Cytosolic mRNA Levels Research Articles

Anota: analysis of differential translation in genome-wide studies

Translational control of gene expression has emerged as a major mechanism that regulates many biological processes and shows dysregulation in human diseases including cancer. When studying differential translation, levels of both actively translating mRNAs and total cytosolic mRNAs are obtained where the latter is used to correct for a possible contribution of differential cytosolic mRNA levels to the observed differential levels of actively translated mRNAs. We have recently shown that analysis of partial variance (APV) corrects for cytosolic mRNA levels more effectively than the commonly applied log ratio approach. APV provides a high degree of specificity and sensitivity for detecting biologically meaningful translation changes, especially when combined with a variance shrinkage method for estimating random error. Here we describe the anota (analysis of translational activity) R-package which implements APV, allows scrutiny of associated statistical assumptions and provides biologically motivated filters for analysis of genome wide datasets. Although the package was developed for analysis of differential translation in polysome microarray or ribosome-profiling datasets, any high-dimensional data that result in paired controls, such as RNP immunoprecipitation-microarray (RIP-CHIP) datasets, can be successfully analyzed with anota. The anota Bioconductor package, www.bioconductor.org.

Identification of differential translation in genome wide studies

Regulation of gene expression through translational control is a fundamental mechanism implicated in many biological processes ranging from memory formation to innate immunity and whose dysregulation contributes to human diseases. Genome wide analyses of translational control strive to identify differential translation independent of cytosolic mRNA levels. For this reason, most studies measure genes' translation levels as log ratios (translation levels divided by corresponding cytosolic mRNA levels obtained in parallel). Counterintuitively, arising from a mathematical necessity, these log ratios tend to be highly correlated with the cytosolic mRNA levels. Accordingly, they do not effectively correct for cytosolic mRNA level and generate substantial numbers of biological false positives and false negatives. We show that analysis of partial variance, which produces estimates of translational activity that are independent of cytosolic mRNA levels, is a superior alternative. When combined with a variance shrinkage method for estimating error variance, analysis of partial variance has the additional benefit of having greater statistical power and identifying fewer genes as translationally regulated resulting merely from unrealistically low variance estimates rather than from large changes in translational activity. In contrast to log ratios, this formal analytical approach estimates translation effects in a statistically rigorous manner, eliminates the need for inefficient and error-prone heuristics, and produces results that agree with biological function. The method is applicable to datasets obtained from both the commonly used polysome microarray method and the sequencing-based ribosome profiling method.

Transcription of Hepatic Cytosolic Phosphoenolpyruvate Carboxykinase Gene in Newborn Dogs

Physiological studies hypothesized that unsuppressed gluconeogenesis by insulin in newborn dogs may be a mechanism responsible for neonatal hyperglycemia. In the present study, we determined the effects of fasting and the infusion of insulin, glucose, and/or epinephrine on the liver cytosolic mRNA levels of the gene for the key regulatory enzyme of gluconeogenesis, phosphoenolpyruvate carboxykinase (PEPCK; EC 4.1.1.32), in newborn dogsin vivoto further test the hypothesis. We observed the following: (i) Fasting increased the hepatic PEPCK mRNA level in newborn dogs. The hepatic PEPCK mRNA level was not detectable at birth; the PEPCK mRNA level at 4 h was arbitrarily determined as 100.0 ± 27.8%, was 108.1 ± 18.4% at 10 h, and stayed at the same level at 24 h (109.1 ± 8.2). (ii) Euglycemic hyperinsulinemia did not significantly reduce the hepatic PEPCK mRNA levels in newborn dogs; however, the same treatment resulted in the repression of the liver PEPCK mRNA to undetectable levels in adult dogs. (iii) Under hyperinsulinemia, a moderate hyperglycemia lowered the liver PEPCK mRNA in newborn dogs to undetectable levels. (iv) In newborn dogs, despite the presence of hyperinsulinemia and hyperglycemia, the infused epinephrine was still able to elevate the liver PEPCK mRNA from undetectable levels to 79% of the control levels. We suggest that unsuppressed neonatal gluconeogenesis in the presence of hyperinsulinemia may be evidence of insulin resistance in newborn dogs and that the stimulatory effect of epinephrine on gluconeogenesis overriding insulin and glucose in the liver of the newborn dogs may be a mechanism for inducing neonatal hyperglycemia.

Effect of thyroid hormones on glucokinase gene transcription in rat liver

Thyroid hormones contribute to the regulation of blood sugar by accelerating the turnover of glucose. The mechanism by which thyroid hormones stimulate the rate of glucose utilization in the liver was determined by investigating the effect of different thyroid states on the expression of the glucokinase gene, a key enzyme of glycolysis. In euthyroid rats the mass of glucokinase mRNA increased 8-fold during the first 4 h of refeeding a high carbohydrate diet to 48-h starved rats. In hypothyroid rats under the same conditions only a 2-fold induction was observed. In euthyroid rats a 5-fold increase was obtained 1 h after refeeding, while hypothyroid rats displayed no significant response in glucokinase mRNA within this time. Basal levels of glucokinase mRNA in starved rats were the same observed in eu- and hypothyroid rats. Injection of 3,3',5-triiodothyronine (T3) into hypothyroid rats restored the mRNA levels of refed hypothyroid rats to euthyroid levels within 24 h. However, a 3-fold increase over untreated animals was already observed 3 h after T3 administration. Even subphysiological doses of T3 (0.1 microgram/100 g body weight) led to an significant increase in glucokinase mRNA levels (1.5-fold, p less than 0.05) in hypothyroid rats, whereas higher doses (100 micrograms/100 g body weight) restored the mRNA levels to those of euthyroid controls. Parallel increases in the cytosolic mRNA levels and rate of glucokinase gene transcription were detected when hypo- and euthyroid fasted rats were compared after 4 h of refeeding. It is concluded that thyroid hormones are permissive for the induction of glucokinase during refeeding but have no effect during starvation. They rapidly enhance the rate of gene transcription within the range of their physiologically circulating concentrations. The results suggest a major importance of thyroid hormones in regulating glucose utilization.

Thyroid hormone regulates transcription of the gene for cytosolic phosphoenolpyruvate carboxykinase (GTP) in rat liver

Using an in vitro assay with isolated rat nuclei, we have determined that thyroid hormone causes a 4-6-fold increase in the synthesis of mRNA coding for phosphoenolpyruvate carboxykinase. Proportional changes were seen in the steady-state cytosolic mRNA levels for phosphoenolpyruvate carboxykinase. Dibutyryladenosine cyclic 3',5'-monophosphate, which stimulates transcription of the phosphoenolpyruvate carboxykinase gene in normal rats, remained effective in hypo- or hyperthyroid animals. The effect of epinephrine on transcription of the gene for phosphoenolpyruvate carboxykinase appears to be modulated by thyroid hormone.