Publications

1Co-first author
*Co-corresponding author

2020

R. Shang1, S. C. Baek1, K. Kim, B. Kim, V. N. Kim, E. C. Lai  (2020) “Genomic Clustering Facilitates Nuclear Processing of Suboptimal Pri-miRNA Loci” Molecular Cell, 78(2):303–316.

J. W. Bae, S. C. Kwon, Y. Na, V. N. Kim*, and J. S. Kim* (2020) “Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution” Nature Structural & Molecular Cell Biology, 27:678-682.

D. Kim1, J.-Y. Lee, J.-S. Yang, J. W. Kim, V. N. Kim*, and H. Chang* (2020) “The architecture of SARS-CoV-2 transcriptome” Cell, 181(4):914-921.e10.

H. Kim1, J. Kim1, S. Yu, Y.-Y. Lee, J. Park, R. J. Choi, S.-J. Yoon, S.-G. Kang, V. N. Kim  (2020) “A mechanism for microRNA arm switching regulated by uridylation” Molecular Cell, in press

S. Yu and V. N. Kim  (2020) “A tale of noncanonical tails: gene regulation by post-transcriptional RNA tailing” Nature Reviews Molecular Cell Biology, in press

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., published online.

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.

2019

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. KimK. T. You, M. J. Chang, C. B. Chang, S. B. Kang, J. S. KimV. 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. JeongY. ChoiS. A. KimH. 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. Kim1J. Kim1K. KimH. ChangK. YouV. N. Kim (2019) “Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification” Nucleic Acids Research, 47(5): 2630-2640.

S. C. KwonS. C. BaekY. G. ChoiJ. YangY. LeeJ.-S. Woo*V. N. Kim* (2019) “Molecular basis for the single-nucleotide precision of primary microRNA processing” Molecular Cell, 73(3):505–518.

2018

J. YeoV. N. Kim (2018) “U-tail as a guardian against invading RNAs” Nature structural & molecular biology, 25, 903–905.

Y. Kim1J. 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.

J. Lim1D. Kim1Y. Lee1M. HaM. LeeJ. YeoH. Chang, J. Song, K. Ahn, V. N. Kim (2018) “Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation” Science, eaam5794.

H. Yi1J. Park1M. HaJ. LimH. ChangV. N. Kim (2018) “PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay” Molecular Cell, 70(6):1081-1088.e5..

B. KimV. N. Kim (2018) “fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: Lessons from DROSHA” Methods, S1046-2023(18)30064-1.

T. A. Nguyen1J. Park1, T. L. Dang, Y. G. ChoiV. N. Kim (2018) “Microprocessor depends on hemin to recognize the apical loop of primary microRNA” Nucleic Acids Res., 46(11):5726-5736.

A. Son1J.-E. Park1V. N. Kim (2018) “PARN and TOE1 Constitute a 3′ End Maturation Module for Nuclear Non-coding RNAs” Cell Reports, 23(3):888-898.

H. Chang1J. Yeo1, J.-g. Kim, H. KimJ. LimM. Lee, H. H. Kim, J. Ohk, H.-Y. Jeon, H. Lee, H. Jung, K.-W. Kim and V. N. Kim (2018) “Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos” Molecular Cell, 70(1):72-82.e7.

K. Kim1, T. D. Nguyen1, S. Li, T. A. Nguyen (2018) “SRSF3 recruits DROSHA to the basal junction of primary microRNAs” RNA, 24(7):892-898.

V. N. Kim (2018) “RNA-targeting CRISPR comes of age” Nature Biotechnology, 36:44–45.

2017

B. Kim1K. Jeong1V. N. Kim (2017) “Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates” Molecular Cell, 66(2):258-269.

2016

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.

2015

K. T. YouJ. Park, and V. N. Kim (2015) “Role of the small subunit processome in the maintenance of pluripotent stem cells” Genes & Development, 29:2004-2009.

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*, and 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. KwonH. ChangV. 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.

T. A. Nguyen, M. H. Jo, Y.-G. ChoiJ. ParkS. C. Kwon, S. Hohng, V. N. Kim*J.-S. Woo* (2015) “Functional Anatomy of the Human Microprocessor” Cell, 161(6):1374-1387.

B. Kim1M. Ha1, L. Loeff1H. 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. Jang1H. 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.

2014

J. Lim1M. Ha1H. Chang1S. C. Kwon, D. K. Simanshu, D. J. Patel, and V. N. Kim (2014) “Uridylation by TUT4 and TUT7 marks mRNA for degradation” Cell, 159(6):1365-1376.

M. LeeY. ChoiK. KimH. JinJ. LimT. A. NguyenJ. 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. Kim1J. Yeo1J. H. Lee1J. Cho, D. Seo, J. Kim, and V. N. Kim (2014) “Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP” Cell Reports, 9:1061–1074.

M. LeeB. Kim and V. N. Kim (2014) “Emerging roles of RNA modifications: m6A and U-tail” Cell, 158:980-987.

M. Ha and V. N. Kim (2014) “Regulation of microRNA biogenesis” Nature Reviews Molecular Cell Biology, 15, 509–524.

Y. KimJ. H. LeeJ.-E. ParkJ. ChoH. Yi and V. N. Kim (2014) “PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator” Genes & Development, 28: 1310-1322.

H. Chang1J. Lim1M. Ha, and V. N. Kim (2014) “TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications” Molecular Cell, 53(6):1044-1052.

J.-S. Woo, and V. N. Kim (2014) “MeCP2 Caught Moonlighting as a Suppressor of MicroRNA Processing” Developmental Cell, 28(5):477-478.

