[FEATURES OF tRNA GENES AND YOUNG SUBFAMILIES Alu-REPEATS EXPRESSION IN PROLIFERATION AND APOPTOSIS].

Using human U937 cell culture, we studied the expression of the RNA polymerase III-directeci genes--tRNAi(Met)1, tRNA(His) and Alu-repeats belonging to the youngest subfamilies AluY (AluYa5 and AluYb8) - du- ring camptothecin-induced apoptosis. The level of tRNAiMetl increased 1.5-fold, tRNAHis level did not change, and the level of AluY-RNA increased 4-10-fold after 6 hours of CAM treatment compared to control (non-apoptotic) cells. We also studied the level of AluYb8 DNA methylation at apoptosis U937. We have shown that the level of AluYb8 DNA methylation does not change at different stages of apoptosis, and does not differ in apoptotic and control cells. We assume that the increase in gene expression of young AluY repeats and tRNAi(Met)1 plays a role in the apoptosis pathway realization in the cell.

[Role of the expression of mobile elements sine and the genes directed by RNA polymerase III in the regulation of intracellular processes].

Small non-translated RNA genes directed by RNA polymerase III (class III genes) comprise substantial part of mammal genomes--about 10%. Besides well-known class III genes--5S rRNA, tRNA, 7SL RNA genes, mobile elements SINEs--a number of new RNA polymerase III-directed genes with poorly studied functions was revealed. According to the latest data, different class III genes can have significantly different expression regulation mechanisms. These data support the existence of gene-specific, tissue-specific and cell state-specific (resting, stress, apoptosis) mechanisms for the regulation of these gene transcription. The review is devoted to the consideration of known small non-translated RNA genes, possible mechanisms of their expression regulation (by the example of some SINEs), and the role of their transcription products in the intracellular processes regulation.

[Computational search for potential post-translational modification sites in human RNA polymerase III subunits].

The transcription of small stable non-translated RNA genes (class III genes), directed by RNA polymerase III, is strictly regulated in accordance to physiological state of the cell (growth rate, cell cycle stage, apoptosis, etc.) Post-translational modifications of the polymerase may play the important role in class III gene transcription regulation. Using computational programs searching for potential post-translational modifications sites in proteins (MotifScan, NetPhos 2.0, and Yin-Yan 1.2), possible sites of phosphorylation were identified in all 17 subunits of human RNA polymerase III, and possible sites of reciprocal phosphorylation and glycosilation ("yin-yan" sites) - in 13 subunits. Among the identified sites -17 sites of phosphorylation in seven subunits are conservative in human, Saccharomyces cerevisiae and Schizosaccharomyces pombe, including two "yin-yan" sites in two subunits. The data obtained can be used for experimental identification of RNA polymerase III modification sites in vivo in cells being in different physiological states.

[RNA polymerase III transcription apparatus: structure and transcription regulation].

RNA polymerase III is a complex multi-subunit enzyme directing transcription of small stable non-translated RNA genes: tRNAs, 5S rRNA, Alu-RNA, U6 snRNA genes and some others (class III genes). Because of its complexity the enzyme is the worst studied among three forms of eukariotic RNA polymerases, but it draws more attention of the researchers in recent years. The reason is that new data appeared about an essential role of RNA polymerase III RNA products in such important cell processes as growth, proliferation and differentiation. It was shown that the RNA product levels are changed depending on cell growth rate and cell cycle stage, during cancer transformation, virus infection and heat shock, and either depend on physiological state of the cell (slow and active proliferation and apoptosis). In this review we consider the structure and function of RNA polymerase III, its general transcription factors and holoenzyme, the structure of different class III gene promoters, the preinitiation complex assembly and the transcription cycle. The second part of the review is devoted to the regulation of class III gene transcription in dependence on cell cycle stage, growth factor influence and cell growth rate, during cell transformation and apoptosis.

Small stable RNA level depends on the physiological state of the cell.

