RNA methylation and control of eukaryotic RNA biosynthesis: processing and utilization of undermethylated tRNAs in CHO cells

Expression of targeted ribozyme against telomerase RNA causes altered expression of several other genes in tumor cells

Telomeres are tandem repeat sequences present at chromosome end that are synthesized by RNA-protein enzyme called telomerase. The RNA component (TR) serves as template for telomerase reverse transcriptase (TERT) for generating telomere repeats. TERT is overexpressed in actively dividing cells including cancerous cells, absent in differentiated somatic cells whereas human telomerase RNA (hTR) is present in normal as well as in cancer cells. Telomerase overexpression in cancer cells ensures telomere length maintenance that actually provides proliferative advantage to cells. Stable expression of ribozyme against hTR in HeLa cells results in reduction of hTR levels, telomerase activity, and telomere length which is accompanied by altered cell morphology and expression of several specific cellular genes. The altered genes deduced from differentially display PCR and 2D gel electrophoresis upon hTR knockdown have function in ribosome biogenesis, chromatin modulation, cell cycle control, and p63-dependant pathways. Our observations shows hTR participates in diverse cellular functions other than telomere maintenance, validates as a possible drug targets in p53- and pRB-negative status, and indicated possible cross-talks between telomerase and other cellular pathways.

Mapping and significance of the mRNA methylome

Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.

Evidence that the methylation inhibitor cycloleucine causes accumulation of a discrete ribosomal RNA precursor in hamster mitochondria

A novel RNA fraction, 'Cy RNA,' that accumulates in mitochondria when hamster cells are treated with the methylation inhibitor cycloleucine, has been characterized by high resolution acrylamide gel electrophoresis and DNA-RNA hybridization. Cy RNA ran in gels as a discrete band, with an apparent chain length of 2 600. It hybridized specifically to restriction fragments containing genes for the mitochondrial ribosomal RNAs. We infer that Cy RNA is a discrete polycistronic ribosomal RNA precursor transcript, whose processing is dependent on normal methylation.

Effects of sinefungin on rRNA production and methylation in the yeast Saccharomyces cerevisiae

The antifungal agent, Sinefungin (SF), has been shown to be an inhibitor of transmethylation reactions. We report here the effects of SF on the production and methylation of rRNA in the yeast, Saccharomyces cerevisiae. Under conditions of SF treatment which have been shown to affect the regulation of cell proliferation in this yeast, pulse-chase labeling experiments using [methyl-3H]methionine and [3H]uracil indicated that methyl incorporation into rRNA during a short labeling period was inhibited, and stable 18 S rRNA production was differentially decreased. Other experiments quantitating modified nucleotides in newly produced rRNA showed that stable molecules were methylated. Taken together, these results suggest that SF slows methylation of rRNA, and is associated with differential loss of undermethylated 18 S rRNA species.

Activity patterns of aminoacyl-tRNA synthetases, tRNA methylases, arginyltransferase and tubulin: tyrosine ligase during development and ageing of Caenorhabditis elegans

As a step in the characterization of development and ageing in the nematode Caenorhabditis elegans, the activities of different groups of enzymes that supposedly exert modulating functions in and after protein synthesis have been determined. From embryonic (E), the four juvenile larval stages (L1-L4) and the gravid adult (A,A+), the selection of defined developmental stages extends to two different preparations of aged nematodes (S10, S12). Some aminoacyl-tRNA synthetase activities remain nearly unchanged in all stages up to the adult, some increase continuously during the larval stages and the remaining activities show stage-specific alterations. Upon ageing all activities except the one for tryptophan decrease sharply, tRNA methylase activities increase from E to L4, decrease from L4 to adult and to aged nematodes with only qualitative alterations in substrate specificity. The activity of tubulin: tyrosine ligase exhibits a parallel pattern, while arginyltransferase activity has a plateau between L2 and L4. The results are consistent with the idea of a modulation of protein synthesis and other cellular processes by quantitative activity changes during development and ageing.

