The control of ribosomal RNA transcription in lymphocytes. Evidence that the rate of chain elongation is the limiting factor

Phosphorylated nucleolar Tau protein is related to the neuronal in vitro differentiation

Tau is a multifunctional protein, originally identified as a cytoplasmic protein associated with microtubules. It is codified by the MAPT gene, and the alternative splicing, in the neuronal cells, results in six different isoforms. Tau was subsequently observed in the cell nucleus, where its function is not yet clearly understood. Here, we studied the MAPT gene and the cellular localization of the AT8 and Tau-1 epitopes of Tau protein, in the SK-N-BE cell line, which differentiates in neuronal-like cells after retinoic acid treatment. These epitopes correspond to the phosphorylated Ser202/Thr205 and unphosphorylated Pro189/Gly207 amino acid residues, respectively, possibly involved in conformational changes of the protein. Our results demonstrated the presence of the smaller Tau isoform (352 amino acids), whose amount increases in differentiated SK-N-BE cells, with Tau-1/AT8 nuclear distribution related to the differentiation process. Tau-1 showed a spot-like nucleolar localization, in both replicative and differentiated cells, while AT8 was only detected in the differentiated cells, diffusely occupying the entire nucleolar region. Moreover, in the replicative cells exposed to actinomycin-D, AT8 and Tau-1 move to the nucleolar periphery and colocalize, in few spots, with the upstream binding transcription factor (UBTF). Our results, also obtained with lymphocytes exposed to the mitogenic compound phytohaemagglutinin, indicate the AT8 epitope of Tau as a marker of neuronal cell differentiation, whose presence in the nucleolus appears to be related to rDNA transcriptional inactivation.

Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling

Synthesis of the 45S rRNA by RNA polymerase I limits cell growth. Knowledge of the mechanism of its regulation is therefore key to understanding growth control. rRNA transcription is believed to be regulated solely at initiation/promoter release. However, we found that stimulation of endogenous 45S rRNA synthesis by epidermal growth factor (EGF) and serum failed to induce an increase in RNA polymerase I engagement on the rRNA genes, despite robust enhancement of 45S rRNA synthesis. Further, endogenous transcription elongation rates were measured and found to be directly proportional to 45S rRNA synthesis. Thus, elongation is a rate-limiting step for rRNA synthesis in vivo. ERK phosphorylation of the HMG boxes of UBF, an RNA polymerase I factor essential for transcription enhancement, was shown to directly regulate elongation by inducing the remodeling of ribosomal gene chromatin. The data suggest a mechanism for coordinating the cotranscriptional assembly of preribosomal particles.

Accurate and statistically verified quantification of relative mRNA abundances using SYBR Green I and real-time RT-PCR

Among the many methods currently available for quantifying mRNA transcript abundance, reverse transcription-polymerase chain reaction (RT-PCR) has proved to be the most sensitive. Recently, several protocols for real-time relative RT-PCR using the reporter dye SYBR Green I have appeared in the literature. In these methods, sample and control mRNA abundance is quantified relative to an internal reference RNA whose abundance is known not to change under the differing experimental conditions. We have developed new data analysis procedures for the two most promising of these methodologies and generated data appropriate to assess both the accuracy and precision of the two protocols. We demonstrate that while both methods produce results that are precise when 18S rRNA is used as an internal reference, only one of these methods produces consistently accurate results. We have used this latter system to show that mRNA abundances can be accurately measured and strongly correlate with cell surface protein and carbohydrate expression as assessed by flow cytometry under different conditions of B cell activation.

The relative rDNA content of a NOR determines its level of expression and its probability of becoming active. A sequential silver staining and in-situ hybridization study

Silver staining was used to estimate the expression of nucleolar organizing regions (NORs), and in-situ hybridization (ISH) with rDNA probes was used to estimate the relative content of rDNA in each NOR in chromosome preparations of the dormouse, Eliomys quercinus, a species with two NOR-bearing chromosome pairs. Both types of signals were sequentially investigated on every NOR by using an Ag-ISH sequential staining method, which made it possible to demonstrate that the relative amount of rDNA in a NOR in comparison with the other chromosomes of the complement determines its level of expression and its likelihood of becoming active, regardless of whether the NORs are homologous or not. We suggest that the NORs in each cell are activated in accordance with an established hierarchy. We propose a two-stage model to relate NOR structure and function, which is consistent with these results and with current knowledge on the molecular regulation of NOR transcription.

