Uridylate-rich sequences in rapidly labelled RNA of mammalian cells

The Cid1 poly(U) polymerase

The Schizosaccharomyces pombe cytoplasmic protein Cid1 acts as a poly(U) polymerase (PUP). Polyadenylated actin mRNA, a target of this activity, is uridylated upon arrest in S phase and is likely to be one of many such Cid1 targets. This RNA uridylation pathway appears to be conserved, as Cid1 orthologs in Arabidopsis thaliana, Caenorhabditis elegans and humans display PUP activity either in vitro or in Xenopus laevis oocytes. Here, we review the literature on Cid1, other PUPs and uridylation, a conserved and previously under-appreciated mechanism of RNA regulation.

Simple repetitive DNA sequences are transcribed in early embryonal stages of Xenopus laevis

We have isolated and sequenced three cDNA clones from early embryonal stages of Xenopus laevis containing highly repetitive sequences. By means of poly A+ RNA hybridization we could show that simple repeats of the type AC/TG are ubiquitously transcribed in the ovary and in early embryonal stages of Xenopus laevis.

Interstrand duplexes in Friend erythroleukemia nuclear RNA. The interaction of non-polyadenylated nuclear RNA with polyadenylated nuclear RNA and with small nuclear RNAs

Intermolecular duplexes among large nuclear RNAs, and between small nuclear RNA and heterogeneous nuclear RNA, were studied after isolation by a procedure that yielded protein-free RNA without the use of phenol or high salt. The bulk of the pulse-labeled RNA had a sedimentation coefficient greater than 45 S. After heating in 50% (v/v) formamide, it sedimented between the 18 S and 28 S regions of the sucrose gradient. Proof of the existence of interstrand duplexes prior to deproteinization was obtained by the introduction of interstrand cross-links using 4'-aminomethyl-4,5',8-trimethylpsoralen and u.v. irradiation. Thermal denaturation did not reduce the sedimentation coefficient of pulse-labeled RNA obtained from nuclei treated with this reagent and u.v. irradiated. Interstrand duplexes were observed among the non-polyadenylated RNA species as well as between polyadenylated and non-polyadenylated RNAs. beta-Globin mRNA but not beta-globin pre-mRNA also contained interstrand duplex regions. In this study, we were able to identify two distinct classes of polyadenylated nuclear RNA, which were differentiated with respect to whether or not they were associated with other RNA molecules. The first class was composed of poly(A)+ molecules that were free of interactions with other RNAs. beta-Globin pre-mRNA belongs to this class. The second class included poly(A)+ molecules that contained interstrand duplexes. beta-Globin mRNA is involved in this kind of interaction. In addition, hybrids between small nuclear RNAs and heterogeneous nuclear RNA were isolated. These hybrids were formed with all the U-rich species, 4.5 S, 4.5 SI and a novel species designated W. Approximately equal numbers of hybrids were formed by species U1a, U1b, U2, U6 and W; however, species U4 and U5 were significantly under-represented. Most of these hybrids were found to be associated stably with non-polyadenylated RNA. These observations demonstrated for the first time that small nuclear RNA-heterogeneous nuclear RNA hybrids can be isolated without crosslinking, and that proteins are not necessary to stabilize the complexes. However, not all molecules of a given small nuclear RNA species are involved in the formation of these hybrids. The distribution of a given small nuclear RNA species between the free and bound state does not reflect the stability of the complex in vitro but rather the abundance of complementary sequences in the heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 400 WORDS)

Double stranded RNA in heterogeneous nuclear RNA from normal and chronic lymphocytic leukemic lymphocytes

Tritium labelled heterogeneous nuclear RNA (HnRNA) from normal and chronic lymphocytic leukemic (CLL) lymphocytes was investigated before and after fractionation into non-poly(A) containing (-HnRNA) and poly(A) containing (+HnRNA) HnRNA with respect to double stranded RNA (dsRNA). Statistically significant higher amounts of rapidly labelled RNA were recovered from CLL lymphocytes when compared to normal cases. Within the CLL cases a significant linear correlation (r = 0.95) was found between white blood cell counts and the amount of dsRNA in total HnRNA. After fractionation into (-) and (+) HnRNAs the ratios of dsRNAs, expressed as the dsRNA in (-) HnRNA divided by the dsRNA in (+) HnRNA, was lower than the corresponding values in normal cases for all the CLL cases except one. The relationship between (+) HnRNA and the total dsRNA level was different when comparing CLL and normal lymphocytes indicating a RNA processing abnormality.

Poly(A)-binding RNAs from nuclei and polysomes of BHK-21 cells

The presence in nuclei and cytoplasm of cultured BHK-21/C13 cells (baby hamster fibroblasts) of RNA species with high affinity for poly(A) was detected using either a Millipore-poly(A)-binding assay or columns of poly(A)-Sepharose 4B. The nuclear species which labels rapidly is metabolically unstable and appears to be a specific subclass of heterogenous nuclear RNA. Digestion with T1 RNAase gives rise to a low level (1%) of oligonucleotide fragments of a disperse size range which are relatively rich in uridylate residues. The cytoplasmic species with affinity for poly(A) is similar in size to polyadenylated messenger RNAs and also associates with polysomes. However it appears to be distinct from the polyadenylated messenger RNAs by virtue of an unusual base composition and relative metabolic instability.

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.

