Ailong Ke
Assistant Professor

Ailong Ke




Department of Molecular Biology & Genetics
251 Biotechnology Building
Cornell University
Ithaca, NY 14853-2703


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Department Profile

Lab Website


1995 B.S. in Biology. University of Science and Technology, China.
2002 Ph.D. in Biophysics. Johns Hopkins University School of Medicine. (Advisor: Dr. Cynthia Wolberger)
2002-05 Postdoc at University of California, Berkeley. (Advisor: Dr. Jennifer Doudna)

Research Description

Research in my lab centers around the biology of RNA. In eukaryotic cells, stable RNAs are transcribed with a 3’ extension that is subsequently trimmed from 3’-to-5’, whereas aberrantly processed RNAs are subject to rapid degradation. A conserved 300 – 400 kDa exoribonuclease protein complex, the exosome, plays crucial roles in both the RNA 3’-end formation and turnover processes (Fig. 1). The nuclear exosome is required for the 3’ end formation of 5.8S rRNA, small nuclear and nucleolar RNAs; and involved in the degradation of inefficiently spliced and hyper– or hypo-adenylated pre-mRNAs. The cytoplasmic exosome is required for the degradation of normal mRNAs as well as those containing premature termination codons, lacking termination codons, or bearing AU-rich elements near the 3’ untranslated region. Using X-ray crystallography and biochemical tools, we aim to understand the architecture, working mechanism, and the regulation of this multi-subunit machinery.


Yibei Xiao, Sherwin Ng, Ki Hyun Nam, Ailong Ke*.
How Type II CRISPR-Cas establishes immunity through Cas1-Cas2 mediated spacer integration.
Nature. 2017 Sep 4. doi:10.1038/nature24020

Yibei Xiao#, Min Luo#, Robert P Hayes, Jonathan Kim, Sherwin Ng, Fran Ding, Maofu Liao*, Ailong Ke*.
Structure basis for directional R-loop formation and substrate handover mechanisms in Type I CRISPR-Cas system.
Cell. 2017 Jun 29;170(1):48-60

Cheulhee Jung, John Hawkins, Stephen K.Jones Jr, Yibei Xiao, Jim R. Rybarski, Kaylee Dillard, Mashelfatema A Saifuddin, Cagri Savran, Andrew Ellington, Ailong Ke, William H. Press, ILya J. Finkelstein.*.
Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips.
Cell. 2017 Jun 29; 170(1):35-37.

Rebort Battaglia, Ian Price, Ailong Ke*.
Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches.
RNA.2017 Apr;23(4):578-585. doi: 10.1261/rna.060186.116. Epub 2017 Jan 17.

Robert P. Hayes, Yibei Xiao, Fran Ding, Paul B. G. van Erp, Kanagalaghatta Rajashankar, Scott Bailey, Blake Wiedenheft, Ailong Ke*.
Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.
Nature. 2016 Feb 25;530(7591):499-503.

Price IR, Gaballa A, Ding F, Helmann JD, Ailong Ke*.
Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.
Molecular Cell. 2015 Mar 19;57(6):1110-23.

Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ailong Ke*.
Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation.
Nat Struct Mol Biol. 2014 Sep;21(9):771-7.

Grigg JC, Ailong Ke*.
Structural determinants for geometry and information decoding of tRNA by T box leader RNA.
Structure. 2013 Oct 1;13: 346-348.

Grigg JC, Chen Y, Grundy FJ, Henkin TM, Pollack L, Ailong Ke*.
T box RNA decodes both the information content and geometry of tRNA to affect gene expression.
Proceedings of National Academy of Sciences U.S.A. 2013 Apr 15;110(18):7240-5.

Complete list of Ailong Ke's publications