The level of 5S rRNA and tRNAi(Met)1 synthesized by RNA polymerase III was investigated in human epidermoid carcinoma cells A431 at different physiological states: low and high proliferation and apoptosis. The real-time RT-PCR method using SYBR Green I was applied to measure certain RNA species in total cellular RNA. The share of 5S rRNA was practically the same in slowly and actively proliferating A431 cells, but increased about 2.5-fold in apoptotic cells. The share of initiator tRNAi(Met)1 in actively proliferating and apoptotic cells was 1.5-2.0 times higher than in slowly proliferating cells. Our results suggest a possible existence of special mechanisms regulating RNA polymerase III-directed transcription from different type promoters in accordance with the physiological state of the cell.

[Use of the real-time RT-PCR method for investigation of small stable RNA expression level in human epidermoid carcinoma cells A431]. / Ispol'zovanie metoda RT-PCR v real'nom vremeni dlia izucheniia urovnia ékspressii malykh stabil'nykh RNK v kletkakh épidermoidnoi kartsinomy cheloveka A431.

Real-time RT-PCR using fluorescence dyes (e.g. SYBR Green I) is currently the most sensitive and precise method for investigation of RNA level and has long been widely used for absolute and relative quantification of mRNA in the cell. This highly sensitive method allows measurement of different type RNA level in the cell based on the kinetics of the corresponding double-stranded cDNA amplification. Upon its binding to the minor groove of double-stranded DNA, SYBR Green I dye increases its fluorescence about 100-fold, and this increase can be recorded even at early cycles of amplification. During the real-time RT-PCR procedure the level of amplified DNA is measured after every cycle of amplification, which permits to perform quantification at the cycles when amplification curve has not yet reached the "plateau" range and corresponds to the range of exponential increase in DNA amount. This approach makes it possible to avoid misinterpretation of data typical of conventional PCR methods "in the end point" and caused by a deficiency of one or more reaction components at the late PCR cycles. We applied for the first time real-time RT-PCR using SYBR Green I for the measurement of the class III genes RNA-product level, that is, small stable non-translated RNAs--ribosomal 5S rRNA, initiator transfer RNAiMet1, and Alu-RNA, synthesized by DNA-dependent RNA polymerase III. We investigated the level of 5S rRNA-, tRNA- and Alu-gene expression in the cell being in different states: with prolonged generation period, activated to proliferation, and apoptotic. The expression level was judged from the content of corresponding RNA-products in the total cellular RNA. The used approach enabled us to find out the specific RNA share in the total cell RNA. Human epidermoid carcinoma cells A431 were used as a model for investigating class III gene expression level in vivo. These cells expose on their surface an abnormally large amount of receptors to epidermoid growth factor (EGF), and the result of EGF action on A431 cells depends on the growth factor concentration. Low concentrations of EGF (0.1 ng/ml) cause active proliferation of A431 cells, but its high concentrations (10-100 ng/ml) cause apoptosis in these cells. Besides, upon growing in serum-free media, A431 cells continue to proliferate, but by this extending the generation period to 48 h, against 30 h on growing in serum-containing media. Hence, A431 cells can serve as a useful model for investigation of specific gene expression level in cells being in different physiological states, in both slowly and actively proliferating cells, and in apoptotic cells. For successful use of real-time RT-PCR in 5S rRNA, tRNAi(Met)1 and Alu-RNA level quantification, we optimized the amplification reaction conditions. We took into account that the share of each particular RNA in the cell may vary--the share of ribosomal RNA is high, tRNAi(Met)1--low, and Alu-RNA--very low. Moreover, the level of some small RNAs (e.g. Alu-RNA) can vary significantly in cells of different lines. This explains why the amount of cDNA, gained by reverse transcription of total cellular RNA, and the concentration of specific primers used for PCR were different in each case. We showed that the expression of different class III genes--5S rRNA-, tRNA- and Alu-genes, was not similarly regulated in response to external stimuli, causing prolongation of generation period, activation of proliferation and apoptosis. 5S rRNA level was practically the same in A431 cells both having prolonged generation period and being activated by EGF in low concentration, but in apoptotic cells this level dramatically fell about 8-fold. Alu-RNA level was equal in cells with prolonged generation period and in apoptotic cells, and increased about 2-fold in cells activated by EGF in low concentration. The initiator tRNAi(Met)1 level in cells activated by EGF in low concentration and in apoptotic cells was by almost two times higher than in cells with prolonged generation period. The data obtained testify that the real-time RT-PCR method using SYBR Green I yields highly reliable and reproducible quantification for the level of class III gene RNA-products--small stable RNAs (5S rRNA, tRNA and Alu-RNA). Examination of each specific RNA level requires individual selection for the amplification reaction conditions: the amount of cDNA and primer concentration in the sample. This is primarily caused by different expression levels in some particular class III genes within the frames of the cells, and by different levels of some small stable RNAs (e. g. Alu-RNA) in different cell lines. Special attention must be paid to the internal control for discriminating between specific RNA levels in proliferating and apoptotic cells, as in the late apoptosis RNAs of most types are degraded (for example, mRNA of "house-keeping" gene for RPLP0 protein, used as a possible internal control in our experiments). As far as the applied approach allows estimation of a specific RNA share in the total cellular RNA, we propose to chose as internal control mRNA, whose share doesn't change during the total RNA degradation in apoptosis and thus, mRNA degradation is not selective (in relation to other type RNAs). In that way, the real-time RT-PCR method, which is currently the most sensitive and precise method for quantification of RNA in the cell, holds much promise for the investigation of not only different mRNAs, but also small stable RNAs, synthesized by RNA polymerase III.

