S. Kim1, S. Kim1, H. R. Chang1, D. Kim1, J. Park, N. Son, J. Park, M. Yoon, G. Chae, Y. -K. Kim, V. N. Kim, Y. K. Kim, J. -W. Nam, C. Shin*, D. Baek* (2021) “The regulatory impact of RNA-binding proteins on microRNA targeting” Nature Communications, 12:5057.
Y. Hong, H. Jeong, K. Park, S. Lee, J. Y. Shim, H. Kim, Y. Song, S. Park, H. Y. Park, V. N. Kim, K. Ahn (2021) “STING facilitates nuclear import of herpesvirus genome during infection” Proceedings of the National Academy of Sciences of the U. S. A., 118(33):e2108631118.
Y. Lee1, J. Kim1, M. Kim1, Y. Kwon, S. Shin, H. Yi, H. Kim, M. Chang, C. Chang, S. Kang, V. N. Kim, J. Kim, J. Kim, S. J. Elledge, C. Kang (2021) “Coordinate regulation of the senescent state by selective autophagy” Develpmental Cell, 56(10):1512-1525.
H. Kim1, Y. Lee1, S. -M. Kim, S. Jang, H. Choi, J. -W. Lee, T. -D. Kim, V. N. Kim (2021) “RNA demethylation by FTO stabilizes the FOXJ1 mRNA for proper motile ciliogenesis” Developmental Cell, 56(8):1118-1130.
Y. Na, H. Kim, Y. Choi, S. Shin, J. H. Jung, S. C. Kwon, V. N. Kim*, J. S. Kim* (2021) “FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo” Nucleic Acids Research, 49(5):e28.
C. Kim1, S. Sung1, J. -S. Kim1, H. Lee, Y. Jung, S. Shin, E. Kim, J. J. Seo, J. Kim, D. Kim Hiroyuki Niida, V. N. Kim, D. Park*, J. Lee* (2021) “Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells” Nature communications, 12:1097.
S. Hwang, H. Jung, S. Mun, S. Lee, K. Park, S. C. Baek, H. Moon, H. Kim, B. Kim, Y. Choi, Y. Go, W. Tang, J. Choi, J. Choi, H. Cha, H. Park, P. Liang, V. N. Kim, K. Han*, K. Ahn* (2021) “L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force” Nature communications, 12:880.
S. C. Kwon1, H. Jang1, S. Shen1, S. C. Baek, K. Kim, J. Yang, J. Kim, J.-S. Kim, S. Wang, Y. Shi, F. Li*, V. N. Kim* (2020) “ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8” Nucleic Acids Research, 48(19):11097-11112.
J. W. Bae, S. C. Kwon, Y. Na, V. N. Kim*, J. S. Kim* (2020) “Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution” Nature Structural & Molecular Biology, 27:678-682.
D. Kim1, Y. Lee1, S.-J. Jung1, J. Yeo1, J. J. Seo, Y.-Y. Lee, J. Lim, H. Chang, J. Song, J. Yang, J. S. Kim, G. Jung, K. Ahn, V. N. Kim (2020) “Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing” Nature Structural & Molecular Biology, 27:581–588.
J. Won, S. Lee, M. Park, T. Y. Kim, M. G. Park, B. Y. Choi, D. Kim, H. Chang, V. N. Kim, C. Justin Lee (2020) “Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19)” Exp Neurobiol., 29(2):107-119.
J. Min, T. S. Han, Y. Sohn, T. Shimizu, B. Choi, S. W. Bae, K. Hur, S. H. Kong, Y. S. Suh, H. J. Lee, J. S. Kim, J. K. Min, W. H. Kim, V. N. Kim, E. Choi, J. R. Goldenring, H. K. Yang (2020) “microRNA-30a arbitrates intestinal-type early gastric carcinogenesis by directly targeting ITGA2.” Gastric Cancer., 23:600-613.
S. Shin, J. H. Hong, Y. Na, M. Lee, W. J. Qian, V. N. Kim, J. S. Kim (2020) “Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster” Anal. Chem., 92(7):4926-4934.
