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Ja Yil Lee, Ph.D.
Department of Biological Sciences
Ulsan National University of Science and Technology (UNIST)
Building 110, Room 601-6
UNIST-gil 50 Ulsan 44919, South Korea
Office Phone: +82-52-217-3069
Home Phone: +82-10-4062-2412
E-mail: biojayil@unist.ac.kr
ㅇ EDUCATION & RESEARCH EXPERIENCE
UNIST (Ulsan National University of Science and Technology), Korea 2016-Present
Associate Professor in Department of Biological Sciences
➢ Investigate in-depth mechanism underlying nucleotide excision repair and homologous recombination.
➢ Elucidate DNA repair process in the chromatin context.
➢ Reveal the underlying mechanism of chromatin dynamics and epigenetics
➢ Characterize protein behavior at the collision with other biomolecules.
Columbia University, New York, NY 2008-2016
Associate Research Scientist with Professor Eric C. Greene
➢ Investigated eukaryotic homologous recombination.
➢ Investigated the nucleotide-dependent binding and translocation of DNA translocase, FtsK, using DNA curtains, which is a high-throughput single-molecule technique based on nanofabricated system.
➢ Examined the collisions of FtsK with other proteins (RNA polymerase, EcoRI, RecBCD, and so on).
➢ Developed a combined system of optical tweezers and DNA curtains and studied protein-DNA interaction (nucleosomes and RNA polymerase) under the mechanical strain to DNA.
➢ Developed actin filament curtains to study the formin dynamics.
Korea University, Seoul, South Korea 2006-2008
Research Professor in Dept. of Physics with Professor Seok-Cheol Hong
➢ Developed a combined system of single-molecule fluorescence spectroscopy and magnetic tweezers.
➢ Investigated the initiation of Holliday junction under torsion and tension to DNA.
➢ Examined the DNA triplex formation using single-molecule FRET spectroscopy.
Seoul National University, Seoul, South Korea 2003-2006
Ph.D. in Dept. of Physics with Professor Dai-Sik Kim
➢ Thesis: “Studies on conformational dynamics of telomeric DNA via single-molecule FRET”.
➢ Studied the conformational dynamics of G-quadruplex structure in human and protozoan telomeric DNA.
➢ This work was done in collaboration with Taekjip Ha’s group (see References).
Biomedlab Co., Seoul, South Korea 2001-2003
Researcher in Microarray Research Center
➢ Participated in developing a lab-on-a-chip using microfluidcs and confocal detection system.
➢ Participated in developing a sensitive detection instrument for DNA microarray chip.
Samsung SDI, Suwon, South Korea 1999-2001
Assistant Researcher in Center for Research and Development
➢ Participated in developing a slim cathode-ray tube using two electron guns.
➢ Evaluated the display quality.
Seoul National University, Seoul, South Korea 1997-1999
M. S. in Dept. of Physics with Professor Dai-Sik Kim
➢ Studied non-linear optical properties of semiconductor using femto-second pulse laser.
➢ Studied virtual excitation (off-resonance excitation) of electron in bulk GaAs as a function of thickness using a four-wave mixing technique.
Seoul National University, Seoul, South Korea 1993-1997
B. S. in Dept. of Physics
ㅇPUBLICATIONS
Oh J-M, Kang Y, Park J, Sung Y, Kim D, Seo Y, Lee EA, Ra JS, Amarsanaa, E, Park YU, Hwang, JM, Kim H, Scharer OD, Cho SW, Lee C, Takata K, Lee JY*, and Myung K*, MSH2-MSH3 promotes DNA end resection during HR and blocks TMEJ through interaction with SMARCAD1 and EXO1. Nucleic Acids Res (under revision)
Kang Y, An S, Min D, and Lee JY, Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying DNA damage repair. Frontiers in Bioeng and Biotech 2022; 10: 973314-973331.
Ju MK, Lee JR, Lee S, Park SY, Sul HJ, Chung HJ, An S, Choi Y, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y, Kim H, and Zang DY, PWWP2B Regulates Homologous Recombination by Promoting DNA End Resection. EMBO Reports 2022: 23: e53492.
Cheon NY and Lee JY, Studying R-loop recognizing proteins using single-molecule DNA curtain technique and electrophoretic mobility shift assay. R-loops, Methods in Molecular Biology, Springer Protocols, 253-269, 2022 (Book chapter).
