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Open Access Publications from the University of California

Advances in RNA metabolic labeling for profiling nascent transcription

  • Author(s): Nainar, Sarah
  • Advisor(s): Spitale, Robert C
  • et al.

The transcriptional landscape has revealed itself to be highly complex, wherein RNA serves both coding and non-coding functions that are essential for cell differentiation, development and survival. Because the role of RNA has continued to expand, there is increasing need for biochemical methods to label and track RNA transcription, post-transcriptional regulation, and other RNA-based mechanisms. Herein, my doctoral work to expand the scope of metabolic reporters for RNA synthesis details a systematic expansion of chemistries and modifications for nucleoside analogs. This work has also served as a foundation for the development of novel, cell-specific RNA tagging approaches, both chemical and enzymatic. Throughout these studies, I have characterized the limitations of functional group tolerance and in many cases interrogated their effects on cell uptake and metabolism. Furthermore, I have worked to characterize the limitations of current cell-specific methods, with the goal of developing more stringent and robust approaches. These efforts are poised to provide greater context and engineering opportunities for methods to tag, visualize and study RNA gene expression.

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