Multiplex solution hybridization-ribonuclease protection assay for quantitation of different ribonucleic Acid...

We have compiled a protocol for simultaneous quantitation of a variety of gene transcripts in multiple individual brain and pituitary gland dissections for studying pretranslational regulation of neuroendocrine systems in vivo, using experimental designs compatible with meaningful statistical power. To facilitate collection of many samples at a time, the tissue was snap-frozen in chilled liquid Freon and stored at -80 °C until further processing. In this way, as many as five different brain and pituitary gland dissections per rat could be collected from eight rats in about an hour. The snap-frozen tissue was suitable for isolation of separate cytoplasmic and nuclear RNA fractions using homogenization in the presence of detergents. To facilitate homogenization of many samples at a time, we devised a method in which the tissue was repeatedly expelled through a 22 gauge hypodermic needle attached to a 1-ml plastic syringe used as a disposable, ready-to-use homogenizer. In order to promote dissolution of lipid membrane structures which are prevalent in the brain, the lysis buffer has been optimized to include the detergent sodium deoxycholate in addition to Nonidet P-40. Specific RNA transcripts were analyzed using a quantitative solution hybridization-ribonuclease protection assay coupled with polyacrylamide gel electrophoresis. The value of this highly sensitive assay has been expanded by including several molecular probes against a variety of neuroendocrine mRNA sequences simultaneously (e.g. progonadotropin-releasing hormone, proopiomelanocortin, tyrosine hydroxylase, dopamine D2 receptor, prolactin), thus increasing the amount of information obtained from each sample in one assay. Furthermore, each sample was routinely co-assayed for cyclophilin mRNA, an abundant, generally non-regulated mRNA whose levels reflected the individual variability in sample processing, thus serving as an internal reference. Once stored in hybridization solution, as many as 100 samples could be analyzed simultaneously for several different RNA transcripts in one assay. This protocol provides a powerful tool for studying regulation of neuroendocrine systems at the molecular level in vivo, using sample sizes suitable for applying statistical analysis of meaningful statistical power.