Nucleic Acids Research Volume 3 no.6 June 1976 Globin mRNA contains a sequence complementary to double-stranded region of nuclear pre-mRNA. Aleksei P. Ryskov, Olga V.Tokarskaya, Georgii P.Georgiev, Charles Coutelle* and Berndt Thiele* Institute of Molecular Biology, Academy of Sciences of the USSR, Moscow, USSR ABSTRACT 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. INTRODUCTION It was previously shown that the cytoplasmic mRNA from mouse liver or Ehrlich carcinoma cells could form RNAase-stable hybrids with melted ds RNA sequences 1 2 prepared from a nuclear pre-mRNA (hnRNA) ' . About 20 per cent of the ds RNA sequences were involved in a hybridization reaction. It was suggested that the double-stranded hairpin-like structures formed the border-lines between mRNA sequences and the non-informative part of the pre-mRNA.. In the course of processing, part of the ds region would be destroyed resulting in the separation of the mRNA. A part of one branch of ds RNA would remain bound to mRNA and could hybridize with the ds RNA from pre-mRNA . In this paper, similar experiments were made with the individual mRNA (globin mRNA) using different techniques of hybrid detection. The results obtained are similar to those described earlier with total mRNA of mouse cells. The size of the hybridized ds RNA sequences in the complexes of mRNA with ds RNA was determined. MATERIALS AND METHODS Isolation of pre-mRNA. On the 5th day of recovery from phenylhydrazine anaemia an enrichment with nucleated erythroid cells up to 70% can be obtained in the bone marrow 4 of rabbits, using partial in vivo synchronization . The cell suspension enriched in 3 erythroid precursor-cells was incubated for 15 min at 37°C with H uridine (0.85 mCi © Information Retrieval Limited 1 Falconberg Court London W1V5FG England 1487 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 Received 8 March 1976 Nucleic Acids Research /2-10 9 cells, specific activity, 20-30 Q/mmole, UWVR, Praha, CSSR), and nuclear RNA was subsequently extracted by the hot phenol fractionation method . According to this method, pre-rRNA is obtained in the 40°C fraction and pre-mRNA in the fractions extracted above 55°C . 65°Cand 85°C fractions were combined and ultra- centrifuged through a 12 ml linear 5-20% (w/v) sucrose gradient in a buffer containing lOmM Tris-HCl (pH8), 0.1 M Nad, 1 mM EDTA, 0.5% SDS in the Spinco SW 40 The fraction were collected, the aliquots were analyzed and all fractions heavier than 35S were pooled and precipitated with ethanol. Isolation and purification of ds RNA. Pre-mRNA dissolved in 2xSSC was treated with a mixture of pancreatic RNAase (Sigma) and TT RNAase (Galbiochem) as described previously . After incubation, the mixture was treated with pronase (Reanal, 100 fjg/ml), applied to a Sephadex G-75 column (1x80 cm) and eluted with 0.2M sodium acetate buffer . Only the material eluted in the void volume was collected, and treated again with pronase (100 ug/ml) at 25° for 30 min. Thereafter SDS was added to 1% and the mixture was shaken with phenol for 30 min at 60°C. The water phase was treated with a mixture of phenol-chloroform (1:1 v/v) and chloroform at room temperature and the material was precipitated with ethanol in the presence of carrier tRNA. This procedure completely frees ds RNA samples from RNAase contamination. Isolation of globin mRNA of rabbit. Globin 9S mRNA of rabbit reticulocytes was Q isolated according to the technique described by Evans and Lingrel from polysomal RNA by two cycles of ultracentrifugation in sucrose gradients followed by two cycles of chromatography of the material in the 9S peak on poly(U)-Sepharose 4B (Pharmacia). The procedure for producing a phenylhydrazine-induced anemia in rabbits and for 9 preparing a lysate of the reticulocyte rich blood was described previously . Total poly(A) RNA of rabbit liver was isolated from total cytoplasm or from polyribosomes 9a free from cytoplasmic informosomes and monoribosomes as described elsewhere . Reassociation of denatured ds RNA. ds RNA was dissolved in a small volume of water and denatured by heating in small teflon tubes. One tenth of the volume of 20xSSC was added and the samples,5 to 10 pl,(10OO-2000 cpm radioactive material) were incubated at 65°C for the time necessary