RNA Modification

Chuan He, Ph.D., is the John T. Wilson Distinguished Service Professor in the Department of Chemistry and Director of the Institute for Biophysical Dynamics at the University of Chicago. He is also a joint Professor in the Department of Chemical Biology and Director of the Synthetic and Functional Biomolecules Center at Peking University. He was born in P. R. China in 1972 and received his B.S. (1994) from the University of Science and Technology of China. He received his Ph. D. degree from Massachusetts Institute of Technology in chemistry in 2000. After being trained as a Damon-Runyon postdoctoral fellow at Harvard University from 2000-2002, he joined the University of Chicago as an Assistant Professor, and was promoted to Associate Professor in 2008, Professor in 2010 and John T. Wilson Distinguished Service Professor in 2014. He is also a member of the Cancer Research Center at the University of Chicago. His research spans a broad range of chemical biology, epigenetics, cell biology, molecular biology, biochemistry, structural biology, and genomics. His recent research concerns reversible RNA and DNA methylation in biological regulation. His research group discovered the first RNA demethylase and showed that reversible RNA methylation significantly affects post-transcriptional gene expression regulation. He was selected as an Investigator of the Howard Hughes Medical Institute in 2013.

1. Methodology For The High-Throughput Identification and Characterization of tRNA Variants that are Substrates for a tRNA Decay Pathway
Matthew J. Payea, Michael P. Guy, and Eric M. Phizicky
2. Nucleoside Analysis by Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry
Yuriko Sakaguchi, Kenjyo Miyauchi, Byeong-il Kang, and Tsutomu Suzuki
3. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications
Weiling Maggie Cai, Yok Hian Chionh, Fabian Hia, Chen Gu, Stefanie Kellner, Megan E. McBee, Chee Sheng Ng, Yan Ling Joy Pang, Erin G. Prestwich, Kok Seong Lim, I. Ramesh Babu, Thomas J. Begley and Peter C. Dedon
4. Recognition of Specified RNA Modifications by the Innate Immune System
Tatjana Eigenbrod, Patrick Keller, Steffen Kaiser, Katharina Rimbach, Alexander H. Dalpke and Mark Helm
5. Kinetic Analysis of tRNA Methyl Transferases
Ya-Ming Hou and Isao Masuda
6. Preparation of Human Nuclear RNA m6A Methyltransferases and Demethylases and Biochemical Characterization of Their Catalytic Activity
Jianzhao Liu, Yanan Yue, and Chuan He
7. Transcriptome-Wide Mapping of N6-Methyladenosine by m6A-Seq
Dan Dominissini, Sharon Moshitch Moshkovitz, Ninette Amariglio and Gideon Rechavi
8. Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA
Nian Liu and Tao Pan
9. High-resolution mapping of N6-methyladenosine in transcriptome and Genome Using a Photo-Crosslinking-Assisted Strategy
Kai Chen, Guan-Zheng Luo and Chuan He
10. Pseudouridine in Mrna: Incorporation, Detection and Recoding
Guowei Wu, Chao Huang and Yi-Tao Yu
11. Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA
T homas M. Carlile, Maria F. Rojas-Duran and Wendy V. Gilbert
12. Pseudouridine Chemical Labeling and Profiling
Xiaoyu Li, Shiqing Ma and Chengqi Yi
12. Experimental Approaches for Target Profiling RNA Cytosine Methyltransferases
Vahid Khoddami, Archana Yerra, and Bradley R. Cairns
13. RNA 5-Methylcytosine Analysis by Bisulfite Sequencing
Matthias Schaefer
14. Biochemical and transcriptome-wide identification of A-to-I RNA editing sites by ICE-seq
Shunpei Okada, Masayuki Sakurai, Hiroki Ueda, and Tsutomu Suzuki
15. Radical SAM-Mediated Methylation of Ribosomal RNA
Vanja Stojkovic and Danica Galonic Fujimori