Seoul National University Biological Sciences Website

Publications

Systems Mass Spectrometry Lab

2024

Hyunyoung Kim†, Sanghee Shin†,Jeongho Han, Jong-Seo Kim* and Hyungju Park* (2024). Serpina1e mediates the exercise-induced enhancement of hippocampal memory. , (), under review.

Yongwoo Na†, Yeon Choi†, Thi Thanh My Nguyen, Hoang-Anh Pham-Bui, Jeesoo Kim, V. Narry Kim, Mihye Lee* and Jong-Seo Kim* (2024). Gene expression dynamics before and after zygotic genome activation in Drosophila early embryogenesis. iScience, (), under revision.

Seonhwa Lee†, Dong-Gi Jang†, Yeon Ju Kyoung, Jeesoo Kim, Eui-Soon Kim, Ilseon Hwang, Jong-Chan Youn*, Jong-Seo Kim* and In-Cheol Kim* (2024). Proteome-wide characterization and pathophysiology correlation in three non-ischemic cardiomyopathies. Korean Circulation Journal, 54(8), 468-481.

Yeon Choi†, Buyeon Um†, Yongwoo Na, Jeesoo Kim, Jong-Seo Kim*, and V. Narry Kim* (2024). Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle. Molecular Cell, 84(9), 1764-1782.

Sanghee Shin†, Song-Yi Lee†, Myeong-Gyun Kang, Dong-Gi Jang, Jeesoo Kim, Hyun-Woo Rhee* and Jong-Seo Kim* (2024). Super-resolution proximity labeling with enhanced direct identification of biotinylation sites. Communications Biology, 7(1), Article number: 554.

Ara Lee†, Gihyun Sung†, Sanghee Shin, Song-Yi Lee, Jaehwan Sim, Truong Thi My Nhung, Tran Diem Nghi, Sang Ki Park, Ponnusamy Pon Sathieshkumar, Imkyeung Kang, Ji Young Mun, Jong-Seo Kim*, Hyun-Woo Rhee*, Kyeng Min Park*, and Kimoon Kim* (2024). OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools. Nature Communications, 15(1), Article number: 1851.

Isaac Park†, Kwang-eun Kim†, Jeesoo Kim†, Ae-Kyeong Kim, Subin Bae, Minkyo Jung, Jinhyuk Choi, Pratyush Kumar Mishra, Taek-Min Kim, Chulhwan Kwak, Myeong-Gyun Kang, Chang-Mo Yoo, Ji Young Mun, Kwang-Hyeon Liu, Kyu-Sun Lee*, Jong-Seo Kim*, JaeMyoung Suh*, and Hyun-Woo Rhee* (2024). Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis. Nature Chemical Biology, 20(2), 221–233.

Chanhyeok Jeon, Dongju Kim, Kyung-Me Kim, Seung Hoon Lee, Ji-Hyun Lee, Sang-Hyon Kim, Jong-Seo Kim, Young Mo Kang, Sungsin Jo, Tae-Hwan Kim, Chang-Nam Son* (2024). Complement factor H-related protein 5 alleviates joint inflammation and osteoclast differentiation by disrupting RANK-JNK signaling in collagen antibody-induced arthritis mouse model. Cytokine, 184(), 156790.

Ka-Yun Ban, Yong-woo Na, Juhan Song, Jong-Seo Kim and Jimi Kim* (2024). Protein-RNA interaction dynamics reveal key regulators of oncogenic KRAS-driven cancers. Scientific Reports, 14(), Article number: 27119.

Jaejin Kim#, Yeonghyeon Lee#, Taerang Jeon#, Seonmin Ju, Jong-Seo Kim, Mi-Sung Kim, and Chanhee Kang* (2024). Autophagy-dependent splicing control directs translation toward inflammation during senescence. Developmental Cell, (), in press.

Ji-Hyun Lee, Seung Hoon Lee, Chanhyeok Jeon, Jinil Han, Sang-Hyon Kim, Jeehee Youn, Ye-Soo Park, Tae-Jong Kim, Jong-Seo Kim, Sungsin Jo*, Tae-Hwan Kim*, Chang-Nam Son* (2024). The complement factor H-related protein-5 (CFHR5) exacerbates pathological bone formation in ankylosing spondylitis. Journal of Molecular Medicine, 102(4), 571–583.

