back after RNA melting. While the moderately long double-stranded RNA (dsRNA) is renatured at C0t1/2 approximately equal to 5-10(-4), the very long dsRNA shows a higher complexity (C0t1/2 approximately equal to 2-10(-2). They also hybridize to less reiterated class of DNA than moderately long dsRNA. Two classes of dsRNA are represented by different sequences as followed from cross-renaturation experiments. Very long dsRNA forms stable hybrids with 20% of total poly(A)+mRNA of cytoplasm. The properties of different classes of ds structures present in nuclear pre-mRNA are compared and their possible nature is discussed. The presence of very long dsRNA may reflect either the symmetric transcription of structural genes, or the transcription from those DNA sequences which are complementary to each other but located in different parts of the genome.

Intermolecular duplexes in heterogeneous nuclear RNA from HeLa cells

Rapidly sedimenting hnRNA complexes contain regions of stable intermolecular duplex. Disruption of such complexes, as judged by a reduction in sedimentation rate, requires conditions sufficient to denature the duplex regions. Rapidly sedimenting molecules reappear only when the complementary sequences reanneal-that is, the formation of such complexes is dependent upon time and the concentration of homologous RNA. These experiments lead us to the conclusion that rapidly sedimenting hnRNA complexes consist of two or more largely single-stranded RNA molecules held together by short duplex regions. Precisely such structures have been visualized in the electron microscope. Rapidly sedimenting fractions of native nuclear RNA from preparative sucrose gradients consist primarily of large, multi-molecular complexes interconnected by duplex regions averaging 300 base pairs in length. Exposure of the RNA to severely denaturing conditions eliminates such complexes. Reannealing of the RNA reconstitutes complexes which are indistinguishable from those observed in preparations before denaturation.

Comparative studies on the '5'-cap' and in vitro translational activity of cytoplasmic and nuclear poly A(+) RNA1

The translational activities of cytoplasmic poly A(+)RNA of normal rat liver and Novikoff hepatoma cells in the wheat germ cell free system were found to be approximately 15-20 times greater than tose of the corresponding nuclear poly A(+) RNA. The translationsl activities were 85 and 62 pmoles 3H-leucine incorporated/micron g cytoglasmic poly A(+) RNA for the liver and tumor respectively and 3-4 pmoles 3H-leucine incoporated/micron g nuclear poly A(+)RNA. Inasmuch as intergity of the '5'-cap' of mRNA is essential for its translational activity, quantitative comparisons were made of its content in these RNA fractions. Of the total 32P incorporated into the tumor cytoplasmic poly A(+) RNA, 0.41% was in the '5'-cap'; in nuclear poly A(+) RNA, the '5'-cap' contained 0.11%. After periodate oxidation and labeling with KB3H4, m7 guanosine, the 5'-terminal nucleoside in both liver and Novikoff hepatoma nuclear poly A(+) RNA contained approximately 20% as much isotope as in the cytoplasmic poly A(+) RNA. These results suggest the lower translational activity of nuclear poly A(+) RNA is partly related to its lower content of the '5'-cap'. Molecular selection of poly A(+) RNA for transport out of the nucleus or further cytoplasmic processing may account for the higher percentage of the '5-cap' and the greater translational activity of the cytoplasmic poly A(+) RNA. During these studies, it was also found that the m7 guanosine of the '5'-cap' was not removed during translation of the mRNA in the wheat germ system; this result suggests that the '5'-cap' may associate with allosteric binding sites of initiation factor(s).

Conformational states of 18 S rRNA from HeLa cells detected by gel electrophoresis

Gel electrophoretic analysis has been used to study some of the conformational properties of 18 S rRNA from HeLa cells. After isolation and treatment by heat or denaturants, the mobility of the RNA in 3% acrylamide/0.5% agarose composite gels was found to be altered; often there were two or more distinct components. Several of these forms could be interconverted by heating to 40 degrees C or by use of dimethyl sulfoxide. Although these comformers were easily distinguishable (by their electrophoretic properties), their melting profiles were very similar. Only a single electrophoretic form was detected when electrophoresis was performed at 40 degrees C. The conformational differences observed are probably derived by variations in base pairing and stacking that result when the parent form is cooled.

Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences

Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...

A model for cytoplasm-governed gene regulation

A model of cytoplasm-governed transcription is presented. The nuclear membrane has a selective permeability towards nuclear pre-mRNA molecules which are provided with group-specific non-translated "passwords". RNA transcription on the chromatin proceeds under a dual control. One of them is gene regulation according to the Britten-Davidson and Georgiev models. The other is cytoplasm-governed regulation mediated through the selective transport of mRNA from nucleus to cytoplasm. Pre-mRNA molecules which are not "in immediate demand" by the cytoplasm and therefore accumulating the nucleus repress their own synthesis by end-product inhibition. The interrelationship of the two types of regulation in the course of cell development is discussed.