Cheon NY, Kim S, and Lee JY, Biophysical and biochemical approaches for R-loop sensing mechanism. Gene Expression 2022 (Book chapter, online published).
Kang Y, Bae S, An S, and Lee JY, Deciphering molecular mechanism of histone assembly by DNA curtain technique. J Visual Exp 2022; e63501.
Kang Y, Cho C, Lee KS, Song JJ, and Lee JY, Single-molecule imaging reveals the mechanism underlying histone loading of Schizosaccharomyces Pombe AAA+ ATPase Abo1. Mole and Cells 2021; 44: 79-87.
Cha J and Lee JY, A Novel High-Throughput Single-Molecule Technique: DNA Curtain. J Korean Phys. Soc. 2021; 78: 442-448.
***This paper is an invited paper***
Kang HJ††, Cheon NY††, Park H, Jeong GW, Ye BJ, Yoo EJ, Lee JH, Hur JH, Lee EA, Lee K, Choi SY, Lee-Kwon W, Myung K*, Lee JY*, and Kwon HM*, TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution. Nucleic Acids Research. 2021; 49: 269-284.
Kang Y, Cheon NY, Cha J, Kim A, Kim H, Lee L, Kim KO, Jo K, and Lee JY, High-throughput single-molecule system using nanofabricated trenches and fluorescent DNA-binding proteins. Biotechnology and Bioengineering. 2020; 117: 1640-1648.
Kang W, Ha KS, Uhm H, Park K, Lee JY, Hohng, S, and Kang C, Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA. Nature Communications. 2020; 11: 450-458.
Jang HJ, Lim S, Kim JM, Yoon S, Lee CY, Hwang HJ, Shim JW, Shin KJ, Kim HY, Park KI, Nam D, Lee
JY, Yea K, Hirabayashi Y, LEE YJ, Chae YC, Suh PG, and Choi JH, Glucosylceramide synthase regulates adipo-osteogenic differentiation through synergistic activation of PPARγ with ClcCer. FASEB Journal. 2020; 34: 1270-1287.
Cho C, Jang JW, Kang Y, Watanabe H, Uchihashi T, Kim SJ, Kato K, Lee JY*, and Song J-J*, Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone. Nature Communications. 2019; 10: 5764-5776.
Cheon NY, Kim HY, Yeo J-E, Scharer OD and Lee JY, Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B. Nucleic Acids Research. 2019; 47: 8337-8347.
***This paper was chosen as NAR Breakthrough
Lee JY, Steinfeld JB, Qi Z, Kwon Y, Sung, P, and Greene EC, Sequence imperfections and base triplet recognition by the Rad51/RecA family of recombinases. Journal of Biological Chemistry. 2017; 292: 11125-11135.
**This paper was chosen as Editors’ pick
Lee JY, Qi Z, and Greene EC, ATP hydrolysis promotes duplex DNA release by the RecA presynaptic complex. Journal of Biological Chemistry. 2016; 291: 22218-22230.
**
**This paper was chosen in Faculty of 1000.
Lee JY, Tsuyoshi T, Qi Z, Steinfeld JB, Redding S, Kwon YH, Gaines WA, Zhao X, Sung P, and Greene EC, Base triplet stepping during DNA strand exchange by the Rad51/RecA family of recombinases.
Science. 2015; 349: 977-981.
Qi Z, Redding S, Lee JY, Gibb B, Kwon YH, Niu H, Gaines W, Sung P, and Greene EC, DNA sequence alignment by microhomology sampling during homologous recombination. Cell. 2015; 160: 856-869.
Lee JY, Finkelstein IJ, Arciszewska LK, Sherratt DJ, and Greene EC, Single-molecule imaging of FtsK translocation reveals mechanistic features contributing to the outcomes of protein-protein collisions on DNA. Molecular Cell. 2014; 54: 832-843.
Courtemanche N*, Lee JY*, Pollard TD, and Greene EC, Tension modulates actin filament polymerization mediated by formin and profilin. Proceedings of National Academy of Sciences of USA. 2013; 110: 9752-9757.
**
**This paper was featured in Science Editor’s Choice. Science. 2013: 341: 110-111.
Fazio TA*, Lee JY*, Wind SJ, and Greene EC, Assembly of DNA curtains using hydrogen silsesquioxane as barriers to lipid diffusion. Analytical Chemistry. 2012; 84: 7613-7617.
Lee JY, Wang F, Fazio TA,Wind SJ, and Greene EC, Measuring Intermolecular rupture forces with a combined TIRF-optical trap microscope and DNA curtains. Biochemical and Biophysical Research Communications. 2012; 426: 565-570.
