A simple and efficient method to remove ribonuclease contamination from pancreatic deoxyribonuclease preparations

Association of rapidly-labelled RNAs with actin in nuclear matrix from mouse L5178Y cells

More than 90% of rapidly-labelled nuclear RNA was associated with a nuclear matrix prepared from mouse leukemia L5178Y cells. The binding was not affected with up to 4 M NaCl; however, these RNAs were released from the nuclear matrix by treatment with a low ionic strength buffer (5 mM Tris-HCl buffer, pH 7.5, containing 1 mM ATP, 1 mM dithiothreitol, 0.2 mM ethylenediaminetetraacetic acid (EDTA) and 0.4 mM calcium chloride), without destruction of the sphere of the nuclear matrix. Actin filaments in the nuclear matrix were depolymerized with this buffer accompanied with rapidly-labelled RNAs. When the depolymerization was inhibited by slight modifications of the low ionic strength buffer (replacement of ATP by the same concentration of GTP; replacement of calcium ion by the same concentration of magnesium ion; addition of 20 micrograms/ml of phalloidine, which is a specific inhibitor of actin depolymerization), the release of rapidly-labelled RNAs from the nuclear matrix was also inhibited. The complex containing rapidly-labelled RNAs and matrix proteins was solubilized by a sonication from the nuclear matrix, and subjected to cesium chloride equilibrium centrifugation. Rapidly-labelled RNAs were concentrated on the bottom of the gradient accompanied with a small number of proteins (68K, 60K, 43K and 40K). The 43K protein was identified as actin by immunoblotting. By RNase digestion before equilibrium centrifugation, actin in the bottom fractions disappeared. These results suggest that rapidly-labelled RNAs anchor on the actin filaments in the nuclear matrix.

Transcriptional regulation of rat liver glutathione S-transferase genes by phenobarbital and 3-methylcholanthrene

The relative rates of transcription of the rat liver glutathione S-transferase Ya-Yc and Yb genes were determined in purified liver nuclei isolated at different times after phenobarbital or 3-methylcholanthrene administration. The transcriptional rates of the Ya-Yc and Yb genes were elevated approximately fivefold 8 and 6 h, respectively, after phenobarbital administration. In contrast, the transcriptional rates of the Ya-Yc genes were elevated approximately eightfold at 16 h after 3-methylcholanthrene administration, whereas the transcriptional rates of the Yb genes were elevated approximately fivefold at 6 h after the administration of this xenobiotic. The elevation in transcriptional activity of the glutathione S-transferase genes is sufficient to account for the increase in glutathione S-transferase mRNA levels determined previously by RNA blot hybridization [C. B. Pickett, C. A. Telakowski-Hopkins, G. J-F. Ding, L. Argenbright, and A. Y. H. Lu (1984) J. Biol. Chem. 259, 5182-5188]. Therefore, it appears that phenobarbital and 3-methylcholanthrene elevate the level of the rat liver glutathione S-transferases primarily by augmenting the transcriptional rates of their respective genes.

Regulation of creatine kinase induction in differentiating mouse myoblasts

The regulation of creatine kinase (CK) induction during muscle differentiation was analyzed with MM14 mouse myoblasts. These cells withdraw from the cell cycle and commit to terminal differentiation when fed with mitogen-depleted medium. Myoblasts contained trace amounts of an isozyme of brain CK (designated BB-CK), but differentiation was accompanied by the induction of two other isozymes of muscle and brain CKs (designated MM-CK and MB-CK). Increased CK activity was detectable within 6 h of mitogen removal, 3 h after the first cells committed to differentiation and 6 h before fusion began. By 48 h, MM-CK activity increased more than 400-fold, MB-CK activity increased more than 150-fold, and BB-CK activity increased more than 10-fold. Antibodies prepared against purified mouse MM-CK cross-reacted with muscle and brain CKs (designated M-CK and B-CK, respectively) from a variety of species and were used to demonstrate that the increase in enzymatic activity was paralleled by an increase in the protein itself. CK antibodies were also used to aid in identifying cDNA clones to M-CK. cDNA sequences which corresponded to protein-coding regions cross-hybridized with B-CK mRNA; however, a subclone containing the 3'-nontranslated region was unique and was used to quantitate M-CK mRNA levels during myoblast differentiation. M-CK mRNA was not detectable in myoblasts, but within 5 to 6 h of mitogen withdrawal (6 to 7 h before fusion begins) it accumulated to about 30 molecules per cell. By 24 h, myotubes contained approximately 1,100 molecules per nucleus of M-CK mRNA.