to obtain the appropriate Cot value. To calculate the Q)t value, it was assumed that the specific radioactivity of ds RNA was equal to that of heavy pre-mRNA. After annealing, the samples were diluted with 2xSSC and the proportion of RNAase-stable acid insoluble radioactive material was 1488 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 rotor at 23°. Nucleic Acids Research estimated as described elsewhere 10 . In control experiments, the proportion of RNAase-stable material without annealing of denatured ds RNA was determined. Hybridization experiments. For hybridization, ds RNA was melted by heating; about 1000 cpm (~0.02 (jg) of radioactive material was taken, mixed with mRNA and annealed in 2xSSC at 65° for different time intervals to make ds RNA-driven -4 -4 Cot equal to 1x10 to 3x10 . The proportion of acid-insoluble radioactive For prepar- ative isolation of hybridized sequences, aboutlO.OOO to 15,000 cpm of melted radioactive ds RNA (with specific activity 50,000 cpm/^ig) was mixed with 600 pg of globin mRNA and annealed in 3 ml of 2xSSC at 65° for 12 min. At the end of the annealing, 30 pg of pancreatic RNAase (Sigma) were added and the mixture was incubated for 30 min at room temperature. to stop the reaction. 200 pg of pronase (Reanal) were added The RNAase-resistant material was deproteinized with 0.5% SDS and phenol at 60°C with a mixture of phenol+chloroform (1:1 v/v), with chloroform at room temperature and then precipitated with ethanol in the presence of tRNA as carrier. The precipitated material was dissolved in water, denatured by heating and used in electrophoretic experiments. In control experiments, the same procedure was applied to the same amount of ds RNA annealed without mRNA under the same conditions. Detection of hybrid complexes on poly(U)-Sepharose. Hybridization mixture containing melted ds RNA and globin mRNA was annealed as described above and applied to a poly(U)-Sepharose 4B (Pharmacia) at room temperature in 0.4 M Nad -0.01 M EDTA - 0.01 M Tris-HCl (pH 7.5) - 0.2% SDS (buffer 1). The column was washed with the same buffer and the bound material eluted with the buffer 1 lacking NaCl (buffer 2) at 50°C. The acid-insoluble radioactive material was collected on Millipore or fiberglass filters and counted in a toluene scintillator. In control experiments, the same procedure was applied to ds RNA alone, to ds RNA mixed with globin mRNA just before chromatography without annealing, and to ds RNA annealed with a vast excess (40 to 80 ug) of tRNA or commercial poly(A) (Reanal). Polyacrylamide gel electrophoregis of RNA. RNA samples were analysed on poly- acrylamide gel using a modification of the Loening method as described in the legend tc fig.4. Electrophoresis in formamide was carried out according to Hnder e t a l . 1 . 5S ribosomal 4S transfer, i tRNA a (20 nucleotides long) and oligo(U)10 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 material stable to RNAase was determined as described previously . Nucleic Acids Research were used as markers. The gels containing non-labeled markers were stained with "Stains All" (Eastman-Kodak). The gels containing radioactive material were sliced into 2 mm fractions, dissolved in "Tissue solubilizer" (Amersham/Searle) or in "Aquasol" (New England Nuclear, Boston, Mass.) and counted in toluene. RESULTS Characterization of ds RNA prepared from pre-mRNA of rabbit bone marrow cells. fractionation procedure , and the ds sequences were prepared from the high-molecular weight fraction of pre-mRNA as described previously . It should be pointed out that 300 3- 200 20 30 Slice No Fig. 1. Polyacrylamide gel electrophoresis in formamide of the melted ds RNA from pre-mRNA of rabbit bone marrow cells, ds RNA was isolated, purified and melted as described in Material and Methods. The gels contained 12%acrylamide, with a ratio of acrylamide to bisacrylamide of 30 : 1 in de-ionized formamide containing 0.02 M diethylbarbituric acid (pH 9.0). Seven cm gels were prepared and allowed to polymerise for 2 hr at room temperature. RNA samples in 98% formamide were heated at 95°C for 2 min, chilled and applied to the gels. Electrophoresis was performed at 100 V for 5 hr at 24° C with an electrode solution of 0.02 M sodium chloride. The direction of migration was from left to right, and the position of non-labeled markers run in the parallel gel are indicated by the arrow. 