[Phosphorylation and dephosphorylation of rna polymerase III holoenzyme are modifications regulating the level of transcription in vitro]. / Fosforilirovanie-defosforilirovanie kholoénzima RNK-polimerazy III--modifikatsii, reguliruiushchie uroven' transkriptsii in vitro.

Two subforms of RNA polymerase III-IIIa and IIIb--were identified in human placenta nuclei. These subforms differed in molecular weight of one subunit, and in buoyant density in glycerol concentration gradient. Protein kinase activity, which phosphorylates at least four subunits of RNA polymerase IIIa and three subunits of RNA polymerase IIIb in vitro, was copurified with both the subforms. Protein kinase activity was inhibited by wortmannin, a specific PI3-kinase inhibitor. RNA polymerase III dephosphorylation by alkaline phosphatase in vitro decrease the transcription level on specific Alu-template. The associated protein kinase was not able to phosphorylate dephosphorylated RNA polymerase IIIa and to restore the transcription level up to the control one.

[DNA-dependent RNA polymerase I from human placental nuclei]. / DNK-zavisimaia RNK-polimeraza I iz iader platsenty cheloveka.

This paper describes a large-scale method for solubilisation and purification of DNA-dependent RNA-Polymerase I from mature human placenta. The solubilisation method involves homogenization of the whole human placenta, isolation of cell nuclei, sonication of separated nuclei at high ionic strength and ammonium sulfate precipitation. The purification method consists of chromatography of RNA-Polymerase I activity on DEAE-Sephadex A-25 and Phosphocellulose P-11, and glycerol-density gradient centrifugation. In result, RNA-Polymerase I of human placenta nuclei has been shown to be completely resistant to alpha-amanitin. Besides dependence of RNA-Polymerase I on different Mg2+ and Mn2+ concentrations, glycerol concentration and ionic strength was studied. Using our results, an optimal RNA-Polymerase I assay mixture was developed. The subunit composition of RNA-Polymerase I was investigated by dodecylsulfate-gel electrophoresis. The RNA-Polymerase I molecule of human placenta consists of 13-14 polypeptides.

[Extracellular DNA of blood after irradiation]. / Vnekletochnaia DNK krovi posle oblucheniia.

