The choice of resuspension medium for isolated rat liver nuclei: effects on nuclear morphology and in vitro transcription

Isolation of Catharanthus roseus (L.) G. Don Nuclei and Measurement of Rate of Tryptophan decarboxylase Gene Transcription Using Nuclear Run-On Transcription Assay

Background

An accurate assessment of transcription ‘rate’ is often desired to describe the promoter activity. In plants, isolation of transcriptionally active nuclei and their subsequent use in nuclear run-on assays has been challenging and therefore limit an accurate measurement of gene transcription ‘rate’. Catharanthus roseus has emerged as a model medicinal plant as it exhibits an unsurpassed spectrum of chemodiversity, producing over 130 alkaloids through the terpenoid indole alkaloid (TIA) pathway and therefore serves as a ‘molecular hub’ to understand gene expression profiles.

Results

The protocols presented here streamline, adapt and optimize the existing methods of nuclear run-on assay for use in C. roseus. Here, we fully describe all the steps to isolate transcriptionally active nuclei from C. roseus leaves and utilize them to perform nuclear run-on transcription assay. Nuclei isolated by this method transcribed at a level consistent with their response to external stimuli, as transcription rate of TDC gene was found to be higher in response to external stimuli i.e. when seedlings were subjected to UV-B light or to methyl jasmonate (MeJA). However, the relative transcript abundance measured parallel through qRT-PCR was found to be inconsistent with the synthesis rate indicating that some post transcriptional events might have a role in transcript stability in response to stimuli.

Conclusions

Our study provides an optimized, efficient and inexpensive method of isolation of intact nuclei and nuclear ‘run-on’ transcription assay to carry out in-situ measurement of gene transcription rate in Catharanthus roseus. This would be valuable in investigating the transcriptional and post transcriptional response of other TIA pathway genes in C. roseus. Isolated nuclei may also provide a resource that could be used for performing the chip assay as well as serve as the source of nuclear proteins for in-vitro EMSA studies. Moreover, nascent nuclear run-on transcript could be further subjected to RNA-Seq for global nuclear run-on assay (GNRO-Seq) for genome wide in-situ measurement of transcription rate of plant genes.

SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles

PURPOSE

To evaluate a semi-parametric, model-based approach for obtaining transcription rates from mRNA and protein expression.

METHODS

The transcription profile input was modeled using an exponential function of a cubic spline and the dynamics of translation; mRNA and protein degradation were modeled using the Hargrove-Schmidt model. The transcription rate profile and the translation, and mRNA and protein degradation rate constants were estimated by the maximum likelihood method.

RESULTS

Simulated datasets generated from the stochastic, transit compartment and dispersion signaling models were used to test the approach. The approach satisfactorily fit the mRNA and protein data, and accurately recapitulated the parameter and the normalized transcription rate profile values. The approach was successfully used to model published data on tyrosine aminotransferase pharmacodynamics.

CONCLUSIONS

The semi-parametric approach is effective and could be useful for delineating the genomic effects of drugs.

AVAILABILITY

Code suitable for use with the ADAPT software program is available from the corresponding author.

CONTACT

murali@acsu.buffalo.edu.

Heme: a regulator of rat hepatic tryptophan 2,3-dioxygenase?

The hepatic cytosolic hemoprotein tryptophan 2,3-dioxygenase (TDO) is the rate-limiting enzyme in tryptophan catabolism and thus plays a key role in regulating the physiological flux of tryptophan into relevant metabolic pathways. The TDO protein is induced by corticosteroids such as dexamethasone (DEX) and is stabilized by its prosthetic heme. In rats, acute chemically induced hepatic heme depletion reduces the functional hepatic TDO levels to 25-30% of basal levels within 1 h, and this decrease persists beyond 28 h of heme depletion at which time only 25-30% of the protein is available for heme incorporation. Since this could stem from impaired de novo synthesis and/or instability of the newly synthesized apoTDO protein in the absence of heme, we examined the specific role of heme in these events in a previously validated rat model of acute hepatic heme depletion triggered by the P450 suicide substrate 3, 5-dicarbethoxy 2,6-dimethyl-4-ethyl-1,4-dihydropyridine. We now show that exogenous heme can reverse the functional impairment of the enzyme observed during hepatic heme depletion and fully restore the impaired DEX-mediated induction of the enzyme to normal. Furthermore, through Northern/slot blot analyses coupled with nuclear run-on studies, we now document that this heme regulation of TDO is exerted primarily at the transcriptional level. Immunoblotting analyses also reveal corresponding changes in the TDO protein, thereby establishing that heme is necessary for DEX-inducible TDO mRNA transcription and subsequent translation. Thus, the TDO gene may contain heme-regulatory elements in addition to the reported glucocorticoid-responsive elements. Together, these findings suggest that clinically, hepatic heme deficiency may enhance the tryptophan flux into synthetic (serotonergic) pathways, not only by depriving prosthetic heme for a functionally competent TDO hemoprotein, its primary catabolic enzyme, but also by impairing the de novo synthesis of this enzyme.