Y. Tian1, D. K. Simanshu1, J.-B. Ma, J.-E. ParkI. HeoV. 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.

2013

Y.-K. Kim1, G. Wee1J. Park, J. Kim, D. Baek, J.-S. Kim*, and V. N. Kim* (2013) “TALEN-based knockout library for human microRNAs” Nature Structural and Molecular Biology, 20(12):1458-1464.

S. C. KwonH. 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.

C. Joo, M. Fareh, V. N. Kim (2013) “Bringing single-molecule spectroscopy to macromolecular protein complexes” Trends in Biochemical Sciences, 38(1):30-37.

2012

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.

J. Cho1H. Chang1S. C. KwonB. KimY. Kim, J. Choe, M. Ha, Y. K. Kim and V. N. Kim (2012) “LIN28A is a suppressor of ER-associated translation in embryonic stem cells” Cell, 151: 765-777. Suppl.

I. Heo1M. Ha1J. LimM.-J. YoonJ.-E. ParkS. C. KwonH. 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. JinV. 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.

H. JinV. N. Kim* and S. Hyun* (2012) “Conserved microRNA miR-8 controls body size in response to steroid signaling in Drosophila” Genes & Development, 26:1427-1432.

Y.-K. KimJ. YeoB. KimM. Ha and V. N. Kim (2012) “Short Structured RNAs with Low GC Content Are Selectively Lost during Extraction from a Small Number of Cells” Molecular Cell, 46:893-895.

Y. Kim and V. N. Kim (2012) “MicroRNA Factory: RISC Assembly from Precursor MicroRNAs” Molecular Cell, 46:384-386.

2011

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. Park1I. Heo1, Y. Tian, D. K. Simanshu, H. ChangD. 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.

K.-H. YeomI. Heo, J. Lee, S. Hohng, V. N. Kim* and C. Joo* (2011) “Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation” EMBO Reports, 12:690-969.

2010

Y.-K. KimI. Heo and V. N. Kim (2010) “Modifications of Small RNAs and Their Associated Proteins” Cell, 143:703-709.

2009

S. Hyun1J. H. Lee1H. Jin1J. NamB. 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.

I. Heo and V. N. Kim (2009) “Regulating the Regulators: Posttranslational Modifications of RNA Silencing Factors” Cell, 139:28-31.

H. Jin1M. R. Suh1J. HanK.-H. YeomY. LeeI. HeoM. HaS. Hyun and V. N. Kim (2009) “Human UPF1 Participates in Small RNA-Induced mRNA Downregulation” Molecular and Cellular Biology, 20(21):5789-99.

I. Heo1C. Joo1Y.-K. Kim1M. Ha, M.-J. Yoon, J. ChoK.-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.

V. N. Kim*, J. Han and M. C. Siomi* (2009) “Biogenesis of small RNAs in animals” Nature Reviews Molecular Cell Biology, 10:126-139.

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.

S. Y. Park1, J. H. Lee1, M. Ha, J. W. Nam and V. N. Kim (2009) “miR-29 miRNAs activate p53 by targeting p85a and CDC42” Nature Structural and Molecular Biology, 16(1):23-9.

2008

I. Heo1, C. Joo1, J. Cho, M. Ha, J. Han and V. N. Kim (2008) “Lin28 mediates the terminal uridylation of let-7 precursor microRNA” Molecular Cell, 32:276-284.

V. N. Kim (2008) “Cell cycle micromanagement in embryonic stem cells” Nature Genetics, 40(12):1391-2.

V. N. Kim (2008) “Sorting out small RNAs” Cell, 133:25-26.

2007

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. Y. Sohn1, W. J. Bae1, J. J. Kim, K. H. Yeom, V. N. Kim and Y. Cho (2007) “Crystal structure of human DGCR8 core” Nature Structural and Molecular Biology, 14(9):847-53.

Y.-K. Kim and V. N. Kim (2007) “Processing of intronic microRNAs” EMBO Journal, 26(3):775-83.

J. T. Lee, S. S. Yu, V. N. Kim and S. Kim (2007) “Control of Splicing Efficiency by the Mouse Histone H2a Element in a Murine Leukemia Virus-based Retroviral Vector” Molecular Therapy, 15(1):167-72.

2006

V. N. Kim (2006) “Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes” Genes & Development, 20(15):1993-7.

K. H. YeomY. LeeJ. HanM. R. Suh and V. N. Kim (2006) “Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing” Nucleic Acids Research, 34(16):4622-9.

V. N. Kim and J. W. Nam (2006) “Genomics of microRNA” Trends in Genetics, 22(3):165-73.

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. Han1Y. Lee1,K. H. Yeom1J. 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.

Y. Lee1I. Hur1, S. Y. Park1Y.-K. Kim, M. R. Suh and V. N. Kim (2006) “The role of PACT in the RNA silencing pathway” EMBO Journal, 25(3):522-32.

2005

2004

2003

Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim, J. Yim, J. Lee, P. Provost, O. Radmark, S. Kim, V. N. Kim (2003) “The nuclear RNase III Drosha initiates microRNA processing” Nature, 425(6956):415-9.

2002

Y. Lee, K. Jeon, J. T. Lee, S. Kim and V. N. Kim (2002) “MicroRNA maturation: stepwise processing and subcellular localization” EMBO Journal, 21(17):4663-70.

Books

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

Patents

The inhibition method of microRNA

The recombinant primary microRNA molecule for RNA interference