Isolation of a nuclear RNA fraction resembling DNA in its base composition

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

The localization of long noncoding RNAs (lncRNAs) within the cell is the primary determinant of their molecular functions. LncRNAs are often thought of as chromatin-restricted regulators of gene transcription and chromatin structure. However, a rich population of cytoplasmic lncRNAs has come to light, with diverse roles including translational regulation, signaling, and respiration. RNA maps of increasing resolution and scope are revealing a subcellular world of highly specific localization patterns and hint at sequence-based address codes specifying lncRNA fates. We propose a new framework for analyzing sequencing-based data, which suggests that numbers of cytoplasmic lncRNA molecules rival those in the nucleus. New techniques promise to create high-resolution, transcriptome-wide maps associated with all organelles of the mammalian cell. Given its intimate link to molecular roles, subcellular localization provides a means of unlocking the mystery of lncRNA functions.

Action of Daunomycin on Nucleic Acid Synthesis in Hepatoma Ascites Cells Incubated « in vitro »

The action of Dannomycin, an antibiotic of Rhodomycin group, was studied following the incorporation of Adenine-8-14C into nucleic acid of hepatoma ascites cells incubated « in vitro ». Doses of 20 μg/ml of the antibiotic were able to inhibit the uptake of the precursor by RNA; the activity of the drug appeared to be dependent on the density of the cell population. As it was noted that, under our experimental conditions, a partial inhibition of the incorporation was caused by these doses of Daunomycin, some RNA fractions were isolated from cells and tested for their sensitivity to the antibiotic. A high-activity RNA extracted from nuclei appeared to be the most sensitive to the Daunomycin action. At higher doses of Daunomycin the incorporation into DNA was also lowered.

Messenger ribonucleic acid of cerebral nuclei

1. RNA was isolated from crude nuclear preparations and from ribosomes derived from rat brain and liver. Nuclear RNA was obtained by lysis of the nuclei with sodium dodecyl sulphate, followed by denaturation and removal of DNA and protein with hot phenol. 2. Base composition analyses indicated that the cerebral nuclear RNA preparation contained a higher proportion of non-ribosomal RNA than the analogous hepatic preparation. 3. Sucrose-density-gradient analyses revealed a heterogeneous profile for each nuclear RNA preparation, with two major peaks possessing the sedimentation properties of ribosomal RNA (18s and 28s). 4. Template activities of both preparations were widely distributed through the sucrose density gradients. 5. The cerebral nuclear RNA preparation was more active than the hepatic nuclear RNA preparation in promoting amino acid incorporation in cell-free systems from Escherichia coli and rat brain. 6. Cerebral nuclear RNA stimulated amino acid incorporation in a cerebral ribosomal system even in the presence of an excess of purified E. coli transfer RNA. 7. It is concluded that a significant proportion of cerebral nuclear RNA has the characteristics of messenger RNA.

EFFECT OF ACTINOMYCIN D ON RNA SYNTHESIS AND ANTIBODY FORMATION IN THE ANAMNESTIC RESPONSE IN VITRO

Antibody synthesis in anamnestic lymphoid cells, measured by incorporation of leucine-C¹⁴ into specific antibody, was inhibited at moderate concentrations of actinomycin D. This was accompanied by marked inhibition of synthesis of RNA as measured by incorporation of H³-cytidine monophosphate. However, at low concentrations of actinomycin D, antibody synthesis was unaffected or even increased while RNA synthesis continued to be inhibited. The results obtained suggest that messenger RNA for antibody synthesis, either because it is relatively stable or present in excess, does not become a limiting factor until its synthesis is maximally inhibited. Puromycin, an inhibitor of amino acid coupling, abolished antibody synthesis in low concentration. 6-Mercaptopurine had no effect on the synthesis of antibody or RNA even at high concentration. The data obtained support the view that antibody synthesis follows pathways similar to those utilized for the formation of other types of proteins.