It has been shown that blood extracellular DNA of irradiated rats largely consists of the low-molecular DNA and its oligomers. Molecular masses of oligomers are multiple to molecular mass of monomer fragment with nucleosome size. The low-molecular DNA has linear form. The average content of GC-pairs in low-molecular DNA is higher than in total rat's DNA (48.5% against 41.5%). The low-molecular DNA is a part of complex containing RNA, acidic proteins and lipids. It is assumed that the formation of low-molecular DNA is a result of Ca/Mg-dependent nuclear endonuclease action.

[Probing of the linear distribution of nucleosomes in chromatin]. / Zondirovanie lineinogo raspredeleniia nukleosom v khromatine.

The binding of the antibiotic dyes to chromatin fragmented by various ways and to preparations of "complete" (MH3, 206 DNA base pairs) and "minor" MH1, 155 DNA base pairs) nucleosomes was studied. The latter were obtained from the total hydrolysate of nuclear chromatin hydrolysis by Ca-Mg-dependent endonuclease, using preparative electrophoresis in polyacrylamide gel. In liver chromatin of different vertebrate species the actinomycin D binding is decreased by 70% as compared to DNA binding, while that of ethidium bromide is reduced only by 40%. The splitting of part of internucleosomal DNA by Ca-Mg-dependent endonuclease further decreases the number of binding sites for ethidium bromide, but not for actinomycin D. MH3 bid 24 molecules of actinomycin D per 10(3) of nucleotides; their DNA contain 43.4% of GC-pairs. The GC content in MH1 is 47.7%; they bind 28 dye molecules per 10(3) of nucleotides. The data obtained are discussed in terms of possible predominant localization of nucleosomal cores in GC-pair-rich DNA sites.

[Study of heterogeneity of the chromatin endonuclease fragment by free flow electrophoresis]. / Issledovanie geterogennosti endonukleaznykh fragmentov khromatina elektroforezom v svobodnom potoke.

The oligomer chromatin fragments relatively uniform in size (8--11 nucleosomes) were prepared by a short-term endonycleolysis. The heterogeneity of these fragments with respect to their electrophoretic mobility was revealed using free flow electrophoresis. The individual fragmentated chromatin subfractions were obtained. These subfractions differed in their protein and RNA content per DNA weight unit, in quantitative ratios of different zones of high molecular weight non-histone proteins and in thermal and alkaline denaturation kinetics. It was also found that the parameters investigated are correlated with electronegativeity of the fragmentated chromatin subfractions.

[Analysis of brain chromatin subunit composition using different endonucleases]. / Analiz syb'edinichnoi organizatsii khromatina mozga s pomoshch'iu razlichnykh endonykleaz.

A comparison of the processes of chromatin digestion in brain and liver nuclei by Ca, Mg-dependent and staphylococcal endonucleases demonstrates a similarity of the subunit composition of chromatin from both tissues and reveals the same type of linked DNA regions. However, a formation of low molecular weight DNP fragments during hydrolysis and the DNA spectra of soluble and insoluble DNP fragments suggest that brain chromatin contains these fragments alongside with the regions, which are specific for this particular tissue, predominate in it and are resistant to staphylococcal and, particularly, to Ca, Mg-dependent endonucleases. This is paralleled with a non-histone protein enrichment of different brain chromatin fractions and an expansion of the electrophoretic monomer band towards the fragment with a greater molecular weight. It may be assumed that brain nucleosomes are characterized by a higher size heterogeneity of linked DNA, part of which are mostly covered by non-histone proteins, and/or are characterized by a greater set variety.

[Analysis of brain chromatin subunit organization]. / Analiz subdedinichnoí organizatsiikhromatina mozga.

