@article{THESIS,
      recid = {3038},
      author = {Zhang, Wen},
      title = {Investigation and Characterization of RNA Modifications},
      publisher = {University of Chicago},
      school = {Ph.D.},
      address = {2021-06},
      number = {THESIS},
      pages = {178},
      abstract = {        My thesis focuses on the investigation and  characterization of RNA modifications. RNA is  post-transcriptionally modified on the nucleoside bases  and/or on the ribose-phosphate backbone. RNA modifications  are conserved from prokaryotes to eukaryotes. Each  modification has its own functions in vivo. Efficient and  quantitative detection methods are necessary for the  elucidation of the functions of specific RNA modifications.  Some methods are useful for the detection of a specific  modification, while other methods can detect multiple RNA  modifications simultaneously. In the chapters 2 and 3 of my  thesis, I describe the methods that I developed for the  sensitive and quantitative detection of pseudouridine (Ψ)  and glycosylated queuosine (Q). Chapter 4 is about the  usage of small RNA sequencing methods (MSR-seq) for the  investigation of tRNA modification response under stress  conditions.	Chapter 2 describes the development of a  sensitive and quantitative method called “CLAP” for Ψ  detection. This PCR-based method takes advantages of the  CMC reaction with Ψ which leaves a stop signature during  reverse transcription. This method is useful for sensitive  quantification of the modification fraction of target Ψ  sites in low abundant long non-coding RNAs and mRNAs. CLAP  has the potential of being adapted for the studies of other  RNA modifications.
	Chapter 3 describes an acid denaturing  gel based Northern blot method for the quantitative  detection of glycosylated Q modifications. This method  combines the acid denaturing gel and Northern blot.  Non-radioactive Northern blot probes are used for detection  of Q-modified tRNAs. The acid denaturing gel based Northern  blot is useful for measuring the glycosylated Q  modification levels in tRNAs. By combining the acid  denaturing gel based Northern blot and  3-(Acrylamido)phenylboronic acid (APB) gel based Northern  blot, we investigated the Q modification and glycosylation  kinetics in tRNAs in three human cell lines, HEK293T, HeLa,  and MCF7.
	Chapter 4 describes a study of using small RNA  sequencing method to study tRNA abundance and modification  response under different stress conditions including heat  shock, H2O2, and NaAsO2. We identified new stress responses  by m3C modifications in tRNAs and a tRNA-based regulation  of translational elongation, and a relationship between  tRNA modification and tRNA fragment biogenesis.
	In  conclusion, efficient and simple detection methods are  often required for studying the functional roles of RNA  modifications. The development of quantitative methods of  Ψand glycosylated Q will help the elucidation of the  diverse functions of Ψ in different RNA species and uncover  the mysterious functions of glycosylated Q modifications in  tRNAs.},
      url = {http://knowledge.uchicago.edu/record/3038},
      doi = {https://doi.org/10.6082/uchicago.3038},
}