Impact of RNA isolation protocols on RNA detection by Northern blotting.

We prepared total RNA from the Gram-positive soil bacterium Bacillus subtilis by different RNA extraction procedures to compare their suitability for Northern blot detection of tiny RNAs (~14-mers) or RNAs of intermediate size (100-200 nt) in terms of signal quality, intensity, and reproducibility. Our analysis included two hot phenol methods and two TRIzol extraction procedures. We found that signal intensity/detection sensitivity makes the key difference. Total RNAs prepared by the hot phenol method comprise the length spectrum from tRNAs to large ribosomal RNAs. Larger RNAs are less abundant in TRIzol preparations which instead enrich for RNAs of tRNA size and smaller. Thus, hot phenol methods are the choice for the detection of intermediate-sized and longer RNAs, whereas TRIzol extraction procedures are more suited for the detection of tiny RNAs.

Validation of reference transcripts in strawberry (Fragaria spp.).

Contemporary methods to assay gene expression depend on a stable set of reference transcripts for accurate quantitation. A lack of well-tested reference genes slows progress in characterizing gene expression in high-value specialty crops. In this study, a set of strawberry (Fragaria spp.) constitutively expressed reference genes has been identified by merging digital gene expression data with expression profiling. Constitutive reference candidates were validated using quantitative PCR and hybridization. Several transcripts have been identified that show improved stability across tissues relative to traditional reference transcripts. Results are similar between commercial octoploid strawberry and the diploid model. Our findings also show that while some never-before-used references are appropriate for most applications, even the most stable reference transcripts require careful assessment across the diverse tissues and fruit developmental states before being adopted as controls.

Evaluation and identification of reliable reference genes for pharmacogenomics, toxicogenomics, and small RNA expression analysis.

Pharmacogenomics, toxicogenomics, and small RNA expression analysis are three of the most active research topics in the biological, biomedical, pharmaceutical, and toxicological fields. All of these studies are based on gene expression analysis, which requires reference genes to reduce the variations derived from different amounts of starting materials and different efficiencies of RNA extraction and cDNA synthesis. Thus, accurate normalization to one or several constitutively expressed reference genes is a prerequisite to valid gene expression studies. Although selection of reliable reference genes has been conducted in previous studies in several animals and plants, no research has been focused on pharmacological targets, and very few studies have had a toxicological context. More interestingly, no studies have been performed to identify reference genes for small RNA analysis although small RNA, particularly microRNA (miRNA)-related research is currently one of the fastest-moving topics. In this study, using MCF-7 breast cancer cells as a model, we employed quantitative real-time PCR (qRT-PCR), one of the most reliable methods for gene expression analysis in many research fields, to evaluate and to determine the most reliable reference genes for pharmacogenomics and toxicogenomics studies as well as for small RNA expression analysis. We tested the transcriptional expression of five protein-coding genes as well as five non-coding genes in MCF-7 cells treated with five different pharmaceuticals or toxicants [paclitaxel (PTX), gossypol (GOS), methyl jasmonate (JAS), L-nicotine (NIC), and melamine (mela)] and analyzed the stability of the selected reference genes by four different methods: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method. According to our analysis, a protein-coding gene, hTBCA and four non-coding genes, hRNU44, hRNU48, hU6, and hRNU47, appear to be the most reliable reference genes for the five chemical treatments. Similar results were also obtained in dose-response and time-course assays with gossypol (GOS) treatment. Our results demonstrated that traditionally used reference genes, such as 18s RNA, ß-actin, and GAPDH, are not reliable reference genes for pharmacogenomics and toxicogenomics studies. In contrast, hTBCA and small RNAs are more stable during drug treatment, and they are better reference genes for pharmacogenomics and toxicogenomics studies. To widely use these genes as reference genes, these results should be corroborated by studies with other human cell lines and additional drugs classes and hormonal treatments.

Standard curve for housekeeping and target genes: specific criteria for selection of loading control in Northern blot analysis.