Autodigestion of chromosomal DNA does not take place during the brain nuclei incubation in the presence of Ca2+ and Mg2+. The kinetic of chromatin digestion in brain and liver nuclei by staphylococcal nuclease and the formation of DNP-fragments suggest that subnucleosomes are generated in both cases by digesting of monomer specific sites. This monomer contains 185--200 DNA base pairs and the most starting DNA going throughout it. However the quantity of nuclease-resistant DNA in brain chromatin is more and the rate of subnucleosome formation is less than in liver chromatin. Redigestion of isolated monomers of brain chromatin results in the appearance of subnucleosomes similar to those which are formed under limited digestion of nuclear chromatin. The incubation of brain nuclei in the presence of Ca, Mg-dependent endonuclease prepared from liver nuclei results in the appearance of fragment. DNA-spectra of these fragments are similar to those prepared under digestion of liver chromatin in situ. These data suggest definite resemblance of subunit organization in brain and liver chromatin.

[Effect of adrenocorticotropic hormone on nucleic acid and protein synthesis and content in the brain of rat embryos in the early stages of neurogenesis]. / Vliianie adrenokortikotropnogo gormona na sintez i soderzhanie nukleinovykh kislot i belka v golovnom mozge zarodyshei krys na rannikh stadiiakh neirogeneza.

The injection of adrenocorticotropic hormone (ACTH) of prolonged effect at the doses of 4 and 10 M. U. to the intact rats from the 11th till the 15th day of pregnancy resulted in the twofold increase of protein content in the brain and its decrease in the liver of 15 days old embryos, as compared with the control ones. The content of DNA, RNA and proteins in the placenta of experimental animals increased as well. The rate of incorporation of 3H-thymidine in the liver DNA and 14C-leucine in the liver and brain acid-soluble protein decreased within small intervals of time following the treatment. The total radioactivity of proteins in the liver, brain and placenta calculated per DNA unit was similar to the control one whereas the specific radioactivity of total protein in the liver of experimental embryos was higher than in the control.

[Comparative characteristics of chromatin endonuclease fragments]. / Sravnitel'naia kharakteristika endonukleaznykh fragmentov khromatina.

Soluble fragments of chromatin obtained by Ca, Mg-dependent endonuclease digest of rat liver nuclei, have been separated by gel chromatography on Sepharose 4B into three zones, containing oligomers, tetramers--dimers and monomers, respectively. The content of nonhistone proteins and particularly lysine-rich histones is decreased with a transition from theoligomers to monomers. The average protein/DNA ratio of the monomers is equal to 1.36 and that of histone/DNA ratio--to 0.82. The dependence of the degree of chromatin digest by endonuclease on its protein content and conditions of isolation and incubation of nuclei is discussed. The chromatin monomer formed appears to be made up of a nucleosome and short portions of spacer DNA bound to some part of histone HI and nonhistone proteins.

[Effect of the conditions of isolation and incubation of the nuclei on digestion of DNA chromatin by calcium- and magnesium-dependent endonuclease. Change in the spectrum of chromosomal proteins and possible role of DNA-protein interactions]. / Vliianie uslovii vydeleniia i inkubatsii iader na droblenie DNK khromatina Ca, Mg-zavisimoi endonukleazoi. Izmenenie spektra khromosomal'nykh belkov i vozmozhnaia rol' DNK-belkovykh vzaimodeistvii.

Digesting of chromosomal DNA of interphase rat liver nuclei by Ca, Mg-dependent endonuclease in situ in the presence of chelating agents results in the appearance of the soluble DNP--up to 30% of the total DNA. In addition, 50% of the chromatin is solubilised after mild ultrasonication. In the absence of the chelating agents the degree of fragmentation is considerably increased. The process is accompanied by a loss of some histone and nonhistone chromosomal proteins; the nonhistone proteins are lost selectively. The preliminary removal of the nuclear membrane and significant part of the proteins by tritone X-100 promotes the chromatin degradation and the appearance of low molecular weight fragments. The DNA-fragments of solubilised chromatin are similar to the DNA-fragments of residual chromatin, but in the presence of the chelating agents the latter does not contain monomeric fragments.