Comprehensive analysis of RNA degradation via autophagy in yeast

Background: Autophagy is a bulk degradation system of cellular components induced by nutrient starvation. Recently, we revealed that autophagy is one of the major RNA degradation system in starving yeast. RNA delivered to the vacuole via autophagy was degraded by Rny1, a T2-type ribonuclease. Aim: We propose to characterize the amount and type of RNA destined for degradation by autophagy in the vacuole. In this project, we focus on mRNA, tRNA and other cytoplasmic RNA. Comprehensive analysis will reveal specific target RNA, which potentially useful for biomarker of autophagy. Based on the RNA-seq data, we would like to elucidate the molecular mechanisms and physiological roles of autophagy-dependent selective and/or nonselective RNA degradation. Samples: Purified vacuoles from Rny1 KO cells (RNA degradation defective), and Rny1 and Atg2 double KO cells (both RNA degradation and autophagy defective). Conditions: normal growing condition, Rapamycin treatment and carbon starvation.