mRNA Stability, Tailing, and Modification
Functional atlas of vertebrate viral RNA elements that stabilize RNA and enhance translation J. J. Seo 1 ,
C. Lee 1 ,
D. Lim ,
M. Jeong ,
S.-J. Jung , and
V. N. Kim ✉︎ (corresponding author) Cell
(2026), 189(22):7105-7120.e12
Cite: Functional atlas of vertebrate viral RNA elements that stabilize RNA and enhance translation
RNA stability enhancers for durable base-modified mRNA therapeutics S.-J. Jung 1 ,
J. J. Seo 1 ,
S. Lee 1 ,
S.-I. Hyun ,
J.-e. Lee ,
S. Lee ,
Y. Lee ,
H. Chang ,
H. Lee ,
J.-H. Kim , and
V. N. Kim ✉︎ (corresponding author) Nature Biotechnology
(2026), 44(11):1831-1844
Cite: RNA stability enhancers for durable base-modified mRNA therapeutics
Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle Y. Choi 1 ,
B. Um 1 ,
Y. Na ,
J. Kim ,
J.-S. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2024), 84(9):1764-1782.e10
Cite: Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle
Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution Y.-S. Lee 1 ✉︎ (corresponding author) Y. Levdansky 1 ,
Y. Jung ,
V. N. Kim ✉︎ (corresponding author) E. Valkov ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2024), 31(5):826-834
Cite: Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution
Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex J. Park 1 ,
M. Kim 1 ,
H. Yi 1 ,
K. Baeg 1 ,
Y. Choi ,
Y. Lee ,
J. Lim , and
V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2023), 30(3):330-338
Cite: Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex
RNA demethylation by FTO stabilizes the FOXJ1 mRNA for proper motile ciliogenesis H. Kim 1 ✉︎ (corresponding author) Y. Lee 1 ,
S.-M. Kim ,
S. Jang ,
H. Choi ,
J.-W. Lee ,
T.-D. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Developmental Cell
(2021), 56(8):1118-1130.e6
Cite: RNA demethylation by FTO stabilizes the FOXJ1 mRNA for proper motile ciliogenesis
L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force 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 ✉︎ (corresponding author) K. Ahn ✉︎ (corresponding author) Nature Communications
(2021), 12(1):880
Cite: L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force
A tale of noncanonical tails: gene regulation by post-transcriptional RNA tailing S. Yu and
V. N. Kim ✉︎ (corresponding author) Nature Reviews Molecular Cell Biology
(2020), 21(9):542-556
Cite: A tale of noncanonical tails: gene regulation by post-transcriptional RNA tailing
Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing D. Kim 1 ,
Y. Lee 1 ,
S.-J. Jung 1 ,
J. Yeo 1 ,
J. J. Seo ,
Y.-Y. Lee ,
J. Lim ,
H. Chang ,
J. Song ,
J. Yang ,
J. S. Kim ,
G. Jung ,
K. Ahn , and
V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2020), 27(6):581-588
Cite: Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing
U-tail as a guardian against invading RNAs J. Yeo and
V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2018), 25(10):903-905
Cite: U-tail as a guardian against invading RNAs
Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation J. Lim 1 ,
D. Kim 1 ,
Y. Lee 1 ,
M. Ha ,
M. Lee ,
J. Yeo ,
H. Chang ,
J. Song ,
K. Ahn , and
V. N. Kim ✉︎ (corresponding author) Science
(2018), 361(6403):701-704
Cite: Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation
PABP cooperates with the CCR4-NOT complex to promote mRNA deadenylation and block precocious decay H. Yi 1 ,
J. Park 1 ,
M. Ha ,
J. Lim ,
H. Chang , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2018), 70(6):1081-1088.e5
Cite: PABP cooperates with the CCR4-NOT complex to promote mRNA deadenylation and block precocious decay
PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs A. Son 1 ,