Changes in the base composition of nuclear ribonucleic acid of neurons during a short period of enhanced protein production

Nuclei from isolated nerve cells were sampled by microdissection. The content and composition of the nuclear RNA was studied and compared with that of the cytoplasmic RNA of Deiters' nerve cells of rabbits. Analyses were made of control nerve cells and of cells in which an enhanced RNA and protein production had been induced by chemical means, tricyano-amino-propene, for 60 minutes. The nuclear RNA content of the control nerve cells was 56 µµg, i.e. 3 per cent of the total RNA content of the nerve cell. The base ratios were: adenine 21.3, guanine 26.6, cytosine 30.8, uracil 21.3. Purine-pyrimidine analyses showed that the nuclear RNA differed significantly from the cytoplasmic RNA in having higher adenine and uracil values. The guanine and cytosine values were high, however, and the ratio G/C was 0.86 as compared with 1.16 for the cytoplasmic RNA. The composition of the nuclear RNA was interpreted as reflecting the extraordinarily strong development of the nucleolus in these neurons. During the 60 minutes of enhanced neuronal RNA production (+25 per cent) the guanine value increased and the uracil value decreased significantly in the nuclear RNA. In the cytoplasmic RNA the guanine value also increased although not so much as the nuclear guanine. The cytoplasmic cytosine value decreased. The result indicated that the production of the characteristic cytoplasmic RNA had been influenced by the change in the nuclear RNA

METHODS FOR THE PURIFICATION OF THYMUS NUCLEI AND THEIR APPLICATION TO STUDIES OF NUCLEAR PROTEIN SYNTHESIS

Procedures are described for the purification of calf thymus nuclei using mild hypotonit shock to break intact cells, and layering techniques to remove cytoplasmic debris. Ficolc (a high polymer of sucrose) was dissolved in isotonic sucrose to give dense solutions suitable for gradient centrifugation. The method yields nuclei which can incorporate amino acids in vitro. Thymus nuclei isolated under isotonic conditions were incubated with C¹⁴-amino acids and later purified by centrifugation through dense sucrose solutions. The distribution of radioactivity in different nuclear proteins was measured and it was found that isotopic amino acids are actively incorporated into characteristically chromosomal proteins, such as the arginine-rich and lysine-rich histones. Protein synthesis in the nucleus is markedly inhibited by puromycin and by agents, such as 2,4-dinitrophenol, which inhibit ATP synthesis. The synthesis of histones is also inhibited by puromycin, but the uptake of several amino acids into the lysine-rich histone fraction seems less sensitive to puromycin inhibition than is uptake into the arginine-rich histones or other proteins of the nucleus. High resolution autoradiography using tritiated leucine and observing grain distribution over thin sections of isolated nuclei and whole cells shows that amino acid incorporation occurs within the nucleus and is not due to cytoplasmic contamination.

THE BASE COMPOSITION OF RIBONUCLEIC ACID IN LAMPBRUSH CHROMOSOMES, NUCLEOLI, NUCLEAR SAP, AND CYTOPLASM OF TRITURUS OOCYTES

The base composition of RNA's extracted from chromosomes, nucleoli, nuclear sap, and cytoplasm of Triturus oocytes has been determined by microelectrophoresis. The chromosomal RNA has a content of guanine+cytosine equal to that of DNA, but there is no complementarity in the composition as for DNA. Nuclear sap contains a highly variable RNA with a tendency towards high uracil values. Nucleolar and cytoplasmic RNA's are similar in composition and both are of the guanine-cytosine rich type. The chromosomes and nucleoli contain roughly equivalent amounts of RNA, somewhat less than is present in the nuclear sap. The RNA/DNA ratio of the whole chromosomes is about 10. However, the ratio in the synthetically active regions, the loops, is much higher, since the loops contain all the chromosomal RNA but only a small fraction of the DNA.