Transcription unit of the rabbit beta 1 globin gene

We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

Regulation of creatine kinase induction in differentiating mouse myoblasts

The regulation of creatine kinase (CK) induction during muscle differentiation was analyzed with MM14 mouse myoblasts. These cells withdraw from the cell cycle and commit to terminal differentiation when fed with mitogen-depleted medium. Myoblasts contained trace amounts of an isozyme of brain CK (designated BB-CK), but differentiation was accompanied by the induction of two other isozymes of muscle and brain CKs (designated MM-CK and MB-CK). Increased CK activity was detectable within 6 h of mitogen removal, 3 h after the first cells committed to differentiation and 6 h before fusion began. By 48 h, MM-CK activity increased more than 400-fold, MB-CK activity increased more than 150-fold, and BB-CK activity increased more than 10-fold. Antibodies prepared against purified mouse MM-CK cross-reacted with muscle and brain CKs (designated M-CK and B-CK, respectively) from a variety of species and were used to demonstrate that the increase in enzymatic activity was paralleled by an increase in the protein itself. CK antibodies were also used to aid in identifying cDNA clones to M-CK. cDNA sequences which corresponded to protein-coding regions cross-hybridized with B-CK mRNA; however, a subclone containing the 3'-nontranslated region was unique and was used to quantitate M-CK mRNA levels during myoblast differentiation. M-CK mRNA was not detectable in myoblasts, but within 5 to 6 h of mitogen withdrawal (6 to 7 h before fusion begins) it accumulated to about 30 molecules per cell. By 24 h, myotubes contained approximately 1,100 molecules per nucleus of M-CK mRNA.

Transcription unit of the rabbit beta 1 globin gene

We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

Secretory rhythm of growth hormone regulates sexual differentiation of mouse liver

The secretory pattern of growth hormone (GH) differs between the sexes; in males it is more pulsatile than in females. Experiments were performed to test the hypothesis that differences in the secretory rhythm of GH are responsible for sex-dependent liver functions of mice. Continuous delivery of GH was achieved either by introducing metallothionein-GH fusion genes into the germ line or by implanting minipumps. Pulsatile delivery of GH was mimicked by injection. The effects of these treatments on production of hepatic prolactin/GH receptors, albumin, and major urinary protein (MUP) were monitored. The results suggest that induction of MUP mRNA requires pulsatile occupancy of GH receptors, which is achieved naturally in males or by injection of GH, whereas chronic occupancy of GH receptors is inhibitory. In contrast, induction of prolactin/GH receptors requires chronic stimulation of GH receptors, which is approximated in normal female mice or results from increased GH levels in mice with foreign genes or undergoing infusions from minipumps.

Mapping restriction sites on large DNAs by electron microscopy

We have developed a novel technique to map restriction sites on large duplex DNAs by electron microscopy. In this method, the sample DNA is first cut with a restriction enzyme. The resulting fragments are briefly digested with Escherichia coli exonuclease III, and treated with wheat germ RNA polymerase II to fill-in with RNA the resulting gaps. These small RNAs, complementary to sequences immediately adjacent to either side of the restriction site, are isolated from the DNA template and R-looped to the full-length DNA. When this material is prepared by the formamide-cytochrome spreading technique, small bubbles are visible wherever there is a restriction site on the DNA. Improved methods of mapping are outlined.