J.-E. Park 1 , and
V. N. Kim ✉︎ (corresponding author) Cell Reports
(2018), 23(3):888-898
Cite: PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs
Terminal uridylyltransferases execute programmed clearance of maternal transcriptome in vertebrate embryos H. Chang 1 ,
J. Yeo 1 ,
J.-g. Kim ,
H. Kim ,
J. Lim ,
M. Lee ,
H. H. Kim ,
J. Ohk ,
H.-Y. Jeon ,
H. Lee ,
H. Jung ,
K.-W. Kim , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2018), 70(1):72-82.e7
Cite: Terminal uridylyltransferases execute programmed clearance of maternal transcriptome in vertebrate embryos
mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development J. Lim 1 ,
M. Lee 1 ,
A. Son ,
H. Chang , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2016), 30(14):1671-1682
Cite: mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development
Regulation of poly(A) tail and translation during the somatic cell cycle J.-E. Park 1 ,
H. Yi 1 ,
Y. Kim 1 ,
H. Chang , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2016), 62(3):462-471
Cite: Regulation of poly(A) tail and translation during the somatic cell cycle
Uridylation by TUT4 and TUT7 marks mRNA for degradation J. Lim 1 ,
M. Ha 1 ,
H. Chang 1 ,
S. C. Kwon ,
D. K. Simanshu ,
D. J. Patel , and
V. N. Kim ✉︎ (corresponding author) Cell
(2014), 159(6):1365-1376
Cite: Uridylation by TUT4 and TUT7 marks mRNA for degradation
Emerging roles of RNA modifications: m6A and U-tail M. Lee ,
B. Kim , and
V. N. Kim ✉︎ (corresponding author) Cell
(2014), 158(5):980-987
Cite: Emerging roles of RNA modifications: m6A and U-tail
TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications H. Chang 1 ,
J. Lim 1 ,
M. Ha , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2014), 53(6):1044-1052
Cite: TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications
Structural and functional insights into Dom34, a key component of no-go mRNA decay 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 ,
S. J. Lee ,
H. J. Yoon ,
S. J. Kim ,
B. G. Lee ,
H. K. Song ,
V. N. Kim ,
C. M. Park , and
S. W. Suh Molecular Cell
(2007), 27(6):938-950
Cite: Structural and functional insights into Dom34, a key component of no-go mRNA decay
Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation S. J. Yim 1 ,
Y. S. Lee 1 ,
J. A. Lee ,
D. J. Chang ,
J. H. Han ,
H. Kim ,
H. Park ,
H. Jun ,
V. N. Kim , and
B. K. Kaang Journal of Neurochemistry
(2006), 98(2):420-429
Cite: Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation
Viral Regulatory RNAs and mRNA Therapeutics
Functional atlas of vertebrate viral RNA elements that stabilize RNA and enhance translation J. J. Seo 1 ,
C. Lee 1 ,
D. Lim ,
M. Jeong ,
S.-J. Jung , and
V. N. Kim ✉︎ (corresponding author) Cell
(2026), 189(22):7105-7120.e12
Cite: Functional atlas of vertebrate viral RNA elements that stabilize RNA and enhance translation
Identification of the SARS-CoV-2 genome packaging signal in the nsp12-coding region Y. Park ✉︎ (corresponding author) J. Lim ,
H. Cho ,
A. Son ,
M. Jeong ,
Y.-s. Lee ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Nature Communications
(2026), 17(1):8500
Cite: Identification of the SARS-CoV-2 genome packaging signal in the nsp12-coding region
RNA stability enhancers for durable base-modified mRNA therapeutics S.-J. Jung 1 ,
J. J. Seo 1 ,
S. Lee 1 ,
S.-I. Hyun ,
J.-e. Lee ,
S. Lee ,
Y. Lee ,
H. Chang ,
H. Lee ,
J.-H. Kim , and
V. N. Kim ✉︎ (corresponding author) Nature Biotechnology
(2026), 44(11):1831-1844
Cite: RNA stability enhancers for durable base-modified mRNA therapeutics
Human cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion S. Lee ,