Synthesis and behaviour of small RNA species of CHO cells submitted to a heat chick

Incubation of Chinese hamster ovary (CHO) cells for 1 hour at 43 degrees C results in an inhibition of high molecular weight RNA synthesis while most of the ow molecular weight RNAs are still synthesized. In cells returned to 37 degrees C, the transcription of high molecular weight RNA is reinitiated after 7 h recovery. The synthesis of snRNA A, C, D which are transcribed by RNA polymerase B (II) is inhibited in cells incubated at 43 degrees C while the synthesis of 4S, 5S, L and K components is not affected. During the recovery period the synthesis of low molecular weight RNA is increased variously according to the components relative to control cells : x 1.5 for 5S RNA to x 8 for snK. After 9 h recovery at 37 degrees C, snA and SnD are again synthesized but newly synthesized snC does not appear in the nucleus while a putative preC component accumulates in the cytoplasm. On the other hand, the distribution of all the pre-existing low molecular weight RNAs is not affected by the heat shock.

Differences between transfer RNA methylase activity in human diploid fibroblasts during in vitro and in vivo aging

The change of the specific activity of S-adenosylmethionine: tRNA methyltransferase in cultures of human diploid fibroblasts at different passages has been measured and compared with that in the same type of cells derived from donors of different ages. Whereas the specific activity of tRNA methylase in the in vitro aged cells was found to decline gradually with increasing passage number of the culture, a different activity--age relationship was observed for this enzyme in cells derived from donors of different ages. The activity of tRNA methylase is high in the fetal cells and drops drastically in the "newborn" cells. After a further 10% decline, the activity of this enzyme reaches a steady low level in the postnatal cells from donors ranging in age from 3 months to 94 years. These findings cast doubt on the validity of the assumption that the results obtained from in vitro aging experiments reflect the biochemistry of aging in vivo. The "fetal" enzyme can methylate the "aged" tRNA but the "aged" enzyme cannot methylate the "fetal" tRNA. The fetal cells contain enzyme activities specific for the formation of m1A, m5C and m1G. These activities are low or deficient in "aged" cells. Control experiments showed that all of these results are due neither to the presence of inhibitor or stimulator in the extract nor to effects related to the population density, sex or growth rate of the culture.

Methionine metabolism in BHK cells: preliminary characterization of the physiological effects of cycloleucine, an inhibitor of s-adenosylmethionine biosynthesis

Cycloleucine is in vitro a competitive inhibitor of methionine adenosyltransferase, an enzyme involved in S-adenosylmethionine biosynthesis. The physiological effects of this drug on baby hamster kidney cells have been studied. When cells are grown in a medium containing 10 micron methionine, cycloleucine is an inhibitor of cell proliferation; high concentrations of methionine are able to withdraw this inhibition suggesting that cycloleucine toxicity is related to methionine metabolism. The drug does not primarily affect methionine uptake and its subsequent use for protein biosynthesis. Cycloleucine toxicity is correlated with a block of SAM biosynthesis and nucleic acids methylations. The actions of cycloleucine on progression in the cell cycle and DNA, RNA and protein biosynthesis are studied. The implications of these results are discussed.

Biosynthesis and utilization of extensively undermethylated poly(A)+ RNA in CHO cells during a cycloleucine treatment

The role of RNA methylations in the control of mRNA maturation and incorporation into polysomes has been investigated through a study of the effects in vivo of cycloleucine, a specific inhibitor of S-adenosyl-methionine mediated methylation. During the cycloleucine treatment, the rate of biosynthesis of hnRNA and its subsequent polyadenylation were only slightly reduced as compared with untreated cells. However a significant lag-time in the cytoplasmic appearance of poly(A)+ undermethylated molecules was observed, in parallel with a transient shift in the average size of hnRNA towards higher molecular weight. Nevertheless, the total amount of pulse-labelled poly(A)+ mRNA transferred to cytoplasm after a long chase time (3 h.) was approximately the same for both cycloleucine-treated and control cells. Extensively undermethylated poly(A)+ cytoplasmic RNAs, possessing a 5' terminal cap were incorporated into polysomes in proportions very similar to control messenger molecules. These results suggest that a normal level of methylation is not stringently required for the production of the functional mRNA molecules although it appears to be of importance for the kinetics of the maturational process.