Chromatin-like structure of adeno-associated virus DNA in infected cells

Adeno-associated virus (AAV) is a single-stranded DNA virus which requires adenovirus as a helper for productive infection. We studied whether intracellular AAV DNA in KB cells was present in a chromatin-like structure by digesting infected cell nuclei with micrococcal nuclease. Virus DNA was detected by agarose gel electrophoresis followed by blotting and hybridization to nick-translated [32P]DNA probes. After coinfection with adenovirus, AAV DNA was present in nucleosome-like structures which were similar to cell nucleosomes and were double stranded as judged by insensitivity to S1 nuclease digestion. In the absence of adenovirus, intracellular AAV DNA also formed similar nucleosome-like structures which were also insensitive to S1 digestion and were formed in both the presence and absence of hydroxyurea. These latter structures probably formed on AAV duplexes created either by reassociation of infecting parental single-stranded DNA or by covalent integration into the cell genome rather than by de novo AAV DNA synthesis. These results have implications for the mechanism of AAV genome replication, transcription, and integration into the cell genome.

Rapid suppression of alpha 1-fetoprotein gene transcription by dexamethasone in developing rat liver

The administration of glucocorticosteroid hormones to newborn rats interrupts selectively (and reversibly, if the hormone is withdrawn) the hepatic production of alpha 1-fetoprotein (AFP). This results from a decreased concentration of AFP mRNA in the liver [Bélanger, L., Frain, M., Baril, P., Gingras, M.C., Bartkowiak, J., & Sala-Trepat, J.M. (1981) Biochemistry 20, 6665]. We have delineated further the mechanism and time course of this hormonal action in 4-day-old rats treated with dexamethasone (DEX). DNA from a recombinant plasmid containing a 578-bp insert of rat AFP cDNA was used to develop a cell-free nuclear run-off system and directly assess AFP gene transcription activity. Five minutes after DEX injection, AFP gene transcription activity is unchanged, but after 30 min, it drops to 25% that of the control; this correlates with the time required for translocation of DEX receptors to the nucleus. Dose-response curves also show that the degree of AFP gene suppression is closely correlated with the amount of DEX receptor translocated to the nucleus. The nuclear concentration of AFP mRNA, monitored by dot-blot hybridization, decreases to undetectable levels within 48 h, whereas that of albumin mRNA increases slightly, which indicates the selectivity of DEX action. These results show that DEX suppresses AFP gene expression at the transcriptional level and suggest a direct negative action of DEX-receptor complexes on the AFP chromatin transcription unit.

A practical approach for quantitating specific mRNAs by solution hybridization

The preparation and use of a specific cDNA probe for quantitating mRNA by solution hybridization is described. Cloned DNA sequences are nick translated, denatured, hybridized to single-stranded M13 clones containing message strand (mDNA) sequences, and separated chromatographically on Bio-Gel A50 under first native and then denaturing conditions to yield a single-stranded cDNA probe. The details of a solution hybridization assay in which the single-stranded cDNA is used to quantitate mRNA in total nucleic acid samples are described. As little as 0.5 pg of mRNA can easily be detected within a day of sample isolation. Thus, the assay is both rapid and sensitive and can be used to measure RNAs complementary to any cloned DNA sequence. It is ideally suited to situations when accurate quantitation of multiple samples is anticipated.

Expression of integrated viral DNA sequences outside the transforming region in eight adenovirus-transformed cell lines

The expression of early and intermediate-early viral regions in eight adenovirus type 5 transformed cell lines was analyzed by radioimmuno-inhibition and RNA-DNA hybridization techniques. Details on the arrangement of the integrated viral DNA sequences in these cell lines have already been published (Visser, L., Wassenaar, A.D.C., Van Maarschalkerweerd, M.W. and Rozijn, T.H. (1981) J. Virol, 39, 684-693). In all cell lines tested, proteins encoded by the transforming region E1 are present. Dependent on the viral DNA content, additional early regions are expressed in most cell lines. In two of the cell lines polypeptides related to the adenoviral terminal protein, encoded by the recently described region E2b, could be detected. The viral DNA sequence encoding the body of the terminal protein mRNA is probably integrated intact, but the promoter region and at least some of the leaders are lacking in these cell lines.

Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units

Electron microscopy shows that complexes of the single-strand DNA binding protein (SSB) of Escherichia coli and phage fd DNA appear as beaded fiber loops containing an average of 38 beads, 1 per 170 bases of DNA. Extensive digestion of native unfixed SSB-fd DNA complexes with micrococcal nuclease reveals a protected DNA fragment of 145 bases, while shorter digestion periods result in a sequence of fragments in multiples of 160 +/- 25 bases. Digestion of these complexes with DNase I produces a repeating pattern of bands, multiples of approximately 15 bases with strong bands at 60, 105, 118, 130, 145, 150, and 210 bases. Isopycnic banding in CsCl solution yields densities of 1.272 and 1.700 g/ml, respectively, for SSB alone and for fd DNA and, after fixation, of 1.388 g/ml for fd DNA-SSB beaded fibers and 1.373 g/ml for the individual protein-DNA beads. Based on these data and the molecular weights of SSB and fd DNA, we suggest that the nucleoprotein chain consists of eight molecules of SSB bound to 145 bases of DNA, with these units linked by roughly 30 bases of protein-free DNA. The excellent concord between results obtained by enzyme digestion of unfixed native samples and, after fixation, by electron microscopy and density banding supports the conclusion that SSB organizes single-stranded DNA in a manner similar to the organization of duplex DNA by histones.

The role of RNA primer in discontinuous DNA replication in isolated nuclei from HeLa cells

RNA-primed discontinuous DNA synthesis was studied in an in vitro system consisting of washed nuclei from synchronized S-phase HeLa cells. A new technique proved useful for the purification of short nascent fragments of DNA (Okazaki fragments). Mercurated dCTP was substituted for dCTP in the DNA synthesis reaction. Short nascent pieces (4-6 S) of mercurated DNA were found to bind preferentially to sulfhydryl-agarose, and could be eluted with mercaptoethanol. The isolated fragments were assayed for the presence of covalently linked RNA by the spleen exonuclease method described by Kurosawa et al. (Kurosawa, Y., Ogawa T., Hirose, S., Okazaki, T. and Okazaki, R. (1975) J. Mol. Biol. 96, 653-664). Following a 30 s incubation with [3H]TTP in the absence of added ribonucleotides, approximately 20% of the nascent strands synthesized in washed nuclear preparations had RNA attached. These RNA primers either preexisted in the nuclei or were formed from endogenous ribonucleotides. The 5' ends of the primers appeared to be largely in a phosphorylated state. In the absence of added ribonucleotides, these RNA-DNA linkages disappeared with 2 min, whereas if ribonucleotides were added, the number of RNA primers increased to 40% and remained at this level for greater than 2 min. To obtain maximal levels of RNA primer, the addition of all three of the ribonucleotides, rCTP, rGTP, rUTP (0.1mM), as well as high levels of rATP (5mM) was required. Addition of ribonucleotides also markedly enhanced the amount of nascent DNA fragments synthesized. However, in the absence of added ribonucleotides, after RNA primers had disappeared, nascent DNA fragments were still initiated at a significant rate. These results suggest that RNA primers play an important role in the initiation of Okazaki fragments but that synthesis can also be initiated by alternative mechanisms. An important role for ATP in RNA primer synthesis is suggested.

Affinity labelling of yeast phenylalanyl-tRNA synthetase with a 3'-oxidised tRNAPhe. Isolation and sequence of the labelled peptide

Yeast phenylalanyl-tRNA synthetase was specifically labelled with a 3'-oxidised tRNAPhe. Stoichiometric inactivation was achieved with the incorporation of 2 mol oxidised tRNA Phe/mol enzyme which corresponds exactly to the stoichiometry of tRNA binding. The labelled peptide has been isolated using a quick chromatographic procedure which can be applied to any covalent complex formed between a tRNA and an aminoacyl tRNA synthetase. The isolated peptide (18 amino acids) was found to encompass the unique cysteine sequence of the smaller beta subunit of the enzyme.