1490 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 Nuclear pre-mRNA was isolated from bone marrow cells using the hot phenol Nucleic Acids Research a loop in the hairpin is digested by RNAase during ds RNA isolation and therefore the melting converts ds RNA into single-stranded RNA. These ds RNA sequences were characterized in respect to size and renaturation kinetics. Fig.l shows that the melted ds RNA from bone marrow cells displays a rather heterogeneous distribution upon polyacrylamide gel electrophoresis with a maximum in the region of chains of 80-150 nucleotides long. It was also observed that during of melted ds RNA did not decrease (data not shown). Kinetic studies on the renatura- tion of the melted ds RNA (fig 2) showed that about 20% of the sequences (in different -4 -2 experiments from 15 to 25%) renature at low Cot values from 10 to 2x10 , while the rest of the material renatures at higher Cot values. 2 These results are quite similar to those obtained with mouse liver and carcinoma ds RNA. One can conclude that about 20% of total ds RNA is represented by a material which is rather homogeneous in sequence and consists of ds RNA of one or a few kinds. From data represented in fig.2, the conditions for the hybridization reaction were chosen. 3 o £ «f a Fig.2. The renaturation curve of denatured ds RNA from pre-mRNA of rabbit bone marrow cells, ds RNA was isolated, purified, melted and renatured as described in Materials and Methods. 1491 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 short incubation under hybridization conditions (1-2 hr at 65°C), the molecular weight Nucleic Acids Research The ds RNA Cot was chosen sufficiently low (1-3)K10 -4 Hybridization of melted ds RNA with globin mRNA. , to minimize its renaturation. Unlabeled globin mRNA was prepared from rabbit reticulocytes in the usual way by polysome pelleting, isolation of polysomal poly(A) RNA followed by purification of 9S poly(A) RNA. electrophoretically pure. This RNA was It can be completely bound to poly(U)-Sepharose and programmes globin synthesis in a heterogeneous cell-free system . formation was detected using two techniques (table 1). The first one was the detection of RNAase-stable material. In control experiments which werecarried out in the absence of mRNA, 5 to 10 per cent of the melted ds sequences were RNAase-stable under the conditions used. The addition of mRNA immediately followed by RNAase treatment did not increase the amount of RNAasestable material while after annealing with mRNA, the amount of RNAase-stable 3 material increased significantly. For an mRNA/ds RNA ratio of about 10 the difference in respect to the control figure reached 7-9%. A further increase of the mRNA/ds RNA ratio did not lead to an increase in the amount of RNAase stable material. It was observed previously that the 2 3 hybridization reaction was species but not tissue specific ' . In agreement with these data the globin mRNA of rabbit failed to hybridize with the mouse Ehrlich carcinoma ds RNA, whereas mRNA prepared from rabbit liver efficiently binds bone marrow ds RNA (Table 1). Another technique used in detecting hybrid complexes was the binding of hybrids to poly(U)- Sepharose through the poly(A)-end of mRNA. Fig. 3 demonstrates that a significant proportion of the ds RNA binds to poly(U)-sepharose after annealing with mRNA. In control experiments where mRNA was not added, the binding to poly(U)-Sepharose did not exceed 2%. The same background values were obtained when ds RNA was annealed with tRNA or with a vast excess of poly(A) or when mRNA was added to ds RNA just before passing through the poly(U)-Sepharose. The highest binding of ds RNA observed in our experiments after annealing with mRNA was 30 to 35% (Table 1). It should be pointed out that the proportion of the poly(U)-Sepharose bound material was much higher than that of RNAase- stable material after annealing under the same conditions. 