Determination of nucleotide sequences from double-stranded regions of HeLa cell nuclear RNA

Double-stranded regions which comprise about 4% of isolated HeLa cell heterogeneous nuclear RNA have been characterized by RNA fingerprinting and sequencing analysis. The simplicity of the pattern in two-dimensional RNA fingerprints suggests a sequence complexity of about 1000 nucleotides. The nucleotide sequences of six prominent RNase T₁-resistant oligonucleotides (ranging in size from 7 to 9 bases) have been determined using isolated double-stranded nuclear RNA labeled in vivo with ³²P-labeled inorganic phosphate. We conclude that (here exists a substantial subpopulation of simple, potentially complementary sequences common to much of the heterogeneous nuclear RNA population and interspersed with other kinds of sequences.     

Ribonucleoprotein organization of polyadenylate sequences in HeLa cell heterogeneous nuclear RNA.

Ribonucleoprotein particles containing heterogeneous nuclear RNA (Pederson, 1974) were isolated from HeLa cells and digested with ribonucleases A and T₁ at high ionic strength. The nuclease-resistant material, comprising 9.4% of the initial acid-insoluble [³H]adenosine radioactivity, was further fractionated by poly(U)-Sepharose chromatography. The bound fraction eluted from the column with 50% formamide and banded in cesium sulfate gradients (without aldehyde fixation) at a buoyant density characteristic of ribonucleoprotein (1.45 g/cm³). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of this material revealed two Coomassie blue-stained bands. The major polypeptide had a molecular weight of 74,000 a less prominent band had a molecular weight of 86,000. The RNA components contained 74.4 mol % AMP and 17.7 mol % UMP. Polyacrylamide gel electrophoresis of the RNA, labeled with [³H]adenosine, demonstrated the presence of molecules 150 to 200 nucleotides in length (poly(A)), as well as molecules 20 to 30 nucleotides long (oligo(A)). Both poly(A) and oligo(A) sequences have previously been identified in HeLa heterogeneous nuclear RNA. These data demonstrate that both the poly (A) and oligo(A) sequences in HeLa heterogeneous nuclear RNA exist in vivo tightly complexed with specific proteins.     

The methylated nucleotide sequences in HELA cell ribosomal RNA and its precursors

The methylated nucleotide sequences in HeLa cell ribosomal RNA and its nucleolar precursors were examined by RNA fingerprinting and sequencing methods. 18 S RNA was found to contain approximately 46 methyl groups, 28 S RNA some 70 methyl groups and 5.8 S RNA one methyl group. Most methyl groups occur in different T₁ ribonuclease oligonucleotides, and most of these were recovered approximately once per molecule of 18 S or 28 S RNA. There are also, however, several multiply methylated oligonucleotides, a few short products that occur more than once and a few “fractional” products. The great majority of methylations occur at the level of 45 S RNA, but six further methylations occur late during the maturation of 18 S RNA, and one fractional one occurs during 28 S maturation. The transcribed spacer regions of the precursor molecules are unmethylated. Chemical analysis of the methylated components and sequences indicates that all except five “early” methylations are on ribose groups, the remaining five being on bases within the 28 S sequence. The late methylations are all on bases, four of those on 18 S RNA giving rise to the sequence, … Gpm₂^post6Apm₂^post6ApCp… The product, pCmpUp, previously reported by Choi &; Busch (1970) as being the 5′ end-group of rat hepatoma 28 S, 32 S and 45 S RNA, is not present in HeLa cell 28 S RNA or its precursors. Implications of this work are discussed.     

Clustering of the DNA sequences complementary to repetitive nuclear RNA of HeLa cells.

We have studied the hybridization profile of heterogeneous nuclear RNA from HeLa cells across DNA density gradients, and found that components in the high molecular weight fraction of heterogeneous nuclear RNA of HeLa cells hybridize to discrete density fractions on the light and heavy sides of the DNA. The conditions used for hybridization in this work allowed the detection of only those components in the RNA complementary to reiterated sequences in the DNA. These sequences in HnRNA are known to include double-stranded regions, which can be isolated readily. The double-stranded RNA shows a pattern of hybridization across a DNA density gradient which is similar to that of total HnRNA. It is concluded that the repeated sequences in HnRNA are complementary to clusters of repeated sequences in the DNA.     

