Application of the Invader RNA assay to the polarity of vertebrate mRNA decay

Quantitative analysis of mRNA translation in mammalian spermatogenic cells with sucrose and Nycodenz gradients

BACKGROUND

Developmental and global regulation of mRNA translation plays a major role in regulating gene expression in mammalian spermatogenic cells. Sucrose gradients are widely used to analyze mRNA translation. Unfortunately, the information from sucrose gradient experiments is often compromised by the absence of quantification and absorbance tracings, and confusion about the basic properties of sucrose gradients.

METHODS

The Additional Materials contain detailed protocols for the preparation and analysis of sucrose and Nycodenz gradients, obtaining absorbance tracings of sucrose gradients, aligning tracings and fractions, and extraction of equal proportions of RNA from all fractions.

RESULTS

The techniques described here have produced consistent measurements despite changes in personnel and minor variations in RNA extraction, gradient analysis, and mRNA quantification, and describes for the first time potential problems in using gradients to analyze mRNA translation in purified spermatogenic cells.

CONCLUSIONS

Accurate quantification of the proportion of polysomal mRNA is useful in comparing translational activity at different developmental stages, different mRNAs, different techniques and different laboratories. The techniques described here are sufficiently accurate to elucidate the contributions of multiple regulatory elements of variable strength in regulating translation of the sperm mitochondria associated cysteine-rich protein (Smcp) mRNA in transgenic mice.

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

The thermodynamic contributions of rA·dA, rC·dC, rG·dG and rU·dT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°(37), ΔH° and melting temperature (T(m)) of duplexes containing these single mismatches within an average of 0.33 kcal/mol, 4.5 kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rG·dG > rU·dT > rA·dA > rC·dC. The stability trend for the base pairs 5' of the single internal mismatch is rG·dC > rC·dG > rA·dT > rU·dA. The stability trend for the base pairs 3' of the single internal mismatch is rC·dG > rG·dC >> rA·dT > rU·dA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST.

A+U-rich instability elements differentially activate 5'-3' and 3'-5' mRNA decay

The A+U-rich elements (or AREs) are cis-acting sequences that activate rapid mRNA decay, yet the overall polarity of this process is unknown. The current study describes an unbiased approach to this using the Invader RNA assay (Third Wave Technologies, Inc.) to quantify the decay of each of the three exons of human beta-globin mRNA without added instability elements or with the AREs from c-fos or granulocyte-macrophage colony-stimulating factor (GM-CSF) mRNA in the 3' untranslated region. Each of these genes under tetracycline operator control was stably transfected into cells, and beta-globin mRNA was quantified with exon-specific probes following transcription termination. There was little overall evidence for polarity in stable mRNA decay. Adding the c-fos ARE activated rapid and simultaneous decay from both ends of the mRNA. In contrast, the GM-CSF ARE activated decay primarily from the mRNA 5' end. These data were supported by reciprocal RNA interference knockdowns, and we present evidence that the 5'-3' and 3'-5' decay pathways are functionally linked.