Geurim Son, Yongwoo Na, Yongsung Kim, Ji-Hoon Son, Gregory D. Clemenson, Simon Schafer, Apua Paquola, Hyunsu Do, Dayeon Kim, Insook Ahn, Mingyu Ju, Chanhee Kang Younghee Ju, Youngjin Park, Se-Bum Paik, Junho Hur, Yong-Mahn Han, Fred H. Gage, Jong-Seo Kim and Jinju Han* (2024). miR-124 coordinates metabolic regulators acting at early stages of human neurogenesis. Communications Biology, 7(1), 1393.

Chewon Yim#, Yeonji Chung#, Sungjoon Son, Jeesoo Kim, Jong-Seo Kim, Hyun Kim* (2024). Abundance of the membrane proteome in yeast cells lacking Spc1, a non-catalytic subunit of the signal peptidase complex. J. Membr. Biol., 257(3-4), 207–214.

Jinseul Kyung, Daesong Jeong, Hyunjoo Eom, Jeesoo Kim, Jong-Seo Kim, Ilha Lee* (2024). C-TERMINAL DOMAIN PHOSPHATASE-LIKE 1 promotes flowering with TAF15b by repressing the floral repressor gene FLOWERING LOCUS C. Molecules and Cells, 47(10), 100114.

Jun-Yeong Ahn+, Somi Kim+, Chang Rok Kim, Ji-Hyun Lee, Jong Min Kim, Thomas M. Klompstra, Yoon Ha Choi, Yoon Jeon, Yongwoo Na, Jong-Seo Kim, Yuki Okada, Ho Lee, Ik Soo Kim*, Jong Kyoung Kim*, Bon-Kyoung Koo*, and Sung Hee Baek* (2024). Dual function of PHF16 in reinstating homeostasis of murine intestinal epithelium after crypt regeneration. Developmental Cell, (), S1534-5807(24)00492-1.

2023

Yun-Bin Lee, Minkyo Jung, Jeesoo Kim, Afandi Charels, Wanda Christ, Myeong-Gyun Kang, Chulhwan Kwak, Jonas Klingström, Anna Smed Sörenson, Jong-Seo Kim*, Ji-Young Mun*, and Hyun-Woo Rhee* (2023). Super-resolution proximity labeling reveals antiviral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Reports, 42(8), 112835.

Thi Thanh My Nguyen†, Choijamts Munkhzul†, Jeesoo Kim, Yeonju Kyoung, Michele Vianney, Sanghee Shin, Seonmin Ju, Pham Bui Hoang Anh, Junhyung Kim, Jong-Seo Kim*, and Mihye Lee* (2023). In vivo profiling of the Zucchini proximal proteome in Drosophila ovary. Development, 150(4), dev201220.

Hyun Sik Lee#,Injin Bang#, Junghyun You, Tae-Kyeong Jeong, Chang Rok Kim, Minsang Hwang, Jong-Seo Kim, Sung Hee Baek, Ji-Joon Song, Hee-Jung Choi* (2023). Molecular basis for PHF7-mediated ubiquitination of histone H3. Genes & Development, 37(21-24), 984–997.

Nari Kim, Tae-Hyeon Kim, Jee-Eun Lee, Chaelim Kim, Myeong-Gyun Kang, Sanghee Shin, Minkyo Jung, Jong-Seo Kim, Ji Young Mun, Hyun-Woo Rhee, Seung-Yeol Park, Yongdae Shin, Joo-Yeon Yoo (2023). Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Developmental Cell, 58(19), 1950-1966.e8.

Sun-Il Yun, Chulhwan Kwak, Song-Yi Lee, Sanghee Shin, Changsuk Oh, Jong-Seo Kim, Hyun-Woo Rhee*, Kyeong Kyu Kim* (2023). Binding of USP4 to cortactin enhances cell migration in HCT116 human colon cancer cells. The FASEB Journal, 37(5), e22900.

2022

Sungwon Lee, Hyewon Kim, Ari Hong, Jaewon Song, Sungyul Lee, Myeonghwan Kim, Sung-yeon Hwang, Dongjoon Jeong, Jeesoo Kim, Ahyeon Son, Young-suk Lee, V. Narry Kim, Jong-Seo Kim, Hyeshik Chang* and Kwangseog Ahn* (2022). Functional and molecular dissection of HCMV long non-coding RNAs. Scientific Reports, 12(), Article number: 19303.