The election of the correct loading control in Northern blot normalization is something essential to obtain valid results. Housekeeping genes are widely used as loading control and the assumption is made that they counteract load differences between samples. We have found, however, that uneven sample load is capable to alter the results despite normalization, considering no influence of the experimental conditions on housekeeping gene regulation takes place. Normalization ratio (transcript of interest/housekeeping gene) is determined as the pattern of variation in the ratio between densitometric signals of transcripts--both target and control--and the amount of total RNA. The fact that this relationship is specific for each transcript means different ratios will exist depending on the chosen control gene. Actually, loading differences of only 2 microg may induce a 2.5-fold difference between normalized ratios, depending on the housekeeping gene selected for normalization. In order to select the appropriate loading control, it becomes essential to establish a standard curve for each transcript of interest and several housekeeping. Only the one yielding a constant ratio of normalization along the total RNA range used is to be taken into consideration.

A comparison of various "housekeeping" probes for northern analysis of normal and osteoarthritic articular cartilage RNA.

Several approaches are commonly used to normalize variations in RNA loading on Northern blots, including: ethidium bromide (EthBr) fluorescence of 18S or 28S rRNA or autoradiograms of radioactive probes hybridized with constitutively expressed RNAs such as elongation factor-1alpha (ELF), glyceraldehyde-3-phosphate dehydrogenase (G3PDH), actin, 18S or 28S rRNA, or others. However, in osteoarthritis (OA) the amount of total RNA changes significantly and none of these RNAs has been clearly demonstrated to be expressed at a constant level, so it is unclear if any of these approaches can be used reliably for normalizing RNA extracted from osteoarthritic cartilage. Total RNA was extracted from normal and osteoarthritic cartilage and assessed by EthBr fluorescence. RNA was then transferred to a nylon membrane hybridized with radioactive probes for ELF, G3PDH, Max, actin, and an oligo-dT probe. The autoradiographic signal across the six lanes of a gel was quantified by scanning densitometry. When compared on the basis of total RNA, the coefficient of variation was lowest for 28S ethidium bromide fluorescence and oligo-dT (approximately 7%), followed by 18S ethidium bromide fluorescence and G3PDH (approximately 13%). When these values were normalized to DNA concentration, the coefficient of variation exceeded 50% for all signals. Total RNA and the signals for 18S, 28S rRNA, and oligo-dT all correlated highly. These data indicate that osteoarthritic chondrocytes express similar ratios of mRNA to rRNA and mRNA to total RNA as do normal chondrocytes. Of all the "housekeeping" probes, G3PDH correlated best with the measurements of RNA. All of these "housekeeping" probes are expressed at greater levels by osteoarthritic chondrocytes when compared with normal chondrocytes. Thus, while G3PDH is satisfactory for evaluating the amount of RNA loaded, its level of expression is not the same in normal and osteoarthritic chondrocytes.

Differential expression of type II, IV and cytosolic PLA2 messenger RNA in human intrauterine tissues at term.

The involvement of phospholipase A2 (PLA2) enzymes in the formation of biologically-active phospholipid metabolites by human gestational tissues has principally been characterized by the use of enzyme activity assays. While such assays have established the presence of functional PLA2 activity, there is a paucity of information concerning the tissue distribution and relative contribution to net activity made by specific PLA2 isozymes. In particular, both secretory and cytosolic isozymes may be involved in gestational tissue phospholipid metabolism. Thus, the aim of this study was to test the hypothesis that phospholipase A2 mRNA transcripts encoding Type II, Type IV and cytosolic PLA2 are tissue-specifically expressed in human amnion, choriodecidua and placenta obtained at term. The relative expression of polyA+ mRNA encoding these PLA2 isozymes was determined by Northern blot analysis and laser densitometry. The data obtained confirm the tissue-specific expression of PLA2 mRNA in human intrauterine tissues. Cytosolic PLA2 mRNA was most abundantly expressed in amnion when compared to either choriodecidua (which was 5-fold less than amnion; P < 0.001) or placenta (72-fold less than amnion; P < 0.001). In contrast, the secretory PLA2 mRNA transcripts (i.e. Type II and Type IV) were most abundantly expressed in placenta. Type II PLA2 mRNA expression in choriodecidua and amnion was 30-fold less than that observed in placenta (both P < 0.001). Type IV PLA2 mRNA expression was 37-fold (P < 0.001) and 73-fold (P < 0.001) less in choriodecidua and amnion respectively. These data support the conclusion that cytosolic PLA2 is the principal PLA2 isozyme mediating phospholipid metabolism and the liberation of fatty acid substrate (i.e. arachidonic acid) in term amnion, while secretory PLA2 isozymes, and in particular, Type II PLA2 play a major role in phospholipid metabolism in term placenta.