Specific in vitro initiation of transcription on the adenovirus type 2 early and late EII transcription units

Three transcription units are present in the adenovirus type 2 region EII. Transcription units EIIaE and EIIaL encode the mRNA for the 72,000-dalton DNA binding protein, early and late in the lytic cycle, respectively, and transcription unit EIIb encodes the mRNA for the protein that binds to the 5' termini of adenovirus DNA. By using a cell-free transcription system in the presence of purified RNA polymerase B (or II), we have obtained specific initiation of transcription from both the EIIaE promoter, which does not contain a T-A-T-A box, and the EIIaL promoter, which does. In addition, we have identified a new EII T-A-T-A box promoter that is located close to the early non-T-A-T-A box promoter and is used both in vivo and in vitro.

Adeno-associated virus RNA transcription in vivo

We have studied RNA transcripts of the defective parvovirus, adeno-associated virus (AAV) present in poly(A)rich and poly-(A)free fractions of nuclear and cytoplasmic RNA prepared from cells infected together with a helper adenovirus. Cytoplasmic poly-(A)rich RNA contains three overlapping spliced AAV RNAs having sizes of 3.9 X 10(3), 3.3 X 10(3) and 2.3 X 10(3) bases respectively. The nuclear precursors of these RNAs appear to be the coterminal unspliced poly(A)-rich RNAs containing 4.2 X 10(3), 3.6 X 10(3) and 2.6 X 10(3) bases respectively. These unspliced RNAs were also found in the cytoplasm. The nuclear poly(A)-free RNA contained a heterogenous population of AAV RNAs that were generally smaller than 2.3 X 10(3) bases. In addition, the Hirt pellet fraction of the nuclear RNA contained two discrete AAV poly(A)-free RNAs having sizes of 2.5 X 10(3) and 2.8 X 10(3) bases. The 4.2 X 10(3) and 3.6 X 10(3)-base unspliced RNAs are more abundant than the coterminal 3.9 X 10(3) and 3.3 X 10(3)-base spliced RNAs whereas the 2.3 X 10(3)-base spliced RNA is much more abundant than the 2.6 X 10(3)-base unspliced RNA. Thus, the cytoplasmic abundance of the AAV spliced RNAs appears to be controlled in part by the post-transcriptional events of splicing or message stability. We also analysed the effects of AAV defective-interfering genomes upon AAV transcription. These studies showed that when synthesis of standard AAV genomes was inhibited more than 10-fold by defective-interfering genomes there was no significant effect on the types or amounts of AAV RNA transcripts which accumulated. These observations indicate that interference by defective-interfering genomes occurs mostly at the level of DNA replication rather than transcription.

T antigen repression of SV40 early transcription from two promoters

The SV40 early mRNAs encode large (T) and small (t) tumor antigens. During the lytic cycle, the 5' termini of the early mRNAs undergo a shift: shortly after infection only an initiation site downstream from the TATA box is utilized; later an upstream initiation site becomes prominent. Both initiation sites are utilized in an in vitro transcription extract. D2T, a T antigen analog, specifically represses transcription in vitro from both initiation sites, but at different concentrations. Binding of D2T to site I suppresses initiation from the site downstream of the TATA box; binding to sites II and I suppresses initiation from the upstream site. The role of T antigen binding in repression of transcription and in the shift of initiation sites on the early strand is discussed.

Generation of transforming viruses in cultures of chicken fibroblasts infected with an avian leukosis virus

During serial passages of an avian leukosis virus (the transformation-defective, src deletion mutant of Bratislava 77 avian sarcoma virus, designated tdB77) in chicken embryo fibroblasts, viruses which transformed chicken embryo fibroblasts in vitro emerged. Chicken embryo fibroblasts infected with these viruses (SK770 and Sk780) had a distinctive morphology, formed foci in monolayer cultures, and grew independent of anchorage in semisolid agar. Bone marrow cells were not transformed by these viruses. Another virus (SK790) with similar properties emerged during serial subcultures of chicken embryo fibroblasts after a single infection with tdB77. The 50S to RNAs isolated from these viruses contained a tdB77-sized genome (7.6 kilobases), 8.7- and 5.7-kilobase RNAs, and either a 4.1-kilobase RNA or a 4.6-kilobase RNA. These RNAs did not hybridize with cDNA's representing the src, erb, mac, and myb genes of avian acute transforming viruses. Cells transformed by any one of the Sk viruses (SK770, SK780, or SK790) synthesized two novel gag-related polyproteins having molecular weights of 110,000 (p110) and 125,000 (p125). We investigated the compositions of these proteins with monospecific antiviral protein sera. We found that p110 was a gag-pol fusion protein which contained antigenic determinants, leaving 49,000 daltons which was antigenically unrelated to the structural and replicative proteins of avian leukosis viruses. An analysis of the SK viral RNAs with specific DNA probes indicated that the 5.7-kilobase RNA contained gag sequences but lacked pol sequences and, therefore, probably encoded p125. The transforming ability, the deleted genome, and the induced polyproteins of the SK viruses were reminiscent of the properties of several replication-defective acute transforming viruses.