Presence of an inhibitor of RNA polymerase I mediated transcription in extracts from growth arrested mouse cells

Extracts obtained from mouse cells growth arrested at stationary phase or under serum starvation exhibit no specific rDNA transcription activity. Experiments with mixed transcriptionally active and inactive whole cell extracts (WCE) obtained from rapidly dividing or growth arrested cells, respectively, demonstrate that rRNA synthesis in vitro can be suppressed by a polymerase I transcription inhibitory activity (PIN), present in inactive extracts. This inhibition effect is not related to increased nuclease activity and affects neither the non-specific Pol I transcription, nor a polymerase II promoter. A comparison of WCE isolated under different growth conditions indicates that PIN changes according to the physiological state of the cell. It reaches a maximal level soon after serum depletion and disappears rapidly when cells are allowed to recover in serum-rich medium. PIN can be clearly demonstrated in WCE but not in nuclear or cytoplasmic extracts and can be also obtained by an additional high salt extraction of nuclei. Furthermore, gel retardation and transcription-in-pellet assays demonstrate that rDNA promoter binding and preinitiation complex stability are similar in active and inactive WCE. This indicates that some later stage(s) of rDNA transcription, rather than the preinitiation complex formation, are attenuated by inactive extracts. Analysis of partially fractionated extracts suggests that PIN is not associated with but can be separated from polymerase I.

Effect of cytokinins on ribosomal RNA gene expression in excised cotyledons of Cucurbita pepo L

Excised pumpkin (Cucurbita pepo L.) cotyledons were used to investigate the effects of two different types of cytokinins: N(6)-benzyladenine and N1-(2-chloro-4-pyridyl)-N2-phenylurea on RNA synthesis in isolated nuclei. Treatment of cotyledons with both cytokinins resulted in a rapid enhancement of nuclear RNA-polymerase-I activity (EC 2.7.7.6). Maximum stimulation of RNA polymerase I, responsible for rRNA synthesis, was observed 4-6 h after the start of cytokinin action. The activity of RNA polymerase II was stimulated much more slowly and to a lesser extent. Uridine 5'-monophosphate-uridine analysis of the alkalidigested nascent pre-rRNA chains showed that the stimulation of RNA-polymerase-I activity was the consequence of an increase of the polyribonucleotide-clongation rate. No significant change in the number of transcribing enzyme molecules was defected after hormone treatment (86·10(3) RNA-polymerase-I molecules per diploid genome).Indications that de-novo protein synthesis is necessary for cytokinin-mediated RNA-polymerase stimulation were derived from experiments showing inhibition by cycloheximide.

Complex RNA chain elongation kinetics by wheat germ RNA polymerase II

Kinetics of RNA chain elongation catalyzed by wheat germ RNA polymerase II have been studied using various synthetic DNA templates in the presence of excess dinucleotide monophosphate primers. With single- or double-stranded homopolymer templates, the double reciprocal plots 1/(velocity) as a function of 1/(nucleotide substrate) exhibit positive, negative or no curvature. With poly(dAT) as template, the mechanism of nucleoside monophosphate incorporation into RNA is not the ping-pong kinetic mechanism which was derived for E. coli RNA polymerase (6). Noncomplementary nucleoside triphosphates inhibit RNA transcription allosterically. Cordycepin triphosphate behaves as ATP, and not only inhibits AMP incorporation but also that of UMP and GMP on appropriate templates. The reason for this complex kinetic behavior is not yet understood. Possibilities are raised that there are several nucleoside triphosphate binding sites on wheat germ RNA polymerase II, that additional nucleoside triphosphate dependent enzymatic activities are required for reaction to occur or that the Km value for incorporation of a given nucleoside monophosphate into RNA is dependent on the length of the RNA chain and/or the nucleotide sequence surrounding the complementary base on the DNA template.

Aurintricarboxilic acid as a tool for investigating the template-bound and unbound forms of RNA polymerase I in permeabilized cells

The presence of template-bound and unbound RNA polymerase I in permeabilized cells was investigated. The two enzyme forms were defined on the basis of their different susceptibilities towards aurintricarboxilic acid (ATA). It was found that addition of ATA to permeabilized cells suppresses initiation of new RNA chains by RNA polymerase I but has no effect on the activity of the enzyme already engaged in transcription. This last activity is not affected even after washing the permeabilized cells for removal of the ATA. The RNA polymerase I activity solubilized from permeabilized cells pre-treated with ATA is 60-70% of that obtained from non-treated controls. The decrease of the solubilized enzyme activity was observed after purification of the enzymes by DEAE-Sephadex columns and cannot be attributed to the presence of inhibitory or activating factors in the enzyme preparations. The simplest interpretation of these findings is that two distinct RNA polymerase I fractions, showing different sensitivities towards ATA are present in permeabilized cells. These fractions should represent the template-bound and unbound RNA polymerase I. The results also show that the amount of ATA-insensitive activity is lower in nuclei than in permeabilized cells, suggesting that detachment of template-bound enzyme occurs during nuclei isolation.

RNA synthesis and number of transcribing polymerase molecules in ischemic liver nuclei

Nuclei isolated from ischemic liver show a consistent reduction of their RNA synthesis. The reduction persists at high ionic strength and in the presence of heparin, when RNA synthesis in vitro is fully activated and occurs in the presence as well as in the absence of alpha-amanitin. Both the number of transcribing polymerase molecules and the rate of elongation of initiated polynucleotide chains seem to be equally affected.