Ye Young Kim, Hagoon Jang, Gung Lee, Yong Geun Jeon, Jee Hyung Sohn, Ji Seul Han, Won Taek Lee, Jeu Park, Jin Young Huh, Hahn Nahmgoong, Sang Mun Han, Jeesoo Kim, Minwoo Pak, Sun Kim, Jong-Seo Kim, and Jae Bum Kim* (2022). Hepatic GSK3β-Dependent CRY1 Degradation Contributes to Diabetic Hyperglycemia. Diabetes, 71(7), 1373–1387.

2021

Jong Woo Bae, Sangtae Kim, V. Narry Kim*, and Jong-Seo Kim* (2021). Photoactivatable ribonucleosides mark base-specific RNA-binding sites. Nature Communications, 12(), Article number: 6026.

Kwang-eun Kim†, Isaac Park†, Jeesoo Kim, Myeong-Gyun Kang, Won Gun Choi, Hyemi Shin, Jong-Seo Kim*, Hyun-Woo Rhee* and Jae Myoung Suh* (2021). Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice. Nature Communications, 12(), Article number: 5204.

Yongwoo Na, Hyunjoon Kim, Yeon Choi, Sanghee Shin, Jae Hun Jung, S. Chul Kwon, V. Narry Kim*, and Jong-Seo Kim* (2021). FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo. Nucleic Acids Research, 49(5), e28.

Chuna Kim†, Sanghyun Sung†, Jong-Seo Kim†, Hyunji Lee, Yoonseok Jung, Sanghee Shin, Eunkyeong Kim, Jenny J. Seo, Jun Kim, Daeun Kim, Hiroyuki Niida, V. Narry Kim, Daechan Park* and Junho Lee* (2021). Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells. Nature Communications, 12(), Article number: 1097.

Sungyul Lee, Young-suk Lee, Yeon Choi, Ahyeon Son, Youngran Park, Kyung Min Lee, Jeesoo Kim, Jong-Seo Kim, V Narry Kim* (2021). The SARS-CoV-2 RNA interactome. Molecular Cell, 81(13), 2838-2850. e6.

Chewon Yim, Yeonji Chung, Jeesoo Kim , IngMarie Nilsson, Jong-Seo Kim, and Hyun Kim (2021). Spc1 regulates the signal peptidase-mediated processing of membrane proteins. Journal of Cell Science, 134(13), jcs258936.

Yeonghyeon Lee, Jaejin Kim, Mi-Sung Kim, Yoojin Kwon, Sanghee Shin, Hyerim Yi, Hyeonkyeong Kim, Moon Jong Chang, Chong Bum Chang, Seung-Baik Kang, V. Narry Kim, Jin-Hong Kim, Jong-Seo Kim, Stephen Elledge, and Chanhee Kang* (2021). Coordinate regulation of the senescent state by selective autophagy. Developmental Cell, 56(10), 1512-1525. e7.

2020

Jihyun Lee†, Jae Hun Jung†, Jeesoo Kim, Won-Ki Baek, Jinseol Rhee, Tae-Hwan Kim, Sang-Hyon Kim, Kwang Pyo Kim*, Chang-Nam Son*, and Jong-Seo Kim* (2020). Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis. Clinical Proteomics, 17(), 20.

Jong Woo Bae, Sung-Chul Kwon, Yongwoo Na, V. Narry Kim* and Jong-Seo Kim* (2020). Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution. Nature Structural & Molecular Biology, 27(7), 678–682.

Chulhwan Kwak†, Sanghee Shin†, Jong-Seok Park†, Minkyo Jung, Truong Thi My Nhung, Myeong-Gyun Kang, Chaiheon Lee, Tae-Hyuk Kwon, Sang Ki Park*, Ji Young Mun*, Jong-Seo Kim*, and Hyun-Woo Rhee* (2020). Contact-ID, a tool for profiling organelle contact site, reveals regulatory proteins of mitochondrial-associated membrane formation. Proc Natl Acad Sci USA, 117(22), 12109-12120.

Sanghee Shin, Ji Hye Hong, Yongwoo Na, Mihye Lee, Wei-Jun Qian, V. Narry Kim, and Jong-Seo Kim* (2020). Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster. Analytical Chemistry, 92(7), 4926-4934.

Yeon Choi†, Kyowon Jeong†, Sanghee Shin†, Joon Won Lee†, Young-suk Lee, Sangtae Kim, Sun Ah Kim, Jaehun Jung, Kwang Pyo Kim, V. Narry Kim* and Jong-Seo Kim* (2020). MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and in vitro chemical labeling. Analytical Chemistry, 92(7), 4980-4989.