Y. Choi1, K. Jeong1, S. Shin1, J. W. Lee1, Y. Lee, S. Kim, S. A. Kim, J. Jung, K. P. Kim, V. N. Kim*, J. S. Kim* (2020) “MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and in vitro chemical labeling” Anal. Chem., 92(7):4980–4989.
S. Shin1, Y. Jung1, H. Uhm, M. Song, S. Son, J. Goo, C. Jeong, J.-J. Song, V. N. Kim, S. Hohng (2020) “Quantification of purified endogenous miRNAs with high sensitivity and specificity” Nature communications, 11(6033).
J. K. Kim, J. Cho, S. H. Kim, H. C. Kang, D. S. Kim, V. N. Kim, J. H. Lee (2019) “Brain somatic mutations in MTOR reveal translational dysregulations underlying intractable focal epilepsy” J Clin Invest., 129(10):4207-4223.
D. Kang1, J. Shin1, Y. Cho, H. S. Kim, Y. R. Gu, H. Kim, K. T. You, M. J. Chang, C. B. Chang, S. B. Kang, J. S. Kim, V. N. Kim, J. H. Kim (2019) “Stress-activated miR-204 governs senescent phenotypes of chondrocytes to promote osteoarthritis development” Science Translational Medicine, 11(486): eaar6659.
J. Jung, K. Jeong, Y. Choi, S. A. Kim, H. Kim, J. W. Lee, V. N. Kim, K. P. Kim, J. S. Kim (2019) “Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics” J Proteome Res., 18(3):1078-1087.
H. Kim1, J. Kim1, K. Kim, H. Chang, K. You, V. N. Kim (2019) “Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification” Nucleic Acids Research, 47(5): 2630-2640.
Y. Kim1, J. Park1, S. Kim1, M. Kim, M. G. Kang, C. Kwak, M. Kang, B. Kim, H. W. Rhee, V. N. Kim (2018) “PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs” Molecular Cell, 71(6):1051-1063.e6.
H. Chang1, J. Yeo1, J.-g. Kim, H. Kim, J. Lim, M. Lee, H. H. Kim, J. Ohk, H.-Y. Jeon, H. Lee, H. Jung, K.-W. Kim, V. N. Kim (2018) “Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos” Molecular Cell, 70(1):72-82.e7.
J. Choi, Y.-K. Kim, K. Park, J. Nah, S. S. Yoon, D. W. Kim, V. N. Kim, R. H. Seong (2016) “MicroRNA-139-5p regulates proliferation of hematopoietic progenitors and is repressed during BCR-ABL-mediated leukemogenesis” Blood, 128(17):2117-2129.
B. Choi1, J. Yu1, T.-S. Han, Y.-K. Kim, K. Hur, B.-C. Kang, W. H. Kim, D.-Y. Kim, H.-J. Lee, V. N. Kim, H.-K. Yang (2016) “Gastric Carcinogenesis in the miR-222/221 Transgenic Mouse Model” Cancer Research and Treatment, 49(1):150-160.
Y.-K. Kim*, B. Kim, V. N. Kim* (2016) “Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis” Proceedings of the National Academy of Sciences of the U. S. A., 113(13):E1881-E1889.
J. Cho1, N.-K. Yu1, J.-H. Choi, S.-E. Sim, S. J. Kang, C. Kwak, S.-W. Lee, J. Kim, D. I. Choi, V. N. Kim*, B.-K. Kaang* (2015) “Multiple repressive mechanisms in the hippocampus during memory formation” Science, 350(6256):82–87.
M. Kampmann, M. A. Horlbeck, Y. Chena, J. C. Tsai, M. C. Bassik, L. A. Gilbert, J. E. Villalta, S. C. Kwon, H. Chang, V. N. Kim, J. S. Weissman (2015) “Next-generation libraries for robust RNA interference-based genome-wide screens” Proceedings of the National Academy of Sciences of the U. S. A., 112(26):E3384-E3391.