Estrogen-induced changes of ribonucleic acid in the rat uterus

The incorporation of [3H]uridine into uterine RNA of immature rats was studied up to 6 h after a single injection of estradiol. Under these experimental conditions, estradiol progressively increased the incorporation of the radioactive precursor into the total RNA. This increase could not be explained by variations in the uptake of [3H]uridine by the tissue. The total RNA and the fractions obtained by differential thermal extraction were analysed by gel electrophoresis. One hour after hormone treatment, a similar increase of incorporation of the labelled precursor in the different RNA species was observed. After a long period of time, [3H]uridine was preferentially incorporated into rRNA as compared to HnRNA and to heterogenous cytoplasmic RNA. Experiments which involved the use of low doses of actinomycin D sufficient to inhibit any rRNA synthesis, confirmed the relatively slight increase in precursor incorporation into non-ribosomal RNA. The distribution of the radioactivity incorporated into the 3 fractions of RNA, obtained by thermal extraction (2 nuclear fractions and 1 cytoplasmic), suggested an increase in the rate of transcription and transport of the RNA during hormonal treatment. The polyA-containing uterine RNA was isolated on a column of oligo(dT)-cellulose and subsequently studied by electrophoresis. There is no preferential incorporation of precursor into the polyA-containing RNA when compared with the total RNA. However, the polyA-containing RNA constitutes the only part of the non-ribosomal RNA whose synthesis continues to increase throughout the period of hormone treatment.

The existence of triphosphorylated 5'-ends in virus-specific RNA isolated from SV-40 transformed cells

The question about the nature of promoters in the transcriptional units containing SV-40 sequences in transformed cells was analyzed. It was found that the pulse-labeled RNA hybridizing to SV-40 DNA contains small but significant amounts of triphosphorylated 5'-ends detected as pppGp in alkaline hydrolyzates of this RNA. In another series of experiments the fragments of RNA containing triphosphorylated 5'-ends about 100 nucleotides in length have been isolated by hydroxyapatite chromatography. Some of them form hybrids with SV-40 DNA. The conclusion is drawn that at least some of SV-40 promoters are used for transcription initiation in SV-40 transformed cells.

The structural organization of nuclear messenger RNA precursor. I. Reassociation and hybridization properties of double-stranded hairpin-like loops in messenger RNA precursor

The hybridization and renaturation properties of double-stranded hairpin-like loops isolated from giant nuclear messenger RNA precursor of mouse liver or ascites carcinoma cells were studied. About half of the hairpins in messenger RNA precursor appear to contain similar sequences, as indicated by the very fast kinetics of renaturation of the denatured double-stranded RNA sequences. These sequences have no tissue specificity. About one third of the hairpin sequences can hybridize to messenger RNA. It is suggested that the long hairpins in messenger RNA precursor play the role of sequences separating messenger RNA sequences from non-informative sequences and that these hairpins are recognized by processing enzymes.

The transcripts of Balbiani rings from Chironomus thummi. Giant RNA molecules with messenger characteristics

Experimental results on the transcription of Balbiani rings BR 1 and BR 2 of Chironomus thummi salivary gland chromosomes are presented. The DNA of Balbiani ring 2, which is the most active puff in larvae, is transcribed into large RNA molecules of about 22 X 10(6) D which resist degradation by heating, formamide or urea treatment. The asymmetrical distribution of electrophoretic profiles of BR 2 RNA and the appearence of a symmetrical BR RNA peak in the nucleoplasm suggest the synthesis of (mainly) one RNA fraction in BR 2. The gel electrophoretic patterns of BR 1 RNA are, on the other hand, characterized by the appearance of two main fractions of high molecular weight RNA, one of which corresponds in molecular weight (about 22 X 10(6) D) to BR 2 RNA. The second RNA fraction is significantly smaller in molecular size (molecular weight: about 10 X 10(6) D) and, like the 22 X 10(6) D RNA fractions of the two Balbiani rings, resistant against heating in 8 M urea. Binding to poly (U) sepharose of a significant part of Balbiani ring RNA suggests the existence of poly (A) and/or oligo (A) sequences in the Balbiani ring RNA. -- In situ hybridization of BR RNA to the salivary gland chromosomes reveals accumulation of silver grains over the Balbiani ring regions only and demonstrates the restriction of BR DNA sequences to the corresponding Balbiani ring.

