mRNA degradation by autophagy

University Of Colorado, Boulder CO

Investigators

Linked publications & trials

Abstract

DESCRIPTION (provided by applicant): Differential localization of messenger ribonucleoprotein particles (mRNPs) to the translation machinery or to mRNP aggregates such as P-bodies and stress granules is a key step to determine the translational fate of an mRNA. Since RNA misregulation underlies several neurodegenerative diseases, I seek to understand the effect of granulophagy, the turnover of mRNP aggregates by autophagy, on mRNA decay. I will investigate if granulophagy induces the decay of mRNAs that associate with mRNP aggregates as it may represent a novel mRNA decay pathway. Using RNA-seq, I have identified mRNAs whose levels are stabilized when autophagy is inhibited in yeast. Interestingly, a subset of mRNAs is enriched in the stabilized mRNAs suggesting that autophagy may preferentially degrade specific mRNAs. I will establish if these mRNAs are targeted for granulophagy by using fluorescent in situ hybridization to test if they associate with mRNP aggregates and localize to the vacuole. Additionally, I will validate that these mRNAs are degraded by autophagy by examining their decay rates in wild type cells and cells that are defective for autophagy. These experiments will corroborate that a novel mRNA decay pathway mediated by autophagy exists in yeast. Our preliminary data also suggests that mRNAs can be preferentially targeted for autophagic decay. To explore this possibility, I will test if cis elements encoded in the mRNAs, RNA binding proteins (RBPs) or segments of the mRNA mediate targeting. First, I will use bioinformatics to test if cis elements are enriched in the targeted mRNAs. Second, I will take a candidate approach and test if known RBPs can mediate specificity. Lastly, I will systematically dissect a mRNA to find domains required for its targeting. These assays will define the requirements for specificity in autophagic mRNA decay. Lastly, I will investigate if autophagic mRNA degradation is a conserved process that occurs in higher eukaryotes such as humans by identifying if mRNAs are targeted to autophagy in HEK293T cells. Upon characterization of human mRNAs subjected to autophagic decay, I anticipate testing if RNA aggregates found in neurodegenerative diseases result from defects in granulophagy or autophagic decay of mRNAs. In summary, I seek to uncover a novel mRNA decay mechanism in yeast and humans, thus, serving as a basis to uncover dysfunctions related to neurodegeneration.