1492 One may suggest that the hybrid contains the duplex region as well as Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 A mixture of an excess of globin mRNA with melted ds RNA was annealed and hybrid Nucleic Acids Research Fig.3. Detection of hybrid complexes on poly(U)-Sepharose column. About 1,000 cpm of radioactive material of melted ds RNA was passed through a 0.5 ml poly(U)Sepharose column after annealing with 75 pg of globin mRNA (-O-), or alone (-A-) as described in Materials and Methods. mRNA driven Cot was about 9 at mRNA/ds RNA ratio of 6500(w/w). Table 1 Hybridization of ds RNA sequences with mRNA Nature of RNAs used In hybridization reaction Rabbit bone marrow ds RNA + rabbit globin mRNA Exp.N 0 Ratio of mRNA to ds RNAa (w/w) ds RNA sequences . hybridized(per cent total ) 1 2 3 4 1.3x10^ 1.3x10, 6.3x10^ 6.3x 10 5 6 6.3x10, 6.3x 10 37 11 7 8 6.3x10, 6.3 x 10 17 30 9 1.8 x 10 1 RNAase 10 1.5 x 104 1.5 RNAase 6 7 9 28 3 Rabbit bone marrow ds RNA + rabbit liver mRNA Mouse carcinoma ds RNA + rabbit globin mRNA Mouse liver ds RNA + rabbit globin mRNA Technique used for analysis RNAase RNAase RNAase poly(U)-Sepharose binding - "- "-"-"RNAase poly( U)-Sepharose binding In the majority of experiments ds RNA-driven C^t was about 3 x 1 0 (it was calculated on the basis of specific radioactivity of pre-mRNA, from which ds RNA was isolated). In exp.N°5 the ds RNA-driven Cot was 5 dmes higher than in the other experiments. Background equals to 5-10% of total counts in the RNAase experiments, and 2% in the poly(U)-Sepharose binding experiments. The background was detected in each experiment and siijtracted from the total counts obtained (see also the reassociation curve in Fig.2, and the control curve in Fig.3). 1493 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 Fraction A/o Nucleic Acids Research the unpaired tail of ds RNA. Such an interpretation is supported by the fact that RNAase treatment of the hybrid bound to the poly(U)-Sepharose column, digests from 30 to 75% of the labeled material. The size of ds RNA-mRNA hybrid. The size of the hybridised sequence originated from ds RNA was determined using polyacrylamide gel electrophoresis. RNA, 5S ribosomal RNA, one quarter tRNA a and oligo(U) Transfer were used as markers. narrow peak in the region of chains of about 30 nucleotides long. Undigested material (original melted ds RNA or RNA eluted from the poly(U)-Sepharose column) as was mentioned above, was located with chains 80-150 nucleotides long. The same location (in the region of sequehces of 80-150 nucleotides long) was observed for 200 E ex. j •3 100 o o 4 10 20 Sties Ho Fig.4. Polyacrylamide gel electrophoresis of the sequence of ^H-labeled ds RNA hybridized with non-labeled globin mRNA. Preparative isolation and purification of hybridized sequences was performed as described in Materials and Methods. The gel contained 15% acrylamide, with a ratio of acrylamide to bisacrylamide of 375 : 1 in 0.09 M Tris-borate buffer (pH 8.3) containing 2 mM EDTA. Seven cm gels were prepared and allowed to polymerise for 1 hr at room temperature. RNA samples in distilled water were heated at 95°C for 2 min, chilled and applied to the gels. Electrophoresis was performed at 100 V for 1.5 hr at 24°C. The direction of migration was from left to right, and the positions of non-labeled markers run in the parallel gel are indicated by the arrows. 1494 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 One can see from Fig.4 that the RNAase-stable material migrates as a rather Nucleic Acids Research RNAase-stable material of ds RNA annealed without mRNA (data not shown). Therefore all values used in Fig.4 were obtained after substracting this background. DISCUSSION The results presented in this paper demonstrate the existence of a short (~ 30 nucleotides long) region in the double-stranded hairpin-like sequence of pre-mRNA which is complementary to a portion of the globin mRNA. In our previous study it was shown length of the complementary sequences was heterogeneous, varying from 10 to 60 nucleotides . The following hypothetical scheme could be drawn from this result as 2 3 13 well as from the previous data obtained with total mRNAs ' ' (Fig. 5). We suggest that in the giant pre-mRNA,a long hairpin structure of about 100-150 base 100-200 tase p r fy( ve fxnt 30 6a%t m t mRNA sequence | | FH VNA I Release of mRNA and | /Wotare t mRNA Fig. 5. A hypothetical model for the localization and functioning of double-stranded regions of pre-mRNA as a "separator" of mRNA from non-informative part of the precursor. 