Date of Award
Spring 2024
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Genetics
First Advisor
Giraldez, Antonio
Abstract
Post-transcriptional mRNA regulation shapes gene expression, yet the full extent of cis-regulatory sequences and how translation shapes the regulation of these elements is poorly understood. To identify conserved cis-regulatory elements shaping mRNA stability, I analyzed the features associated with differential mRNA decay in two vertebrate systems: steady-state HEK293 cells and developing zebrafish embryos. I found that strength of translation initiation (Kozak score), uORF content, codon optimality, AU-rich elements, microRNA binding sites, and ORF length function combinatorially to regulate mRNA stability. Surprisingly, machine learning analysis identified ORF length as the most important conserved feature regulating mRNA decay. I found that mRNAs with long ORFs have lower translation efficiency, thus potentially more ribosome depleted regions. To find factors involved in targeting long ORFs to decay, I used yeast knockout screen that revealed Upf1 as a factor to target “poorly translated/untranslated” mRNA regions of long ORFs. Using a massive parallel reporter assay (MPRA) I show that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate, including mRNAs with uORFs and those with exposed ORFs after stop codons. Additionally, Upf1 knockdown stabilizes mRNAs with long ORFs or containing uORFs. My study emphasizes Upf1’s converging role in surveilling mRNAs with exposed ORFs that are poorly translated including mRNAs with long ORFs, ORF-like 3’UTRs and mRNAs containing uORFs. I propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC-independent NMD pathway that I term ORF Mediated Decay (OMD).
Recommended Citation
Musaev, Damir, "Coding sequence dependent mRNA decay regulation" (2024). Yale Graduate School of Arts and Sciences Dissertations. 1489.
https://elischolar.library.yale.edu/gsas_dissertations/1489