S. Kim1, D. Seo1, D. Kim, Y. Hong, H. Chang, D. Baek, V. N. Kim, S. Lee, K. Ahn (2015) “Temporal Landscape of MicroRNA-Mediated Host-Virus Crosstalk during Productive Human Cytomegalovirus Infection” Cell Host & Microbe, 17(6):838-851.
B. Kim1, M. Ha1, L. Loeff1, H. Chang, D. K. Simanshu, S. Li, M. Fareh, D. J. Patel, C. Joo*, V. N. Kim* (2015) “TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms” EMBO Journal, 35(2):115-236. Suppl.
K. Boo1, J. Bhin1, Y. Jeon, J. Kim, H. J. Shin, J. E. Park, K. Kim, C. R. Kim, H. Jang, I. H. Kim, V. N. Kim, D. Hwang, H. Lee, S. H. Baek (2015) “Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells” Nature Communications, 6:6810.
T.-S. Han, K. Hur, G. Xu, B. Choi, Y. Okugawa, Y. Toiyama, H. Oshima, M. Oshima, H.-J. Lee, V. N. Kim, A. N. Chang, A. Goel, and H.-K. Yang (2015) “MicroRNA-29c mediates initiation of gastric carcinogenesis by directly targeting ITGB1” Gut, 64:203–214.
I. Jang1, H. Chang1, Y. Jun, S. Park, J. O. Yang, B. Lee, W. Kim, V. N. Kim, and S. Lee (2015) “miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data” Bioinformatics, 31(4): 596-598.
M. Lee, Y. Choi, K. Kim, H. Jin, J. Lim, T. A. Nguyen, J. Yang, M. Jeong, A. J. Giraldez, H. Yang, D. J. Patel, and V. N. Kim (2014) “Adenylation of maternally inherited microRNAs by Wispy” Molecular Cell, 56(5):696-707.
Y. Tian1, D. K. Simanshu1, J.-B. Ma, J.-E. Park, I. Heo, V. N. Kim, and D. J. Patel (2014) “A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer” Molecular Cell, 53:606-616.
S. C. Kwon, H. Yi, K. Eichelbaum, S. Föhr, B. Fischer, K. T. You, A. Castello, J. Krijgsveld, M. W. Hentze, and V. N. Kim (2013) “The RNA-binding protein repertoire of embryonic stem cells” Nature Structural and Molecular Biology, 20(9):1122-1130.
S.-R. Ryoo, J. Lee, J. Yeo, H.-K. Na, Y.-K. Kim, H. Jang, J. H. Lee, S. W. Han, Y. Lee, V. N. Kim, and D.-H. Min (2013) “Quantitative and Multiplexed MicroRNA Sensing in Living Cells Based on Peptide Nucleic Acid and Nano Graphene Oxide (PANGO)” ACS Nano, 7(7):5882–5891.
S. Cho, I. Jang, Y. Jun, S. Yoon, M. Ko, Y. Kwon, I. Choi, H. Chang, D. Ryu, B. Lee, V. N. Kim, W. Kim and S. Lee (2012) “miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting” Nucleic Acids Research, 41 (D1): D252-D257.
I. Heo1, M. Ha1, J. Lim, M.-J. Yoon, J.-E. Park, S. C. Kwon, H. Chang and V. N. Kim (2012) “Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs” Cell, 151: 521-532.
J. Kim, M. Choi, J. R. Kim, H. Jin, V. N. Kim and K. H. Cho (2012) “The co-regulation mechanism of transcription factors in the human gene regulatory network” Nucleic Acids Research, 40(18):8849-8861.
S. Kim, S. Lee, J. Shin, Y. Kim, I. Evnouchidou, D. Kim, Y.-K. Kim, Y.-E. Kim, J.-H. Ahn, S. R. Riddell, E. Stratikos, V. N. Kim and K. Ahn (2011) “Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1″ Nature Immunology, 12:984-991.
J.-E. Park1, I. Heo1, Y. Tian, D. K. Simanshu, H. Chang, D. Jee, D. J. Patel and V. N. Kim (2011) “Dicer recognizes the 5′ end of RNA for efficient and accurate processing” Nature, 475:201-205. Suppl.
