Abstract

Regulation of gene expression is essential to life. Post-transcriptional regulation of gene expression is a complex process with many inputs that lead to changes in localization, translation and stability of mRNAs. The translation and stability of many mRNAs is regulated by cis-elements, such as mRNA-structure or codon optimality; and by trans-acting factors such as RBPs and miRNAs. Here I report on the complex interactions between RBPs, miRNAs and characteristics of their target mRNAs in respect to effects on translation and RNA stability.Using a reporter based approach we studied modulation of microRNA-mediated repression by various mRNA characteristics. We observed the influence of codon optimality, 5’UTR structure, uORFs and translation efficiency on the magnitude of miRNA-mediated repression. To study functional interactions between RBPs and miRNAs, we developed a new method: PTRE-seq. This method utilizes a massively parallel reporter library to study the individual and combined effects of RBPs and miRNAs on translation and RNA stability. Using PTRE-seq we observed epistatic interactions between AU-rich elements and miRNA binding sites. In addition to PTRE-seq, we developed a novel method for immunoprecipitation of mRNAs that will facilitate the identification of miRNAs and RBPs bound to mRNAs of interest.

Committee Chair

Sergej Djuranovic

Committee Members

Kathleen Hall, Sheila Stewart, Andrew Yoo, Tim Schedl,

Comments

Permanent URL: https://doi.org/10.7936/K72R3R31

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Molecular Cell Biology)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

Winter 12-15-2017

Language

English (en)

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