Repetitive sequences and hairpin-like structures in giant RNA of pigeon erythroid cells

In giant molecules (>45 S) of HnRNA from pigeon bone marrow and peripheral blood erythroid cells a correlation is demonstrated between the amounts of hairpin-like structures and the sequences transcribed from the DNA repetitions. The same correlation is observed in the >45 S poly(A)⁺ and poly(A)^- subfractions.Abbreviations HnRNA heterogeneous nuclear RNA - poly(A)⁺ RNA RNA molecules containing polyadenylic acid sequences - poly(A)^- RNA RNA molecules which do not contain polyadenylic acid sequences - dsRNA double-stranded RNA - SDS sodium dodecylsulphate     

Adenovirus transcription. V. Quantitation of viral RNA sequences in adenovirus 2-infected and transformed cells.

The concentrations, in copies per cell, of viral RNA sequences complementary to different regions of the genome were determined at 8, 18 and 32 hours after infection of human cells with adenovirus type 2: separated strands of fragments of ³²P-labelled adenovirus 2 DNA, generated by cleavage with restriction endonucleases EcoR1, Hpa1 and BamH1, were added to reaction mixtures at sufficient concentrations to drive hybridizations with infected or transformed cell RNA. Under these conditions, the fraction of ³²P-labelled DNA entering hybrid is directly proportional to the absolute amount of complementary RNA in the reaction.At 8 hours after infection in the presence of cytosine arabinoside, “early” viral messenger RNA sequences are present at a frequency of 300 to 1000 copies per cell. The abundance of early mRNA sequences in different lines of adenovirus 2-transformed rat cells is markedly lower than their concentration in lytically infected cells. Moreover, the abundance of early mRNA in a given transformed rat cell line reflects the number of copies of its template DNA sequences per diploid quantity of cell DNA. After the onset of the late phase of the lytic cycle, the abundance of one early mRNA species, that coding for a single-stranded DNA binding protein required for viral DNA replication, is amplified. Viral RNA sequences complementary to regions of the genome coding for other early mRNA sequences remain at the level observed at 8 hours after infection.Exclusively “late” viral mRNA sequences are present over a range of concentrations, 500 to 10,000 copies per cell, depending on the region of the genome. By 18 hours after infection, the nucleus contains approximately three times as much total, viral RNA as the cytoplasm. The abundant nuclear, viral RNA sequences at 18 hours are transcribed from a contiguous region, 65% of the genome in length. In some cases, viral RNA sequences complementary to mRNA sequences are very abundant in the nucleus. When cytoplasmic and nuclear fractions are mixed and incubated under annealing conditions, some mRNA sequences will anneal with more abundant, anti-messenger nuclear RNA sequences to form double-stranded RNA. Such annealing of nuclear, viral RNA to early, cytoplasmic mRNA sequences probably accounts for the inability to detect, by filter hybridization, certain classes of early mRNA sequences during the late stage of infection.     

Nucleotide sequences from messenger RNA transcribed from the operator-proximal portion of the tryptophan operon of Escherichia coli

³²P-labeled messenger RNA transcribed in vivo from the operator-proximal portion of the tryptophan operon of Escherichia coli was purified by DNA/RNA hybridization. The mRNA preparations obtained were subjected to polyaerylaamide gel electrophoresis, and a number of discrete labeled bands were detected. Characterization of the labeled bands and of purified, unbanded mRNA preparations, by partial sequence analysis of the oligonucleotides obtained following T₁ and pancreatic RNase digestion, revealed that the bands represented discrete segments of the trp mRNA molecule. This observation suggests that endonucleolytic cleavage occurs in vivo at specific sites in the mRNA molecule.     