Effect of 2-allyl-2-isopropylacetamide on poly(adenylic acid)-containing ribonucleic acid

A single administration of 2-allyl-2-isopropylacetamide, a porphyrinogenic drug, enhanced the 32P-labelling of nucleoplasmic as well as cytoplasmic poly(A)-containing RNA in rat liver. The synthesis of total microsomal RNA is only marginally increased under these conditions. The drug enhances the labelling of a variety of cytoplasmic poly(A)-containing RNA species, and this effect is counteracted by the simultaneous administration of haemin. 2-Allyl-2-isopropylacetamide also enhanced the release of RNA from the nucleus to the cytoplasm.

Size of primary transcripts in Ehrlich ascites cells as measured by tetraphosphate determination

A method for the quantitation of 5"-tetraphosphate ends in 32P-labeled RNA has been developed. The tetraphosphate content of different RNA fractions obtained from Ehrlich ascites cells labeled with 32P for different lengths of time has been determined. Ribosomal RNA and poly(U)-binding RNA, labeled for long periods, (mRNA) lack 5'-terminal tetraphosphate. 5S RNA, pulse labeled 4-5S RNA, and poly(U)-binding hnRNA (heterogeneous nuclear RNA) do contain tetraphosphate. From the amount of the tetraphosphate, molecular weight data can be calculated for these RNA fractions which agree with independent determinations by denaturing gel electrophoresis. The results demonstrate that the majority of the poly(A) containing hnRNA molecules are small (less than 28S) and contain the tetraphosphate of the primary transcript. Therefore, they do not originate from the 3'-end of large molecules by processing events.

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.

Direct demonstration of a complementarity between mRNA and double-stranded sequences of pre-mRNA

The total poly(A)-containing mRNA from mouse liver or Ehrlich ascites carcinoma cells was annealed with denatured ds RNA prepared from heavy nuclear 3H-labeled pre-mRNA of the same tissue. The hybrids formed were detected by binding of complexes to poly(U)-Sepharose columns through the poly(A) of mRNA. With this technique, about 30% of labeled ds RNA was bound to poly(U)-Sepharose after annealing it with an mRNA excess. The proportion of hybrid material detected by RNase treatment was two to three times lower than that obtained by poly(U)-Sepharose binding. The length of the RNase-stable acid precipitable hybrid material consisted of heterogeneous sequences of 10-100 nucleotides long when cytoplasmic, and 10-60 nucleotides long when polysomal mRNA was used in the hybridization reaction. The results obtained show that at least some of the mRNA molecules contain sequences complementary to one of the branches of the pre-mRNA hairpins. These results are compatible with the idea that the hairpin-like sequences in pre-mRNA are localized between mRNA and the non-informative part of the precursor molecule.

Precursor mRNA from erythroid-enriched bone-marrow cells of the rabbit. Electron microscope investigation of precursor mRNA molecules, molecular weight about 1.7 X 10(7), containing mRNA-like structures at one end

Precursor mRNA (pre-mRNA) molecules, sedimenting at greater than 45 S, from erythroid-enriched bone marrow cells of the rabbit and hemoglobin mRNA molecules from rabbit reticulocytes were investigated by electron microscopy. Four of 98 measured pre-mRNA molecules had a length between 15 and 17.1 mum. In some of the pre-mRNA molecules a characteristic condensed structure was observed at one end, strikingly resembling the structure of the mRNA molecules.

Polyadenylation of RNA in vitro in isolated chromatin and nuclei

Poly(A) is added post-transcriptionally to RNA transcribed in vitro by endogenous form B DNA-dependent RNA polymerase bound to the template in isolated nuclei or chromatin. It is also added to processed fragments of the products from alpha-amanitin-resistant RNA polymerases A and/or C. The poly(A) segments are of similar size to those found in nuclear RNA pulse-labelled in vivo and are added onto the 3' terminus of RNA chains (whether pre-existing, completed during the incubation in vitro or created by fragmentation of larger RNA transcripts). That poly(A) addition is not directly mediated by any of the nuclear DNA-dependent RNA polymerases is shown by the differential sensitivities of RNA and poly(A) syntheses to increasing ionic strength and transcriptional inhibitors such as the exotoxin from Bacillus thuringiensis.

Methylated constituents of heterogeneous nuclear RNA: presence in blocked 5' terminal structures

A substantial portion of the hnRNA of mouse L cells contains internal residues of N6-methyl adenylate and blocked 5' terminal sequences which are apparently of the type m7G5' ppp5' YmpZp..., in which 7-methyl guanosine is joined by a 5'-5' pyrophosphate linkage to a 2'-0-methylated residue, Ym. These sequences are indistinguishable from those comprising one of the two classes of blocked 5' sequences found in mRNA, and are quite distinct from those comprising the other class. The remarkable similarity in 5' terminal methylated sequences of hnRNA and a major fraction of mRNA appears to extend even to the relative occurrence of each of the four 2'-0-methylated species in position Ym.

