Undergraduate Honors Thesis

 

Characterizing Novel CypA-RNA Interactions Public Deposited

https://scholar.colorado.edu/concern/undergraduate_honors_theses/d217qq72t
Abstract
  • RNA-binding proteins are a diverse and essential class of proteins with critical roles in key processes such as gene regulation, mRNA processing, and cell metabolism1,2. While hundreds of RNA binding proteins (RBPs) have functions relating to RNA executed by well characterized RNA binding domains, a recent set of mRNA pulldown studies has uncovered a rich set of unexpected RBPs with no known binding domains and functions that do not obviously require RNA2-4.  Among these putative RNA binders are proteins belonging to the cyclophilin family, proteins that isomerize the amino acid proline from the lower energy trans conformation to the higher energy cis conformation5.

    Cyclophilin A (CypA), a highly conserved cyclophilin comprising a single isomerase domain6, was among the identified novel RBPs2-4. CypA is ubiquitous in the cell, as it abundant in the nucleus and cytoplasm as well as being secreted6,7. It plays an essential role in protein folding and trafficking, cell signaling, and immune system response6,7 and has recently been shown to interact with key transcription factors to mediate their transcriptional activity8,9.  CypA is also biomedically relevant as the target of the immunosuppressive drug Cyclosporin A and is overexpressed in various cancers7. In addition to the mRNA studies, CypA and homologues have been implicated as RNA binders in several studies10-12 though its isomerase activity does not seem to require RNA. It is thus an exciting model to study novel RNA-protein interactions. Here, I take a two-pronged approach to investigate CypA’s RNA interactome: in vitro binding with previously implicated RNAs and in vivo RNA immunoprecipitation with subsequent bioinformatic analysis to identify relevant endogenous RNA classes that CypA may bind. The in vitro results suggest that CypA binds RNA with some specificity, as certain RNAs interacted with CypA while others did not. The in vivo results differentiate a set of statistically significant enriched genes from a set of depleted genes, suggesting that CypA interacts sets of transcribed genes in the cell whose functional groups relate to known CypA activity.

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  • 2021-04-01
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  • 2021-05-12
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