Purification of globin messenger RNA from dimethylsulfoxide-induced friend cells and detection of a putative globin messenger RNA precursor

Procedures are described that permit the detection and isolation of a specific messenger RNA as well as its precursor from total cell extracts. DNA complementary to the mRNA was elongated by the addition of dCMP residues and annealed with labeled cell RNA. The elongated DNA with RNA hybridized to it was isolated by chromatography on a poly(I)-Sephadex column. The method was used to isolate ³²P-labeled globin mRNA from labeled Friend cells, a mouse erythroleukaemic cell line, induced with dimethylsulfoxide to synthesize hemoglobin. ³²P-labeled globin mRNA isolated by this procedure was estimated to be 80% pure by hybridization analysis and sedimented as a single peak at 10 S. Partial sequences were determined for 16 oligonucleotides derived from the purified ³²P-labeled globin mRNA by RNAase T₁ digestion. The partial sequences for nine oligonucleotides corresponded to those predicted from the amino acid sequences of α and β globin; the other oligonucleotides were presumably derived from non-translated regions.In order to detect a possible precursor to globin mRNA, RNA from induced Friend cells pulse-labeled with [³²P]phosphate for 20 minutes was centrifuged through a sucrose gradient and the resulting fractions were analyzed for globinspecific sequences. Two peaks of globin-specific RNA were detected, a larger one at 10 S, the position of mature globin mRNA, and a smaller one at 15 S.     

Demonstration of the "5-8 S" ribosomal sequence in HeLa cell ribosomal precursor RNA

HeLa cell “5.8 S” ribosomal RNA was digested with T₁ ribonuclease and the digestion products were characterized. In particular several hexa-, or larger, oligonucleotides were well fractionated by T₁ ribonuclease plus alkaline phosphatase fingerprints. The sequences of these large products were determined. The same large products were identified in fingerprints of “native” 28 S RNA, that is, 28 S RNA to which 5.8 S RNA is attached. The products were demonstrably absent in fingerprints of heat-denatured 28 S RNA, which lacks the 5.8 S fragment. The oligonucleotides were present in fingerprints of 32 S RNA, whether previously heated or not. One of the largest 5.8 S oligonucleotides contains an alkali-stable (2′-O-methylated) dinucleotide, Gm-C. This product was identified in fingerprints of methyl-labelled 45 S RNA. These findings prove that the 5.8 S ribosomal sequence is present within HeLa cell ribosomal precursor RNA. In addition to the methylated nucleotide, two pseudouridylate residues were discovered in HeLa cell 5.8 S RNA.     

The nucleotide sequences of some large ribonuclease T1 products from bacteriophage R17 ribonucleic acid

A method of `fingerprinting' high-molecular-weight <sup>32</sup>P-labelled RNA species, using a two-dimensional thin-layer-chromatographic separation of ribonuclease T<sub>1</sub> digestion products, has been applied to RNA from the Escherichia coli bacteriophage R17. The `fingerprinting' technique, besides giving a unique pattern that can be used as a characterization of the RNA, has made it possible to isolate a number of the larger oligonucleotides and to determine their nucleotide sequences.     

Similarity between 5'- and 3'-terminal nucleotide sequences and double-stranded RNA-derived sequences of eukaryotic mRNA

It has been reported recently that parts of the nucleotide sequences present in the 5′- and 3′-terminal regions of cytoplasmic mRNA are derived from double-stranded hairpin structures of heterogeneous nuclear RNA—a putative mRNA precursor (Naora, 1979). In order to explore the nature of double-stranded hairpin structures, using the sequencing data of human and rabbit globin mRNA and hen ovalbumin mRNA, we examined the following possibility: that certain regions of both the 5′- and 3′-terminal nucleotide sequences of mature mRNA were present in double-stranded hairpin structures covalently linked to both sides of the message sequence in the precursor mRNA molecule and that these double-stranded hairpin structures are similar to each other. The results support the above possibility by showing substantial similarity of nucleotide sequences between the 5′- and 3′-terminal regions of these mRNAs in terms of the formation of similar double-stranded hairpin structures.     

Nucleotide sequences within the ribosomal ribonucleic acids of HeLa cells, Xenopus laevis and chick embryo fibroblasts.

Nucleotide sequences within the ribosomal RNAs of HeLa cells, Xenopus laevis cultured kidney cells and chick embryo fibroblasts were compared by “finger-fprinting” procedures, using separate preparations of ³²PO₄-labelled and [¹⁴C] methyl-labelled RNAs. The results revealed extensive similarities between oligonucleotides from the ribosomal RNAs of the three species, and also some characteristic interspecies differences. The following findings were of particular interest.