Reduction of hepatic insulin-like growth factor I (IGF-I) messenger ribonucleic acid (mRNA) during fasting is associated with diminished splicing of IGF-I pre-mRNA and decreased stability of cytoplasmic IGF-I mRNA

The mechanisms by which fasting decreases liver insulin-like growth factor I (IGF-I) messenger RNA (mRNA) abundance have not been defined completely. In the present study, we have examined the effects of fasting in rats on hepatic IGF-I gene transcription, IGF-I pre-mRNA splicing, and cytoplasmic IGF-I mRNA stability. Using the in vitro nuclear run-on transcription technique, we observed that fasting did not change IGF-I gene transcription activity [76 +/- 32 densitometric units (DU) for fasted vs. 58 +/- 23 DU for control-fed rats; P = 0.1], whereas IGF-binding protein-1 (IGFBP-1) gene transcription, a positive control, was increased more than 2-fold (729 +/- 157 DU for fasted vs. 261 +/- 56 DU for control-fed rats; P < 0.05). This implies that fasting-induced reduction of liver IGF-I mRNA is due to events other than a decreased rate of IGF-I gene transcription. By measuring nonspliced (pre-mRNA) and spliced IGF-I transcripts in liver nuclear RNA using ribonuclease protection assays, we found that IGF-I pre-mRNA was increased in fasted rats (measured as the percentage of beta-actin: 34.0 +/- 5.5% for fasted vs. 8.1 +/- 3.8% for control-fed rats; P < 0.01), whereas spliced IGF-I transcript remained unchanged (measured as the percentage of beta-actin: 60.9 +/- 9.2% for fasted vs. 79.0 +/- 6.2% for control-fed rats; P = 0.75). We then compared this pattern of splicing to IGF-I pre-mRNA splicing in hypophysectomized rats subjected to GH stimulation and to IGFBP-1 pre-mRNA splicing in the same fasting experiment. One hour after GH injection, we observed a coordinate increase in both nonspliced and spliced IGF-I transcripts in liver nuclei of hypophysectomized rats. Fasting increased both IGFBP-1 pre-mRNA and spliced transcript. Taken together, these results indicate that the increase in IGF-I pre-mRNA in liver nuclei during fasting is caused by delayed pre-mRNA splicing, rather than increased IGF-I gene transcription. To examine the possible effect of fasting on hepatic IGF-I mRNA stability, we used an in vitro model of nutrient deprivation (fewer amino acids in culture medium) of rat hepatocyte primary culture. Each of the three major IGF-I mRNA species exhibited a shortened half-life in the amino acid-deprived media. The 7.5-kb IGF-I mRNA, however, was degraded faster than the two smaller IGF-I mRNA species. This may indicate that fasting decreases the stability of liver IGF-I mRNA in vivo. In summary, these results suggest that fasting regulates hepatic IGF-I gene expression mainly at the posttranscriptional level by delaying IGF-I pre-mRNA splicing, which attenuates mature IGF-I mRNA generation, and by accelerating the rate of degradation of IGF-I mRNA in cytoplasm.

Peroxisome proliferator-activated receptor (PPAR)-dependent and -independent transcriptional modulation of several non-peroxisomal genes by peroxisome proliferators

To better characterize peroxisome proliferator-induced non-peroxisomal responses, we searched the mRNAs of which the levels were modulated by proliferators. We used the PCR-based methods including differential display. The mRNAs were divided into at least four groups by their time-courses of induction and repression: group 1 very rapidly increased then decreased; group 2 increased after a time lag (well-characterized peroxisomal mRNAs belonged to this group); group 3 decreased reciprocally compared with group 2 mRNAs; group 4 increased after group 2 mRNAs, with a much longer lag period. All of these modulations cannot be explained by peroxisome proliferator action through PPAR and RXR dimerization on the target genes to activate transcription. Another unidentified transcription factor may be involved in some of these modulations. It will also be important to consider PPAR-independent pathways when studying the diverse effects of peroxisome proliferators.

In vivo interpretation of in vitro effect studies with a detailed analysis of the method of in vitro transcription in isolated cell nuclei

In vitro experimental approaches are of central importance to contemporary molecular and cellular biology and toxicology. However, the scientific value or impact of in vitro results depends on their relevance in vivo. In vitro effect studies address inobservable in vivo phenomena through experiments on analogous in vitro phenomena. We present a theoretical basis developed to evaluate the in vivo relevance of in vitro effect studies. As a case study, the procedure for measuring specific gene transcription in isolated cell nuclei (¿nuclear run-off method¿) is analyzed. It is concluded that current evidence fails to justify in vivo interpretations of nuclear run-off experiments within the framework of theoretical models of transcription, implying that quantitative in vivo interpretations are unwarranted. Qualitative interpretations of nuclear run-off experiments may be justified by inferring ¿the best explanation¿, especially when significant in vitro effects follow in vivo perturbations. Elements of a general theory are proposed. It is concluded that quantitative in vivo interpretations are warranted primarily in biochemical quantitation of biomolecules, while studies on biological function should be interpreted qualitatively in terms of causal explanations. Inferences to the best explanations are strengthened through additional evidence and the creation of experimental differences (effects).