Rat hepatoma cells nucleolar DNA. II. A possible model of nucleolar DNA organisation

A model of nucleolar DNA organization has been established. Three clearly defined main components are found in ascites hepatoma cell nucleolar DNA by CsCl gradient analysis. A linear arrangement for nucleolar DNA and a model of DNA organization in the neighbourhood of a set of ribosomal genes, which may play a fundamental role in the elaboration of nucleolar chromatin tertiary structure, are presented.

Salt dissociation of nuclear particles containing DNA-like RNA. Distribution of phosphorylated and nonphosphorylated species

Electrophoresis of proteins from nuclear particles containing DNA-like RNA gave a pattern with 45 bands. The possibility that some of these proteins arose by contamination with ribosomes, chromatin, or soluble nuclear proteins was examined and eliminated. The fate of the proteins of the particles was studied after partial dissociation with 0.25 and 0.70 M NaCl. The individual proteins were released progressively and in different quantities. A group of easily released species (75 and 95% removed with 0.25 and 0.70 M NaCl) was demonstrated. This group contained 8 species between 29,000 and 39,000 daltons which represented approximately one-half of the total number of molecules. It is suggested that they are bound to repetitive sequences of the RNA. At least 30 and 60% of the other proteins were released at 0.25 and 0.70 M NaCl, respectively. There were no specific proteins tightly bound to the RNA, unless the nature of the remaining species is different from that of the released ones of the same molecular weight. The phosphorylated proteins were more tightly bound to the RNA than the nonphosphorylated species of similar molecular weight. In several instances, the 32-P radioactivity was associated with quantitatively minor bands of proteins.

Modified nucleosides and bizarre 5'-termini in mouse myeloma mRNA

Messenger RNAs from mouse myeloma cells contain N-6-methyl adenosine and novel 5' termini having 7-methy-guanosine in a 5', 5' triphosphate linkage with ribose-methylated nucleosides. Ten common 5'-terminal sequences of the forms m-7-G-5'-PPP-5'-NmpNp and m-7-G-5'-ppp-5'-NmpNmpNp are reported. Structures like this may be a general feature of mRNA in eukaryotes.

Effects of gamma-irradiation on biosynthesis of different types of ribonucleic acids in normal and regenerating rat liver

1. The effect of gamma-irradiation (4000rd) on the synthesis of ribosomal (pre-rRNA) and heterogeneous nuclear RNA (pre-mRNA) in normal and in regenerating rat liver was studied by using 40 min labelling with [6(-14)C]orotic acid. 2. Partial hepatectomy caused a sharp transient increase in the specific radioactivity of the endogenous low-molecular-weight RNA precursors in the livers of both normal and irradiated rats. Irradiation of intact animals did not affect the pool. 3. Irradiation enhanced the synthesis of pre-rRNA for at least 12h. The synthesis of pre-mRNA was also enhanced, but only in the first 3h after irradiation. 4. Partial hepatectomy strongly stimulated the synthesis of both pre-rRNA and pre-mRNA. 5. The synthesis of pre-rRNA was enhanced also in regenerating liver of animals irradiated before or after the operation. The conclusion can be drawn that the early increase in the synthesis of ribosomal RNA is a non-specific cellular response to different injuring factors. 6. The only case where irradiation caused an early inhibition of RNA synthesis was that of pre-mRNA in regenerating liver. This supports the hypothesis that ionizing radiation does not suppress the transcription per se but affects the mechanisms of activation of new genes (cellular programming).

Transcription of fractionated mammalian chromatin by mammalian ribonucleic acid polymerase. Demonstration of temperature-dependent rifampicin-resistant initiation sites in euchromatin deoxyribonucleic acid

The chromatin fractionation method of Frenster et al. (1963) as modified by Leake et al. (1972) was used to prepare fragments of euchromatin from rat liver nuclei. These remain soluble in 5mm-MgCl(2), and contain DNA of maximum mol.wt. 1x10(6)-2x10(6). The fragments were separated from condensable chromatin on a sucrose gradient. Euchromatin contains endogenous DNA-dependent RNA polymerase, and most of the nascent RNA labelled in vivo or in vitro. Euchromatin fragments allow initiation of transcription by added purified rat liver form-B RNA polymerase and contain temperature-dependent rifampicin-resistant initiation sites for the form-B enzyme. These findings indicate that transcription of the euchromatin regions of interphase chromosomes is not initiated in condensed chromatin, but is initiated within the euchromatin stretches. Condensable chromatin also contains most of these activities, but is not associated with nascent RNA.