S. Kim ,
H. Kim ,
D. Lee ,
D. Jeong ,
H. Kim ,
J. Park ,
K. Park ,
J. Hur ,
S. Kim ,
V. N. Kim , and
K. Ahn ✉︎ (corresponding author) Nature Microbiology
(2025), 10(9):2275-2290
Cite: Human cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion
SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production J. Kim 1 ,
Y. Park 1 ,
D. Yoon 1 ,
S. Lee 1 ,
H. Kim 1 ,
K.-Y. Ban ,
J. Yang ,
D.-E. Choi ,
J. Kim ,
J.-S. Kim , and
V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2025), 53(14):gkaf674
Cite: SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production
Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site S. Kim 1 ,
J. H. Jeon 1 ,
M. Kim ,
Y. Lee ,
Y.-H. Hwang ,
M. Park ,
C. H. Li ,
T. Lee ,
J.-A. Lee ,
Y.-M. Kim ,
D. Kim ,
H. Lee ,
Y.-J. Kim ,
V. N. Kim ,
J.-E. Park ✉︎ (corresponding author) J. Yeo ✉︎ (corresponding author) Nature Communications
(2024), 15(1):7226
Cite: Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site
Functional viromic screens uncover regulatory RNA elements J. J. Seo 1 ,
S.-J. Jung 1 ,
J. Yang ,
D.-E. Choi , and
V. N. Kim ✉︎ (corresponding author) Cell
(2023), 186(15):3291-3306.e21
Cite: Functional viromic screens uncover regulatory RNA elements
Functional and molecular dissection of HCMV long non-coding RNAs S. Lee 1 ,
H. Kim 1 ,
A. Hong 1 ,
J. Song 1 ,
S. Lee ,
M. Kim ,
S. Hwang ,
D. Jeong ,
J. Kim ,
A. Son ,
Y. Lee ,
V. N. Kim ,
J.-S. Kim ,
H. Chang ✉︎ (corresponding author) K. Ahn ✉︎ (corresponding author) Scientific Reports
(2022), 12(1):19303
Cite: Functional and molecular dissection of HCMV long non-coding RNAs
Analyzing viral epitranscriptomes using nanopore direct RNA sequencing A. Hong 1 ,
D. Kim 1 ,
V. N. Kim , and
H. Chang ✉︎ (corresponding author) Journal of Microbiology
(2022), 60(9):867-876
Cite: Analyzing viral epitranscriptomes using nanopore direct RNA sequencing
The SARS-CoV-2 RNA interactome S. Lee 1 ,
Y. Lee 1 ,
Y. Choi ,
A. Son ,
Y. Park ,
K.-M. Lee ,
J. Kim ,
J.-S. Kim , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2021), 81(13):2838-2850.e6
Cite: The SARS-CoV-2 RNA interactome
The architecture of SARS-CoV-2 transcriptome D. Kim ,
J.-Y. Lee ,
J.-S. Yang ,
J. W. Kim ,
V. N. Kim ✉︎ (corresponding author) H. Chang ✉︎ (corresponding author) Cell
(2020), 181(4):914-921.e10
Cite: The architecture of SARS-CoV-2 transcriptome
Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing D. Kim 1 ,
Y. Lee 1 ,
S.-J. Jung 1 ,
J. Yeo 1 ,
J. J. Seo ,
Y.-Y. Lee ,
J. Lim ,
H. Chang ,
J. Song ,
J. Yang ,
J. S. Kim ,
G. Jung ,
K. Ahn , and
V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2020), 27(6):581-588
Cite: Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing
Development of a laboratory-safe and low-cost detection protocol for SARS-CoV-2 of the coronavirus disease 2019 (COVID-19) J. Won ,
S. Lee ,
M. Park ,
T. Y. Kim ,
M. G. Park ,
B. Y. Choi ,
D. Kim ,
H. Chang ,
V. N. Kim , and
C. Justin Lee ✉︎ (corresponding author) Experimental Neurobiology
(2020), 29(2):107-119
Cite: Development of a laboratory-safe and low-cost detection protocol for SARS-CoV-2 of the coronavirus disease 2019 (COVID-19)
Temporal landscape of microRNA-mediated host-virus crosstalk during productive human cytomegalovirus infection S. Kim 1 ,
D. Seo 1 ,
D. Kim ,
Y. Hong ,
H. Chang ,
D. Baek ,
V. N. Kim ,
S. Lee , and
K. Ahn ✉︎ (corresponding author) Cell Host & Microbe
(2015), 17(6):838-851
Cite: Temporal landscape of microRNA-mediated host-virus crosstalk during productive human cytomegalovirus infection
Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1 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 ✉︎ (corresponding author) Nature Immunology