Adenylate-rich sequences of heterogeneous nuclear RNA from normal and chronic lymphocytic leukaemia lymphocytes

Rapidly labelled high molecular weight heterogeneous nuclear RNA (Hn RNA) from normal and chronic lymphocytic leukaemia (CLL) lymphocytes has been fractionated into two classes by chromatography on poly (U) sephasose. The (+) Hn RNA is bound to poly (U) sepharose and contains both a long poly (A) segment (100-200 nucleotides) and shorter (A) rich sequences (approximately 20-30 nucleotides. (-) Hn RNA is not bound to poly (U) sepharose and lacks the longer poly (A) segment but does contain shorter (A) rich sequences. Partial association of the short (A) rich segments with double-stranded regions was found for both classes of Hn RNA but was most pronounced in (-) Hn RNA from high WBC cases of CLL. Both classes of Hn RNA from CLL lymphocytes contain varying but generally higher amounts of the short (A) rich fraction than those in normals. Similar amounts of the longer poly (A) segments were found in (+) Hn RNA from both CLL and normal lymphocytes.

On the nature of 5' termini in nuclear pre-mRNA of Ehrlich carcinoma cells

5' terminal nucleosides of nuclear pre-mRNA of Ehrlich ascites carcinoma cells were analyzed by a combination of different chromatographic methods and phosphatase treatment. The heavy nuclear pre-mRNA contains mainly unblocked triphosphorylated nucleosides at the 5' end, although some capped 5' ends could also be found. In this respect, it differs from cytoplasmic poly(A)+ mRNA which contains blocked 5' termini and no triphosphorylated ends. The 5' terminal nucleotides in pre-mRNA are pppGp and pppAp (in a ratio of 3:2). The determination of pppNp content in poly (A)+, poly(U)+, and poly (A)-(U)- fragments of RNA has been used as an approach to establish the topography of pre-mRNA. We also established that the technique for isolation of triphosphorylated 5' terminal fragments of RNA based on hydroxyapatite chromatography (Bajszár, Samarina, and Georgiev, 1974) is still valid in the presence of blocked oligonucleotides. The latter do not interfere with fragments containing free triphosphate groups. Using this technique, we showed that a small but significant portion of triphosphorylated 5' end fragments of 100 nucleotides in length contain oligo(U) sequences reacting with poly(A)-Sepharose.

High molecular weight UMP-rich RNA of germinating wheat embryo

The synthesis of a relatively homogeneous RNA fraction was observed in germinating wheat embryo. The fraction synthesised within the first 3 h of germination had a high molecular weight (approx. 2.10(6)) and a specific nucleotide composition. In particular, the UMP content was unusually high (47 mol%). The high UMP content resulted probably from the presence of UMP-rich regions within the newly-synthesised polynucleotide chain. Neither ribosomal nor transfer DNA sequences were transcribed at the same time. It is suggested that the newly-synthesised RNA fraction represents an mRNA precursor and is transcribed in the immediate response of wheat embryo to the environmental stimuli to germinate.

Three distinct forms of nuclear poly(A) polymerase

Poly(A) polymerase activities have been solubilized from rat liver nuclei and purified by chromatography on Bio-Gel A-1.5M, DEAE-Sephadex and CM-cellulose. Three distinct forms of nuclear poly(A) polymerase have been resolved by chromatography on CM-cellulose. According to their sequence of elution from CM-cellulose these enzyme activities have been termed A, B and C. Enzymes A and B are Mn2+ -dependent, enzyme C requires Mg2+. With the same chromatographic step on CM-cellulose the Mn+ -dependent poly(A) polymerase activities were separated from a Mn2+ -dependent enzyme system capable of synthesizing RNA-primed poly(U), poly(G) and poly(C). The effect of different nuclear and cytoplasmic RNA primers on the rate of poly(A) formation suggests enzyme A to be responsible for the elongation of preexisting poly (A) chains. The phosphorylated derivated derivative of cordycepin, 3'-deoxyadenosine 5'-triphosphosphate (3'-dATP), which is known to inhibit nuclear poly(A) synthesis in vivo, also impairs poly(A) formation in vitro. It is shown that 3'-dATP very probably is not incorporated into poly(A)invitro, suggesting that 3'-dATP primarily affects the catalytic activities of the poly(A) polymerase species rather than directly blocking chain elongation.

Hybridization of polyuridylic acid to human DNA immobilized onto nitrocellulose filters

The level of deoxyadenylate (da) regions in human DNA was estimated from formation of poly(U)-poly(da) triplexes on nitrocellulose filters that were RNAase resistant. The (dA) rich sequences were determined following mild ribonuclease treatment of the poly(U)-DNA hybrids (5 mug/ml at 25 degreesC for 30 min), where as exhaustive ribonuclease treatment (5 mug/ml at 25 degrees C for 6 hr) estimated the more (dA) pure sequences. The level of (dA) rich regions was 0.39% of the DNA and for the more (dA) pure regions it was 0.07%. The (dA) regions were widely distributed throughout human DNA regardless of base composition or sequence repetition. However, a concentration of (dA) regions into main band CsC1 gradient fractions of DNA and into repeated DNA was observed.

Heterogeneous nuclear rna from lymphocytes of chronic lymphocytic leukaemia: adenylate-rich and double-stranded regions

Rapidly labelled high molecular weight nuclear RNA from lymphocytes of chronic lymphocytic leukaemia was analysed for ribonuclease-stable adenylate-rich and double-stranded regions. The polyadenylate content corresponds to 0.4-0.5 percent and the content of double-stranded sequences to 2-4 percent of the total nucleotides. Partial association of polyadenylate segments with double-stranded regions was found by comparative analysis of (3H)-adenosine and (3H)-uridine labelled ribonuclease-stable RNA before and after thermal denaturation. Comparison with normal lymphocytes shows lower proportions of polyadenylate-containing RNA binding to poly(U)-Sepharose in leukaemia cells than in normals. Partial degradation of rapidly labelled high molecular weight RNA was found in leukaemia cases with low white cell counts.