The expression-linked copy of a surface antigen gene in Trypanosoma is probably the one transcribed

The antigenic specificity of the living trypanosome seems to be determined by the protein component of a unique glycoprotein species covering the whole surface of the parasite. During chronic infection, a single clone of trypanosomes may successively express a large repertoire of different variable antigen types (VATs). There are probably as many genes as variant-specific antigens (VSAs) (see refs 1-3 for reviews). The expression of the genes coding for the synthesis of these antigens is linked to genomic rearrangements involving duplication of the coding sequence and transposition of the additional copy. The regulation of the expression of the VSA genes is operated at the transcriptional level. It can thus be supposed that their transcription depends on the presence of the additional, transposed copy. We report here that this additional copy is in a chromatin configuration highly sensitive to pancreatic deoxyribonuclease, suggesting that it is the transcribed one.

Study of the interaction between yeast tRNAphe and yeast phenylalanyl-tRNA synthetase by monochromatic ultraviolet irradiation at various wavelengths. Advantages and limits of the method

The interactions between yeast tRNAphe and phenylalanyl-tRNA synthetase were studied by analysis of the covalent adducts obtained upon monochromatic ultraviolet irradiation at different wavelengths (248, 282, 292, 302 and 313 nm). The high extent of inactivation of phenylalanyl-tRNA synthetase, together with the partial modification of tRNA, as well as the peculiar instability of most of the covalent bonds formed upon irradiation constitute severe limitations to the use of the technique and to the interpretation of the results. These disadvantages led us to select an irradiation wavelength of 248 nm and to use only mild isolation procedures allowing a good recovery of the covalent adducts formed. Seven major tryptic peptides of the enzyme were found to be cross-linked to tRNAPhe whereas six major T1-oligonucleotides were covalently linked to the protein, among these, the three cross-linked oligonucleotides previously described by Shoemaker and Schimmel (J. Biol. Chem. 250 (1975) 4440-4444) in the same system. The difference in the number of covalently linked oligonucleotides is discussed in the light of the instability of the covalent linkages. The localization of the six oligonucleotides at the inside of the two branches forming the L-shaped tRNA molecule is similar to that observed in the yeast valine system (Renaud et al., Eur. J. Biochem. 101 (1979) 475-483) and is consistent with the interaction model previously described (Rich and Schimmel, Nucl. Acids Res. 4 (1977) 1649-1665 and Ebel et al. in Transfer RNA: structure, properties and recognition, (1979) pp. 325-343 Cold Spring Harbor Laboratory, NY). The occurrence of covalent cross-linking upon irradiation in the tryptophan absorption band (302 nm) strongly suggests the participation of this residue in the stabilization of the tRNA enzyme complex.

Identification of a 16-S RNA fragment crosslinked to protein S1 within Escherichia coli ribosomal 30-S subunits by the use of a crosslinking reagent: ethyl 4-azidobenzoylaminoacetimidate

The bifunctional reagent ethyl 4-azidobenzoylaminoacetimidate was used to crosslink specifically ribosomal protein S1 to 16-S RNA within 30-S subunits. The reagent was attached to isolated protein S1. The modified protein was reassociated with protein-S1-depleted 30-S subunits and then crosslinked to the RNA molecule. The covalently bound 16-S RNA-protein S1 complex was isolated and the RNA fragment C-U-A-A-C-G-C-G-U-U-A-A-G-U-C-G-A-C-C-G-C-C-U-G-G-G-G-A-G (positions 861-889) was characterized to be crosslinked to protein S1.