Jinuk Kim, Wonhee Han, Taeyong Park, Eun Jin Kim, Injin Bang, Hyun Sik Lee, Yejing Jeong, Kyeonghwan Roh, Jeesoo Kim, Jong-Seo Kim, Chanhee Kang, Chaok Seok, Jin-Kwan Han, Hee-Jung Choi* (2020). Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature Communications, 11(), Article number: 5357.

Dongwan Kim, Young-suk Lee, Soo-Jin Jung, Jinah Yeo, Jenny Seo, Young-yoon Lee, Jaechul Lim, Hyeshik Chang, Jaewon Song, Jihye Yang, Jong-Seo Kim, Guhung Jung, Kwangseok Ahn and V. Narry Kim (2020). Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing. Nature Structural & Molecular Biology, 27(6), 581–588.

Chang Rok Kim, Taichi Noda, Hyunkyung Kim, Gibeom Kim, Seongwan Park, Yongwoo Na, Seiya Oura, Keisuke Shimada, Injin Bang, Se Kyu Oh, Yong Ryoul Kim, Hee-Jung Choi, Jong-Seo Kim, Inkyung Jung, Ho Lee, Yuki Okada, Masahito Ikawa*, and Sung Hee Baek* (2020). PHF7 Modulates BRDT stability and Histone-to-Protamine Exchange during Spermiogenesis. Cell Reports, 32(4), 107950.

Ju-Hyung Lee, Ji-Sun Yoo, Yeonbum Kim, Jong-Seo Kim, Eun-Jin Lee, and Jung-Hye Roe (2020). The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition. mBio, 11(2), e00625-20.

S Chul Kwon, Harim Jang, Siyuan Shen, S Chan Baek, Kijun Kim, Jihye Yang, Jeesoo Kim, Jong-Seo Kim, Suman Wang, Yunyu Shi, Fudong Li*, V Narry Kim* (2020). ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8. Nucleic Acids Research, 48(19), 11097–11112.

Jihyeon Yu, Eunju Cho, Yeon-Gil Choi, You Kyeong Jeong, Yongwoo Na, Jong-Seo Kim, Sung-Rae Cho, Jae-Sung Woo, and Sangsu Bae (2020). Purification of an intact human protein overexpressed from its endogenous locus via direct genome engineering. ACS Synthetic Biology, 9(7), 1591-1598.

Ji-Eun Kim, Joon-Sun Choi, Jong-Seo Kim, You-Hee Cho, and Jung-Hye Roe (2020). Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme. Nucleic Acids Research, 48(5), 2401–2411.

2019

Jaehun Jung, Kyowon Jeong, Yeon Choi, Sun Ah Kim, Hyunjoon Kim, Joon Won Lee, V. Narry Kim, Kwang Pyo Kim and Jong-Seo Kim* (2019). Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics. Journal of Proteome Research, 18(3), 1078-1087.

Eunkyong Ko†, Jong-Seo Kim†, Jong Woo Bae, Jeesoo Kim, Sung-Gyoo Park, and Guhung Jung* (2019). SERPINA3 is a key modulator of HNRNP-K transcriptional activity against oxidative stress in HCC. Redox Biology, (), Jun;24:101217.

Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaitė L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M (2019). NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Research, 47(16), 8720-8733.

Donghyun Kang, Jungkwon Shin, Yongsik Cho, Hyeon-Seop Kim, Young-Ran Gu, Haedong Kim, Kwon Tae You, Moon Jong Chang, Chong Bum Chang, Seung-Baik Kang, Jong-Seo Kim, V. Narry Kim, and Jin-Hong Kim (2019). Stress-activated miR-204 governs senescent phenotypes of chondrocytes to promote osteoarthritis development. Science Translational Medicine, 11(486), eaar6659.

Zee-Won Lee, Byoung Sik Kim, Kyung Ku Jang, Ye-Ji Bang, Suhyeon Kim, Nam-Chul Ha, Young Hyun Jung, Hyun Jik Lee, Ho Jae Han, Jong-Seo Kim, Jeesoo Kim, Pramod K. Sahu, Lak Shin Jeong, Myung Hee Kim, Sang Ho Choi (2019). Small-molecule inhibitor of HlyU attenuates virulence of Vibrio species. Scientific Reports, 9(), 4346.

