Enzymes in RNA Science and Biotechnology Part B

Prof. Ryota Yamagami received his Ph.D degree under the supervision of Prof. Hori at Ehime University in Japan in 2015 where he studied folate-dependent tRNA methyltransferase and tRNA modification network in Thermus thermophilus, a thermophilic bacterium. After his Ph.D course, he had worked in the lab for 1 year as a JSPS postdoctral fellow. He then joined the Bevilacqua Lab at Pennsylvania State University as a postdoctal fellow in 2016 where he has studied RNA folding. Dr. Chun Kit Kwok obtained his B.Sc. in Chemistry (2009) from the Chinese University of Hong Kong, after completing an exchange program at University of California, Los Angeles in 2007-2008. He completed his PhD in Pennsylvania State University (2014), mentored by Professor Philip C. Bevilacqua and Professor Sarah M. Assmann. In Apr 2014, Dr. Kwok worked as a Croucher Postdoctoral Fellow in University of Cambridge under Professor Sir Shankar Balasubramanian. In Oct 2016, Dr. Kwok's joined the City University of Hong Kong as an Assistant professor and has been promoted to Associate professor in July 2021. In 2019, he was one of the recipients of the CityU President Award and Croucher Innovation Award. In 2020, Dr. Kwok's joined the State Key Laboratory of Marine Pollution, City University of Hong Kong. In 2021, Dr. Kwok was recognized as elected member of Hong Kong Young Academy of Science (YASHK) and Hong Kong Institute for Advanced Study Rising Star in Chemistry. In 2022, Dr. Kwok was awarded the NSFC Excellent Young Scientist Fund. Dr. Kwok’s current research focus is to explore the role of RNA structures and interactions in biology, especially the functions of G-quadruplex structures/interactions and non-coding RNA structures/interactions in the mammalian transcriptome and their relevance to gene regulation, RNA metabolism and diseases. Two new research directions in the Kwok lab are to develop targeting tools for detection, imaging, intervention of these important RNA structures and interactions, as well as to invent innovative nucleic acid-based technologies for sensing chemical pollutants and pathogens

Post-transcriptional modification enzymes
1. Quantitative base-resolution sequencing technology for mapping pseudouridines in mammalian mRNA
Li-Sheng Zhang
2. Quantitative base-resolution DAMM-seq for mapping RNA methylations in tRNA and mitochondrial dsRNA
Li-Sheng Zhang
3. Discovering RNA modification enzymes using a comparative genomics approach
Satoshi Kimura
4. Functional analysis of tRNA modification enzymes using mutational profiling
Ryota Yamagami and Hiroyuki Hori
5. Fluorescent labeling of tRNA for rapid kinetic interaction studies with tRNA-binding proteins
Ute Kothe and Sarah Schultz
6. Enzymatic Synthesis of RNA Standards for Mapping and Quantifying RNA Modifications in Sequencing Analysis
Howard Gamper, Caroline McCormick, Amr Makhamreh, Meni Wanunu, Sara Rouhanifard and Ya-Ming Hou

Nucleases
7. Characterizing RNase L-mediated mRNA decay in single cells
James Burke, Renee Cusic and Monty Watkins
8. Characterization of RNase J
Balasubramanian Gopal, Muralidharan Vandanashree and Ankur Singh
9. Pri-miRNA cleavage assays for the Microprocessor complex
Tuan Anh Nguyen, Cong Truc Le and Thi Nhu Y. Le
10. The pre-miRNA cleavage assays for DICER
Tuan Anh Nguyen, Cong Truc Le and Thi Nhu Y. Le
11. Methods for study of ribonuclease targeting chimeras
Matt Disney, Noah Springer, Samatha Meyer, Yuquan Tong, Jessica Childs-Disney and Raphael Isaac Benhamou
12. Profiling the in vivo RNA interactome associated with the endoribonuclease RNase III in Staphylococcus aureus
Winton Wu, Chi Nam Ignatius Pang, Jai Tree and Daniel Giuseppe Mediati