Promoter sequences of eukaryotic protein-coding genes

In vitro genetic techniques were used to study the sequence requirements for the initiation of specific transcription. Deletion mutants were constructed around the putative promoter of the adenovirus-2 major late and chicken conalbumin genes. Specific transcription in vitro by RNA polymerase B together with a HeLa cell cytoplasmic extract was used as the test for promoter function. With this approach sequences which are essential for the initiation of specific transcription in vitro, were shown to be located between 12 and 32 base pairs upstream from the 5' end of these genes.

Comparison of the nuclear ribonucleoproteins containing the transcripts of adenovirus-2 and HeLa cell dna

A method as devised allowing the preparation of hnRNA-containing ribonucleproteins (hnRNP) frm HeLa cells infected with adenovirus type 2 under conditions where the extraction of viral replication complexes as minimal. Approximately 60% of the RNA from such hnRNP hybridized with adenovirus DNA. The hnRNP from infected cells had the same general characteristics as those from uninfected cells. Their size was heterogeneous (30-260 S) and depended upon that of their RNA. Their CsCl densities were identical (1.39-1.40 g/ml), indicating the same protein:RNA ratio. Their proteins were found in the same molecular weight range, between 25 000 and 200 000. The major proteins of hnRNP from HeLa cells were present in hnRNP from adenovirus-infected cells. As 60% of the cellular RNA was replaced by adenovirus RNA in hnRNP, this in dicated that there was not stringent specificity in the RNA-protein interactions. The relative proportions of the proteins were identifical in both cases, suggesting that the hnRNP assembly was independent of nucleotide sequences at least for the major proteins. The hnRNP from infected and uninfected cells differed by the size of their RNA, which was larger after infection, and by the presence of six additional minor polypeptides after infection. However, it cannot be excluded that the presence of these polypeptides in hnRNP resulted from non-specific adsorption.

Specific in vitro initiation of transcription on conalbumin and ovalbumin genes and comparison with adenovirus-2 early and late genes

Specific initiation of transcription of cloned conalbumin and ovalbumin genes has been obtained in a cell-free system in the presence of purified calf thymus RNA polymerase B. Comparison with the adenovirus-2 early (E1A) and major late genes reveals marked variations in transcriptional efficiencies. Specific fragmentation of the conalbumin gene DNA indicates that a short DNA segment 5' to the initiation site is involved in specific transcription.

Complexity of RNA from the neuronal and glial nuclei

The unique DNA expression value in the brain nuclear RNA was much higher than those from other tissues. The origin of this high complexity of brain nuclear RNA was examined using the [3H]DNA-RNA saturation hybridization technique. RNA was extracted from the isolated neuronal and glial nuclei. The experimental results may indicate that the high complexity in the brain nuclei does not result from the summation of many cell types but only from the neuronal nuclei.

Transcription of polyoma DNA by Escherichia coli RNA polymerase: influence of ionic strength on promoter selection

The influence of ionic strength on transcription of polyoma DNA by Escherichia coli RNA polymerase was investigated. At 0.15 M KCl, transcription was highly symmetrical and, due to the lack of reinitiation, a limited extent of RNA synthesis was observed. When the concentration of KCl was raised to 0.45 M, the affinity of the enzyme for its template, as well as its apparent affinity for ribonucleoside triphosphates, was reduced. Under optimal conditions, the rate and extent of RNA synthesis at 0.45 M KCl were greater than at 0.15 M KCl, and transcription was mostly asymmetric. Binding and initiation sites at both ionic strengths were identified; at 0.15 M KCl, transcription was initiated from two major sites, located at 0.99 and 0.06 map unit, whereas at 0.45 M KCl, a unique initiation site, at 0.99 map unit, was selected by RNA polymerase.