STUDIES ON ISOLATED NUCLEI. II. ISOLATION AND CHEMICAL CHARACTERIZATION OF NUCLEOLAR AND NUCLEOPLASMIC SUBFRACTIONS

This paper describes the subfractionation of nuclei isolated from guinea pig liver by the procedure presented in the first article of the series (8). Centrifugation in a density gradient system of nuclear fractions disrupted by sonication permits the isolation of the following subfractions: (a) a nucleolar subfraction which consists mainly of nucleoli surrounded by a variable amount of nucleolus-associated chromatin and contaminated by chromatin blocks derived primarily from von Kupffer cell nuclei; (b) and (c), two nucleoplasmic subfractions (I and II) which consist mainly of chromatin threads in a coarser (I) or finer (II) degree of fragmentation. The protein, RNA, and DNA content of these subfractions was determined, and their RNA's characterized in terms of NaCl-solubility, nucleotide composition, and in vivo nucleotide turnover, using inorganic ₃₂P as a marker. The results indicate that there are at least three types of RNA in the nucleus (one in the nucleolus and two in the nucleoplasm or chromatin), which differ from one another in NaCl-solubility, nucleotide composition, turnover, and possibly sequence. Possible relations among these RNA's and those of the cytoplasm are discussed.

Hybridization properties of sequences adjacent to triphosphorylated 5'-ends of nuclear pre-mRNA from mouse Ehrlich carcinoma

Triphosphorylated 5'-end fragments about 100 nucleotides long were prepared from purified nuclear pre-mRNA using a modified hydroxyapatite method /1/. These fragments as well as fragments of total pre-mRNA of the same size were polyadenylated in vitro by ATP:RNA adenyltransferase and used as templates for the synthesis of [32P] cDNA by reverse transcriptase in the presence of an oligo(dT) primer. The use of cDNA transcribed from the triphosphorylated 5'-end fragments of pre-mRNA (5'-cDNA) and from the total pre-mRNA fragments allows one to calculate the complexity of the 5'-end fraction pre-mRNA and to detect these sequences in polysomal mRNA. Sequences adjacent to 5'-phosphorylated ends of pre-mRNA represent a specific class of sequences with a complexity of about 200 kb. It was also found that about 25% of total pre-mRNA and about a half of sequences adjacent to triphosphorylated 5'-ends are present in polysomal mRNA. A high homology between triphosphorylated 5'-end fragments of pre-mRNA and mRNA sequences may be explained in terms of splicing. Less than 30% of 5'-cDNA hybridized to moderately repetitive DNA while most of them are represented by unique DNA sequences. About 15% of 5'-cDNA contained oligo(dA) sequences originated from oligo(U) in pre-mRNA from which it was transcribed.

Cell-free translation of the globin message within polydisperse high-molecular-weight ribonucleic acid of avian erythrocytes

Polydisperse high-molecular-weight RNA of nucleated avian erythrocytes includes sequences coding for globin chains. The RNA was extracted from immature erythrocytes of ducks and fractionated under denaturing conditions by sucrose density gradient centrifugation in 99% dimethylsulfoxide. The RNA sedimenting faster than 45 S was able to direct the synthesis of duck globins in the Krebs II ascites cell-free protein-synthesizing system. The newly synthesized globin molecules have been identified by their characteristic electrophoretic properties in polyacrylamide gels containing either urea or sodium dodecyl sulfate, and by immunoprecipitation of the released globin chains by rabbit antibodies against duck hemoglobin. In order to rule out the possibility of a contamination of the high-molecular-weight RNA with duck-globin messenger RNA tailing from the 9-10S region, rabbit-globin messenger RNA was added to duck RNA as an internal control. No rabbit-globin messenger RNA activity could be detected in the RNA fractions sedimenting faster than 45 S. It is concluded that high-molecular-weight RNAs in the nucleated erythroid cell contain sequences of globin messenger RNAs covalently attached to larger polynucleotide chains. These results support the view that polydisperse nuclear RNA is the precursor of the cytoplasmic messenger RNA fraction.

Intranuclear distribution of the inducing metal in primary rhabdomyosarcomata induced in the rat by nickel, cobalt and cadmium

In primary rhabdomyosarcomata, induced in the rat by intramuscular implantation of powdered metallic nickel, cobalt and cadmium, at least 50% of the high content of inducing metal that accumulates in the nuclei of each tumour, is bound by the nucleoli. The remainder is distributed approximately equally between the nuclear sap and chromatin.