Quaking RNA binding proteins regulate tissue-specific gene expression

ABSTRACTANALYSIS OF QUAKING RNA BINDING PROTEINS AND THEIR ROLES IN POST-TRANSCRIPTIONAL REGULATION OF GENE EXPRESSIONW. Samuel Fagg Alternative RNA processing can robustly influence gene expression through a diverse set of molecular regulatory mechanisms. One of the most upstream RNA processing steps is splicing, which is the removal of non-coding intronic sequences from a pre-mRNA molecule and ligation of the exons together to make a mature mRNA. There are numerous types of alternative splicing that give rise to different quantitative and qualitative changes in the gene expression program, which can drastically impact cell fate and physiology. RNA binding proteins (RBPs) regulate alternative splicing and other types of RNA processing by binding substrate RNA molecules and altering downstream processing steps. How these processes are regulated for many RBPs is not known.The Quaking (Qk in mouse, QKI in human) family of RBPs regulates many RNA processing steps including splicing, mRNA localization/decay, translation, and microRNA biogenesis. Interestingly, from a single Qk gene multiple Qk transcripts are generated by alternative splicing, but the different protein forms share identical dimerization and RNA binding domains. The studies presented here analyze many different aspects of how Qk regulates RNA processing. First, we determine the structure of the Qk dimerization domain and find mutations that disrupt it reduce protein stability and splicing functions in vivo. Next we show that Qk and PTB regulate overlapping splicing regulatory networks in myoblasts, but during differentiation to myotubes, Qk protein increases while PTB decreases, leading to an increase in Qk splicing function and a decrease in PTB splicing. The next study reports that QKI regulates monocyte to macrophage differentiation through tissue-specific regulation of alternative splicing and mRNA abundance. The following study details isoform-specific functions and auto-regulatory interactions of the Qk5 and Qk6 isoforms, and the final study extends these observations genomewide.The studies presented here identify novel mechanistic details of how Qk regulates RNA targets and shows that Qk regulates tissue specific gene expression during different stem cell types’ differentiation