An effective elimination of false positives isolated from differential display of mRNAs.

A reverse Northern analysis that effectively eliminates the false positives isolated from differential display of mRNAs (DD) is demonstrated. Preparation of probe by one-step labeling in reverse transcription reaction is found to be more effective and specific as compared to the preparation of probe by random priming of reverse transcribed cDNA pool. Reverse Northern assay of DNA fragments isolated from DD prior to their cloning into plasmid, analysis of multiple fragments on single slot blot, and requirement of RNA only in small amounts as compared to conventional Northern makes the protocol quick, effective, and economic.

Variation in expression of genes used for normalization of Northern blots after induction of cell proliferation.

Quantitative knowledge of gene expression can provide valuable information for understanding the action of chemicals that alter cell proliferation and cancer. Accurate quantification of mRNA levels requires the normalization of the gene of interest to a gene with transcriptional levels that do not vary through the cell cycle or with a particular treatment. Changes in expression were examined in proliferating or non-proliferating rat liver for three constitutively expressed 'housekeeping' genes commonly used to normalize mRNA levels from Northern blots. In addition, a direct method of quantifying poly(A)+ mRNA by hybridization with a radiolabelled polythymidylate--poly(T)--probe was compared with traditional methods. Hepatocyte cytolethality and a subsequent wave of hepatocyte proliferation were induced in male Fischer-344 rats by treatment with a single gavage dose of carbon tetrachloride. Induced cell proliferation peaked at 48 h after treatment. Expression of the housekeeping genes actin, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and albumin, as well as the proto-oncogene H-ras, was determined by Northern blot analysis at times from 0.5 h to 4 days after treatment. Time-dependent changes were observed in the expression of these genes relative to the levels observed in the untreated control animals. Actin expression peaked at 3.4-fold over control and GAPDH expression was increased by 1.9-fold over control. Albumin mRNA levels varied the least, 1.4-fold over control, indicating that this gene is more appropriate than actin or GAPDH for normalization of proto-oncogene expression under experimental conditions that induce cell proliferation in rat liver. The direct quantification of poly(A)+ mRNA using a poly(T) probe was not influenced by the induction of cell proliferation. This method may be useful when the expression of housekeeping genes is affected by treatment.

Molar quantification of specific messenger ribonucleic acid expression in northern hybridization using cRNA standards.

Procedures were developed for estimation of specific mRNA expression as measured by Northern hybridization in terms of moles of message present in tissue samples. These procedures use an externally added cRNA pseudomessage standard with cRNA concentration curves for both the standard and the message of experimental interest in order to convert hybridization signals into moles of message per milligram wet weight of tissue. We present a test of these procedures using hybridization to the message for the glucocorticoid-inducible enzyme tyrosine aminotransferase in rat liver. These procedures accommodate for variations in both RNA yield and hybridization signal intensities, and are applicable to the measurement of changes in message expression of twofold or more using triplicate determinations of a single RNA preparation. This approach allows for the integration of data from many individual hybridization experiments, and may be useful in experimental situations that involve population studies and/or long-term comparisons of treatments.

A rapid, accurate, nonradioactive method for quantitating RNA on agarose gels.

In order to study quantitative gene expression with Northern blots, it is important to have an internal standard that can be used to verify even loading or to correct for uneven loading between lanes. In this study it is shown that two-dimensional quantitation of ethidium bromide-intercalated 28S rRNA fluorescence can be used for such standardization. It was found that the film response of the fluorescence was linear with respect to total loaded RNA in the range of 2.5-12.5 micrograms RNA under the conditions used, after which the linear relationship falls off. This method eliminates the use of radiation for internal standardization of Northern blots.