S. Hyun1, J. H. Lee1, H. Jin1, J. Nam, B. Namkoong, Gina Lee, J. Chung and V. N. Kim (2009) “Conserved microRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K” Cell, 139:1096-1108.
H. Jin1, M. R. Suh1, J. Han, K.-H. Yeom, Y. Lee, I. Heo, M. Ha, S. Hyun and V. N. Kim (2009) “Human UPF1 Participates in Small RNA-Induced mRNA Downregulation” Molecular and Cellular Biology, 20(21):5789-99.
I. Heo1, C. Joo1, Y.-K. Kim1, M. Ha, M.-J. Yoon, J. Cho, K.-H. Yeom, J. Han and V. N. Kim (2009) “TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation” Cell, 138:696-708.
Y.-K. Kim, J. Yu, T. S. Han, S. Y. Park, B. Namkoong, D. H. Kim, K. Hur, M. W. Yoo, H. J. Lee, H. K. Yang*, and V. N. Kim * (2009) “Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer” Nucleic Acids Research, 37:1672-1681.
J. Han, J. S. Pederson, S. C. Kwon, C. D. Belair, Y.-K. Kim, K. H. Yeom, W. Y. Yang, D. Haussler, R. Blelloch, and V. N. Kim (2009) “Posttranscriptional crossregulation between Drosha and DGCR8” Cell, 136:75-84.
H. H. Lee, Y. S. Kim, K. H. Kim, I. Heo, S. K. Kim, O. Kim, H. K. Kim, J. Y. Yoon, H. S. Kim, D. J. Kim, H. J. Yoon, S. J. Kim, B. G. Lee, H. K. Song, V. N. Kim, C. M. Park and S. W. Suh (2007) “Structural and functional insights into Dom34, a key component of No-Go mRNA decay” Molecular Cell, 27(6):938-50.
S. J. Yim1, Y. S. Lee1, D. J. Chang, J. H. Han, H. Kim, H. Park, H. Jun, V. N. Kim and B. K. Kaang (2006) “Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation” Journal of Neurochemistry, 98(2):420-9.
J. Han1, Y. Lee1,K. H. Yeom1, J. W. Nam, I. Heo, J. K. Rhee, S. Y. Sohn, Y. Cho, B. T. Zhang, and V. N. Kim (2006) “Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex” Cell, 125(5):887-901.
J. W. Nam, K. R. Shin, J. Han, Y. Lee, and V. N. Kim, B. T. Zhang (2005) “Human microRNA prediction through a probabilistic co-learning model of sequence and structure” Nucleic Acids Research, 33(11):3570-81.
K. Lee, K. Jeon, J. M. Kim, V. N. Kim, D. H. Choi, S. U. Kim and S. Kim (2005) “Downregulation of GFAP, TSP-1, and p53 in human glioblastoma cell line, U373MG, by IE1 protein from human cytomegalovirus” Glia, 51(1):1-12.
M. R. Suh, Y. Lee, J. Y. Kim, S. K. Kim, S. H. Moon, J. Y. Lee, K. Y. Cha, H. M. Chung, H. S. Yoon, S. Y. Moon, V. N. Kim* and K. S. Kim* (2004) “Human embryonic stem cells express a unique set of microRNAs” Developmental Biology, 270(2):488-98.
Y. Lee and V. N. Kim (2007) “In vitro and in vivo assays for the activity of drosha complex” Methods in Enzymology 427:87-106 doi:10.1016/S0076-6879(07) 27005-3
Y. Lee, J. Han, K. H. Yeom, H. Jin and V. N. Kim (2006) “Drosha in primary microRNA processing” Cold Spring Harbor Symposia on Quantative Biology (2006) 71:51-7 doi:10.1101/sqb.2006.71.041
Y. Lee and V. N. Kim (2005) “Preparation and analysis of Drosha” Methods in Molecular Biology 309:17-28
The inhibition method of microRNA
The recombinant primary microRNA molecule for RNA interference