Lee JY*, Finkelstein IJ*, Crozat E, Serratt DJ, and Greene EC. Single molecule imaging of DNA curtains reveals mechanisms of KOPS targeting by the DNA translocase FtsK. Proceedings of National Academy of Sciences of USA. 2012; 109: 6531-6536.
Lee IB, Lee JY, Lee N-K, and Hong S-C. Direct observation of the formation of DNA triplexes by single-molecule FRET measurements. Current Applied Physics. 2012; 12: 1027-1032.
Lee JY and Greene EC. Assembly of recombinant nucleosomes on nanofabricated DNA curtains for single-molecule imaging. Methods of Molecular Biology. 2011; 778: 243-258.
Lee JY† and Kim DS. Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex Nucleic Acids Research. 2009; 37: 3625-3634.
Lee JY, Yoon J, Kihm, HW, and Kim DS. Structural diversity and extreme stability of unimolecular Oxytricha nova telomeric G-quadruplex. Biochemistry 2008; 47: 3389-3396.
Lee JY, Kim SK, and Hong S-C. Characterization of the evanescent field in objective-based total internal
reflection fluorescence (TIRF) microscopy. Journal of Korean Physical Society. 2007; 50: 1340-1345.
Lee JY*, Okumus B, Kim DS, and Ha T. Extreme conformational diversity in human telomeric DNA. Proceedings of National Academy of Sciences of USA. 2005; 102: 18938-18943.
Jho YD, Lee JY, Yahng JS, Yee KJ, Hohng SC, and Kim DS. Real-to-virtual transition in bulk GaAs: the thickness dependence. Journal of Korean Physical Society. 2000; 37: 728-734.
Kim DS, Lee JY, and Pang MG. Male circumcision: a South Korean perspective. British Journal of Urology International. 1999; 83: 28-33.
Hohng SC, Khang DW, Ahn YH, Lee JY, Kihm SY, Kim DH, Kim WS, Woo JC, Kim DS, Cirtrin DS, Woo DH, Kim EK, Kim SH, and Lim KS. Two color picosecond and CW experiements on the anti-Stokes and Stokes carrier transfer phenomena in GaAs/AlxGa1-x and InGaP2/AlxGa1-xAs heterostructures. Physical Review B. 1999; 60: 8883-8889.
† corresponding author
* equally contributed
ㅇGRANTS & Awards
Korean Research Foundation Grant (KRF-2008-357-C00048) 2008-2010
KASBP-Yuhan Fellowship Award 2013
Travel Grant in Korean Society of Molecular Cell Biology 2014
Posco TJ Park Science Fellowship 2017-2019
National Research Foundation Grant (NRF-2017R1A2B4002213) 2017-2019
National Research Foundation Grant (NRF-2020R1A2B5B01001792) 2020-
Samsung Science & Technology Foundation Grant (BA190113468) 2019-
ㅇRegistered Patents
Hong S-C. and Lee JY, DNA selection and detection method using protein binding specific DNA base sequences, registered Korean patent (10-2009-0022569)
Lee JY, Kang Y, and Choen NY, array for single-molecule imaging containing nano-trench structures, registered Korean patent (10-2020-0041079)
ㅇInvited Presentations for international conferences
International Conference of the Genetic Society of Korea 2021
Title: New roles of TonEBP in R-loop resolution
The 14th Asia-Pacific Physics Conference, 2019, Kuching, Malaysia
Title: DNA damage search mechanism using single-molecule imaging
The 62nd Japanese Radiation Research Society Conference, 2019, Kyoto, Japan
Title: Damage search mechanism of XPC-RAD23B
2nd East Asian Symposium on Single-Molecule Biological Sciences, 2019, Seoul, South Korea
Title: Lesion search mechanism of human NER protein
International Conference of the Korean Society of Structural Biology, 2018, Jeju, South Korea (invited speech)
Title: DNA curtain – a novel single-molecule technique to study detailed mechanisms underlying biological reactions
KSMCB International Conference 2017, Seoul, South Korea
Title: Single-molecule approach to molecular mechanism underlying DNA damage repair
KSBMB International Conference 2017, Busan, South Korea
Title: Single-molecule approach to homology search and strand exchange in homologous recombination
UKC 2016 Dallas, TX, USA
Title: Single-molecule study on the homology search and the strand exchange mechanisms in homologous recombination
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