Determination of apolipoprotein mRNA levels by ribonuclease protection assay

The ribonuclease protection assay procedure described enables the relative quantitation of either single mRNAs or multiple mRNA species simultaneously in a sample of total RNA and demonstrates its applicability to two systems of relevance to the study of apolipoproteins, namely, liver tissue and liver-derived cell lines in culture. The main requirements of the method are the availability of cDNA cloned into a vector that directs the transcription of antisense RNA for the preparation of radioactive probes, and choice of suitable restriction endonuclease sites for linearizing the cDNA so that the final protected products of the various mRNA species are sufficiently different in size to allow their separation. For moderately abundant apolipoprotein mRNAs in rat liver, the method is sensitive down to 1 microgram total RNA. Other experimental sources of RNA or the assay of less abundant mRNA species may require a larger amount of starting material. These aspects of the assay need to be determined for each probe/ tissue system to be studied. The need for adjustments to the specific radioactivity of the probes will depend on the relative abundance of the target mRNA molecules and can be readily determined empirically. The rationale for varying the specific radioactivities to facilitate multiple assays as suggested here is both simple and effective. A preliminary assay provides information on the relative levels of the mRNA species of interest, and the step of preparing, in parallel, a sample of unlabeled antisense RNA provides the means for quantitative dilution of specific radioactivity of the 32P-labeled RNA probe where required.