1495 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 that polysomal poly(A) mRNA of mouse can also hybridize to mouse ds RNA, and the Nucleic Acids Research pairs is localized on the border line between the mRNA sequence and the non-informative part of the pre-mRNA. The processing enzyme recognizes the double-helical region, and destroys a significant part of the hairpin. The rest of the hairpin survives and a piece of the right branch of the hairpin about 30 nucleotides long (for globin mRNA of rabbit) remains at the 5'-end of mRNA moving with it into the 14 cytoplasm. A similar possibility is also suggested by Crippa et al. on the basis of Several points of this model should be considered. in the hairpin is unknown. First, the size of the unpaired loop It was shown previously that the mouse ds RNA could hybridize to some of the palindromes present in DNA . The size of the unpaired loop in the palindrome seems to be very small since this structure is not cleaved with DNAase 16 SI . However, it has not been proved that ds RNA in the pre-mRNA is transcribed from the palindrome itself. It could be also transcribed from the complementary sequences identical to palindromic sequences but separated by a long spacer. This question is under investigation in our laboratory. Second, it is not clear whether all, or only a few mRNA molecules contain sequences complementary to ds RNA. In our experiments, the mRNA/ds RNA ratio was 3 (1.3-6.3)xlO . Assuming that the complementary region comprises about 5% of mRNA and 15% of total ds RNA nucleotides, this ratio should be decreased to about 400 to 2000. This ratio is high enough and even if only some of the mRNA molecules have complementary sequences, hybridization should still take place. There is a possibility that further processing of mRNA leads to elimination of the rest of the hairpin in mRNA. The possible absence of the complementary sequence in most of the mRNAs could 17-18 explain the failure to find internal reiteration heterogeneity in mRNAs . To elucidate this question, detailed kinetic experiments are necessary. Third, poly(U)-Sepharose experiments showed that a high proportion of ds RNA can hybridize with mRNA.. It was higher than the content of rapidly renaturing ds RNA. This could be explained by assumption that ds RNA regions contain a short (~30 nucleotides) sequence which is common to most of the ds regions and to most of the different pre-mRNAs, while the other part of the ds region is characterized by a higher sequence heterogeneity. This possibility also has to be checked experi- mentally . 2 19 A possible role of hairpin-like loops as signals for enzymes of processing ' has found support in experiments with procaryotic systems, where it was shown that 1496 Downloaded from http://nar.oxfordjournals.org/ at Penn State University (Paterno Lib) on March 3, 2016 their experimental data. Nucleic Acids Research pre-mRNA and pre-rRNA are processed to mature molecules with the aid of RNAase 20-22 III which is specific for double-stranded RNA . A very rapid attack of the precursor molecules by the enzyme prevented detection of these precursors before the mutants containing defective RNAase became available. A similar situation may exist also in the case of eucaryotic cells. ACKNOWLEDGEMENTS V. Schick and V. Scheinker for the gift of tRNA, \ tRNAVal and oligo(U)10-. * Central Institute of Molecular Biology, Academy of Sciences of the DDR, Institute of Physiological and Biological Chemistry, Humboldt University, Berlin, GDR. REFERENCES 1 Ryskov, A.P., Limborska, S.A., and Georgiev, G.P. (1973) Mol.Biol. Reports 1, 215. 2 Georgiev, G.P., Varshavsky, A.Ja., Ryskov, A. P., and Church, R.B. (1973) Cold Spring Harbor Symp.Quant.Biol. 38, 869. 3 Ryskov, A.P., Kramerov, D.A., Limborska, S.A., and Georgiev, G.P. (1975) Molek.Biol. 9, 6. 4 Coutelle, Ch., Reineke, H.H., Steindamm, E., Meurer, W., Grieger, M., and Rosenthal, S. (in press). Haematologia (Budapest). 5 Georgiev, G.P., Ryskov, A.P., Coutelle, Ch., Mantieva, V.L., and Avakyan, E.R. (1972) Biochim.Biophys. Acta 259, 259. 6 Coutelle, Ch., Thiele, B., Ladhoff, A., Ryskov, A. P., and Papies, B. 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