A simple method for elimination of RNAase contamination from DNAase preparations

RNAase which usually contaminates commercial pancreatic DNAase preparations can be removed by affinity chromatography on agarose-coupled anti-RNAase antibodies. RNA treated with purified DNAase can be re-isolated intact, as determined by polyacrylamide gel electrophoresis under denaturing conditions. This method might be applicable to purification of other preparations which are used in RNA research, such as PNPase (polynucleotide phosphorylase) and specific antibodies for polysome immunoprecipitation. The non-specific binding of DNAase in our system is less than 5% and the loss of specific activity of DNAase I is less than 1%.

Transcription in vitro of adenovirus-2 DNA by RNA polymerases class C purified from uninfected and adenovirus-infected HeLa cells

DNA-dependent RNA polymerase class C (or III) has been solubilized from either uninfected or adenovirus-2-infected HeLa cells and purified by chromatography on phosphocellulose, DNA-cellulose, CM-Sephadex and DEAE-Sephadex. The last column separated the enzyme into three forms CI, CII and CIII, which were completely free of RNA polymerases class A and B and of DNase and RNase. The total and the relative amount of these different enzyme C forms did not vary whether purified from uninfected or infected cells. Irrespective of the stage of purification, the three enzyme forms transcribed deproteinized adenovirus-2DNA very efficiently. This transcription was highly sensitive to elevated ionic strength (especially in the presence of Mg2+) and was accompanied by continuous reinitiation as shown by adding poly(rI), a potent inhibitor of initiation. In addition heparin-resistant initiation complexes could be formed at elevated temperature. The RNA synthesized in vitro on deproteinized intact adenovirus-2 DNA by the different forms of RNA polymerase class C, has been characterized. Analysis of the transcripts by gel electrophoresis, RNA self-annealing, hybridization to separated adenovirus-2 DNA strands and to restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that the various regions of the adenovirus-2 genome were randomly transcribed. In addition, hybridization of RNA transcripts labelled at their 5' end by either [gamma32P]ATP or [gamma-32P]GTP indicated that not only elongation but also initiation occurred randomly through the entire adenovirus-2 genome, irrespective of the form of the enzyme and of the origin of the cells (normal or infected). The results are discussed in terms of the components which are possibly involved in specific transcription.

Estrogen withdrawal in chick oviduct. Characterization of RNA synthesized in isolated nuclei using a mercurated precursor

1. As a prerequisite for analyzing the effect of estrogen on transcription in chick oviduct, we describe suitable methods for the synthesis (under conditions restricting reinitiation), and isolation of RNA transcripts from oviduct nuclei in vitro, utilizing mercurated UTP (Hg-UTP) as an RNA precursor and chromatography on sulphydryl-Sepharose (SH-Sepharose) to recover mercurated RNA (Hg-RNA). The techniques described include treatment of Hg-RNA with p-hydroxymercuribenzoate, to improve the efficiency of binding to SH-Sepharose, and elution of Hg-RNA from SH-Sepharose after treatment with 60% formamide at 90 degrees C, to eliminate contamination by aggregated nucleic acid. 2. RNA synthesized by endogenous form B RNA polymerase (using either UTP or Hg-UTP as precursor) was recovered in nuclear lysates in the form of 30--85-S heterogeneous RNA . protein complexes, and after removal of protein, was 10--12 S in size. 3. The nature of RNA transcripts synthesized in vitro was examined by hybridization. More than 90% of the RNA was complementary to "unique" DNA sequences, and 50--60% of the hybridized RNA could be competed with homologous, steady-state nuclear RNA, indicating a significant degree with homologous, steady-state nuclear RNA, indicating a significant degree of homology between in vitro transcripts and in vivo RNA. The level of homology was similar whether RNA synthesis was performed in low salt, or in high salt in the presence of heparin. Possible reasons for only partial competition in these experiments are discussed. 4. Withdrawal of estrogen from chicks leads to a 50% reduction in endogenous RNA polymerase activities in nuclei within 48 h. Similar levels of competition with Hg-RNA transcripts for "unique" DNA were obtained using oviduct nuclear RNAs isolated before or after estrogen withdrawal, and even with liver nuclear RNA. Thus, in oviduct, those sequences present in primary transcripts, and analyzed under our experimental conditions, are present in different hormonal states and also in other chick tissues.