RESEARCH INTERESTS

research-summary

      Circular RNAs (circRNAs) are a newly discovered class of RNAs that are generated through non-sequential back splicing: their 3’ and 5’ ends are joined to form a closed loop. Unlike mRNAs and other linear RNAs, circRNAs are defined solely by their topology; they lack ends. As a consequence, regulatory elements found on linear RNA, including 5’ caps, 3’ untranslated regions (UTRs), and poly(A) tails are not present on circRNAs. The absence of regulatory features on circRNAs underscores how little is known about these highly-stable RNAs.
    Like their linear RNA counterparts, circRNAs exhibit a range of functions within cells. The most notable examples, so far, are as microRNA sponges and as ribosome templates. However, as new circRNA functions continue to be discovered, the regulation of these various functions and their importance in disease remain poorly understood.
      I will use a combination of molecular, cellular, genomic, and chemical biology to probe the scope of circRNA function in cells and uncover additional layers of regulation. In particular, I am interested in the movement of circRNAs throughout the cell, their interactions with cellular machinery and metabolites, and factors that regulate their formation and degradation. I will investigate the impact of RNA secondary structures and post-transcriptional modifications on circRNA function and regulation. My work will reveal the "life cycle" of circRNAs, establish a cellular atlas of circRNAs, and define the small and macromolecules that contact them. These insights will address a fundamental question in biology of the molecular mechanisms that govern cellular function.

PUBLICATIONS

[FEATURED ARTICLE] Sensing self and nonself circular RNAs by intron identity.
Chen YG, Kim M, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY.
Molecular Cell 67, 1-11 (2017).
This paper was presented as a preview in Molecular Cell 67, 163-164 (2017): Antiviral Immunity and Circular RNA: No End in Sight and in Stanford Medicine’s Blog: RNA circles can spur immune response, protect cells against viruses, Stanford researchers find. Also, YG Chen was featured in Molecular Cell’s Meet the Authors.
Mechanisms of immune system gene regulation by long noncoding RNAs.
Chen YG*, Satpathy AT*, Chang HY.
Nature Immunology 18(9): 962-972 (2017).
LncRNA Seduction of GOT2 Goes Viral.
Chen YG and Chang HY
Immunity 47(6): 1021-1023 (2017).
The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline.
Bailey AS*, Batista PJ*, Gold RS, Chen YG, de Rooij DG, Chang HY, Fuller MT
eLife 6:e26116 (2017).
m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT5/SOCS pathway.
Li HB*, Tong J*, Zhu S*, Batista PJ, Duffy EE, Zhao J, Bailis W, Guangchao C, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA.
Nature 548, 338–342 (2017).
Discovery and biological characterization of geranylated RNA in bacteria.
Dumelin CE, Chen Y, Leconte AM, Chen YG, Liu DR.
Nature Chemical Biology 8, 913-919 (2012).
LC/MS analysis of cellular RNA reveals NAD-Linked RNA.
Chen YG, Kowtoniuk WE, Agarwal I, Shen Y, Liu DR.
Nature Chemical Biology 5, 879-881 (2009).
Performance assessment and validation of a paramagnetic particle-based enzyme-linked immunosorbent assay for chlorpyrifos in agricultural runoff waters.
Sullivan J, Chen YG, Goh K
J Agric Food Chem 55, 6407-16 (2007).
Oxidative dehydrogenation of dihydropyrimidiones and dihydropyrimidines.
Yamamoto K, Chen YG, Buono F
Organic Letters 7, 4673-4676 (2005).
Kinetic measurements of phosphoglucose isomerase and phosphomannose isomerase by direct analysis of phosphorylated aldose–ketose isomers using tandem mass spectrometry.
Gao H, Chen Y, Leary J
International Journal of Mass Spectrometry 240, 291–299 (2005).

ABOUT

research-summary

YE GRACE CHEN, PhD

Postdoctoral Fellow, Howard Chang’s Laboratory

Stanford University School of Medicine

Email: yegracechen [at] stanford [dot] edu



I am currently a postdoctoral fellow in Howard Chang's group at Stanford University School of Medicine. My research interests center around gaining a molecular understanding of how RNA responds to and regulates cellular processes. I am specifically interested in circular RNA and its "life cycle" in healthy and disease states. Outside of lab, I enjoy exploring the outdoors and going on adventures with family.


Education and Training

2013-present
Postdoctoral Fellow, Stanford University
Advisor: Howard Y. Chang, Dept. of Epithelial Biology
2006-2012
PhD in Chemical Biology, Harvard University
Advisor: David R. Liu, Dept. of Chemistry and Chemical Biology
Spring 2006
Research Associate, California Environmental Protection Agency
Advisor: Kean Goh, Dept. of Pesticide Regulation
Fall 2005
Research Fellow, Tsinghua University
Advisor: Bing Zhou, Dept. of Biology
2002-2005
B.S. in Chemical Biology, University of California, Berkeley
Advisors: Tom Alber, Dept. of Molecular and Cellular Biology; Julie Leary, Dept. of Chemistry

Fellowships and Honors

June 2017
Best Poster Award
RNA International Meeting
May 2017
Best Speaker Award
Stanford ChEM-H Conference
2014-2016
T32 Fellowship
National Institute of Health
2013-2014
Dean’s Fellowship
Stanford University
2007-2010
Graduate Research Fellowship
National Science Foundation
July 2010
Best Speaker Award
University of Konstanz’s Chemical Biology Conference
May 2005
Commencement Speaker
University of California, Berkeley College of Chemistry
2002-2005
Regents’ and Chancellor’s Scholarship
University of California, Berkeley
2002-2005
Alumni Leadership Scholarship
University of California, Berkeley