2018

Ko E, Seo HW, Jung ES, Ju S, Kim BH, Cho H, Kim YJ, Park YM, Kim JS, Jung G (2018). PI3Kδ is a new therapeutic target in hepatocellular carcinoma. Hepatology, 68(6), 2285-2300.

Pyo KE, Kim CR, Lee MK, Kim JS, Kim KI, Baek SH (2018). ULK1 O-GlcNAcylation Is Crucial for Activating VPS34 via ATG14L during Autophagy Initiation. Cell Reports, 25(10), 2878–2890.

Choi EJ, Jung D, Kim JS, Lee Y, Kim BM (2018). Chemoselective Tyrosine Bioconjugation through Sulfate Click Reaction. Chem Eur J, 24(43), 10948-10952.

Ko E, Kim JS, Ju S, Seo HW, Chang Y, Kang JA, Park SG, Jung G (2018). Oxidatively modified PDIA3 promotes DKC1-mediated malignancy and survival of hepatocellular carcinoma cells. Hepatology, 68(5), 1851-1864.

Lee M, Kim IS, Park KC, Kim JS, Baek SH, Kim KI (2018). Mitosis-specific phosphorylation of Mis18α by Aurora B kinase enhances kinetochore recruitment of polo-like kinase 1. Oncotarget, 9(2), 1563-1576.

2017

Song-Yi Lee, Myeong-Gyun Kang, Sanghee Shin, Chulhwan Kwak, Taejoon Kwon, Jeong Kon Seo*, Jong-Seo Kim*, and Hyun-Woo Rhee* (2017). Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells. Journal of the American Chemical Society, 139(10), 3651–3662.

2014

Kim Y, Yeo J, Lee JH, Cho J, Seo D, Kim JS, Kim VN. (2014). Deletion of human tarbp2 reveals cellular microRNA targets and cell-cycle function of TRBP. Cell Reports, 9(3), 1061–74.

2013

Jong-Seo Kim, Ziyu Dai, Uma K. Aryal, Ronald J. Moore, David G. Camp II, Scott E. Baker, Richard D. Smith, and Wei-Jun Qian* (2013). Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Analytical Chemistry, 85(14), 6826–32.

Jong-Seo Kim, Matthew E. Monroe, David G. Camp II, Richard D. Smith, and Wei-Jun Qian* (2013). In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. Journal of Proteome Research, 12(2), 910-6.

2012

Jong-Seo Kim*, Jin-Su Song, Yongju Kim, Seung Bum Park, Hie-Joon Kim* (2012). De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature. Anal Bioanal Chem, 402(5), 1911-9.

2011

Jong-Seo Kim*, Mansup Shin, Jin-Su Song, Songhie An, Hie-Joon Kim* (2011). C-terminal de novo sequencing of peptides using oxazolone-based derivatization with bromine signature. Anal Biochem, 419(2), 211-6.

Jong-Seo Kim, Thomas L. Fillmore, Tao Liu, Errol Robinson, Mahmud Hossain, Boyd L. Champion, Ronald J. Moore, Camp David G. II, Richard D. Smith, Wei Jun Qian* (2011). 18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry. Mol Cell Proteomics, 10(12), M110.007302.

Jong-Seo Kim*, Si-Uk Song, Hie-Joon Kim* (2011). Simultaneous identification of tyrosine phosphorylation and sulfation sites utilizing tyrosine-specific bromination. J Am Soc Mass Spectrom, 22(11), 1916-25.

Jong-Seo Kim, Jisoo Kim, Jung Min Oh, Hie-Joon Kim* (2011). Tandem mass spectrometric method for definitive localization of phosphorylation sites using bromine signature. Anal Biochem, 414(2), 294-6.

2009

Jong-Seo Kim, Enshi Cui, Hie-Joon Kim* (2009). Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity. J Am Soc Mass Spectrom, 20(9), 1751-8.

2008

Jong-Seo Kim, Ji-Hyun Kim, Hie-Joon Kim* (2008). Matrix-assisted laser desorption/ionization signal enhancement of peptides by picolinamidination of amino groups. Rapid Commun Mass Spectrom, 22(4), 495-502.

2005

Jong-Seo Kim, Ji-Young Kim, Hie-Joon Kim* (2005). Suppression of matrix clusters and enhancement of peptide signals in MALDI-TOF mass spectrometry using nitrilotriacetic acid. Analytical Chemistry, 15(77), 7483-8.

2001

Jong-Seo Kim, Hie-Joon Kim* (2001). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine. Rapid Commun Mass Spectrom, 15(23), 2296-300.