(2011), 12(10):984-991
Cite: Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1
Cellular Regulation of Exogenous RNAs
Exogenous RNA surveillance by proton-sensing TRIM25 M. Kim ,
Y. Pyo ,
S.-I. Hyun ,
M. Jeong ,
Y. Choi , and
V. N. Kim ✉︎ (corresponding author) Science
(2025), 388(6742):eads4539
Cite: Exogenous RNA surveillance by proton-sensing TRIM25
Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site S. Kim 1 ,
J. H. Jeon 1 ,
M. Kim ,
Y. Lee ,
Y.-H. Hwang ,
M. Park ,
C. H. Li ,
T. Lee ,
J.-A. Lee ,
Y.-M. Kim ,
D. Kim ,
H. Lee ,
Y.-J. Kim ,
V. N. Kim ,
J.-E. Park ✉︎ (corresponding author) J. Yeo ✉︎ (corresponding author) Nature Communications
(2024), 15(1):7226
Cite: Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site
U-tail as a guardian against invading RNAs J. Yeo and
V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2018), 25(10):903-905
Cite: U-tail as a guardian against invading RNAs
PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs Y. Kim 1 ✉︎ (corresponding author) J. Park 1 ,
S. Kim 1 ,
M. Kim ,
M. G. Kang ,
C. Kwak ,
M. Kang ,
B. Kim ,
H. W. Rhee , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2018), 71(6):1051-1063.e6
Cite: PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs
PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator Y. Kim ,
J. H. Lee ,
J.-E. Park ,
J. Cho ,
H. Yi , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2014), 28(12):1310-1322
Cite: PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator
microRNA Biogenesis
The drifting biochemical basis of an essential molecular interaction Y. Park ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Cell Systems
(2026)
Cite: The drifting biochemical basis of an essential molecular interaction
Structural basis for chaperone-guided assembly of RNA-induced silencing complex Y.-Y. Lee 1 ,
M. Jeong 1 ,
H. Lee 1 ,
D. Lee ,
J. Lee ,
J. Park ,
V. N. Kim ✉︎ (corresponding author) S.-H. Roh ✉︎ (corresponding author) Nature
(2026), 655(8125):1339-1348
Cite: Structural basis for chaperone-guided assembly of RNA-induced silencing complex
ERH promotes primary microRNA processing beyond cluster assistance H. Jang ,
J. Park , and
V. N. Kim ✉︎ (corresponding author) Nature Communications
(2025), 16(1):7913
Cite: ERH promotes primary microRNA processing beyond cluster assistance
The biogenesis and regulation of animal microRNAs H. Kim 1 ,
Y.-Y. Lee 1 , and
V. N. Kim ✉︎ (corresponding author) Nature Reviews Molecular Cell Biology
(2024), 26(4):276-296
Cite: The biogenesis and regulation of animal microRNAs
Small and long non-coding RNAs: past, present, and future L.-L. Chen ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Cell
(2024), 187(23):6451-6485
Cite: Small and long non-coding RNAs: past, present, and future
Structural atlas of human primary microRNAs generated by SHAPE-MaP S. Baek 1 ,
B. Kim 1 ,
H. Jang 1 ,
K. Kim ,
I. Park ,
D.-H. Min , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2024), 84(6):1158-1172.e6
Cite: Structural atlas of human primary microRNAs generated by SHAPE-MaP
Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing S. Son 1 ,
B. Kim 1 ,
J. Yang , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2023), 37(9-10):383-397
Cite: Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing
Sequence determinant of small RNA production by DICER Y. Lee 1 ,
H. Kim 1 , and
V. N. Kim ✉︎ (corresponding author) Nature
(2023), 615(7951):323-330
Cite: Sequence determinant of small RNA production by DICER
Structure of the human DICER–pre-miRNA complex in a dicing state Y. Lee 1 ,
H. Lee 1 ,
H. Kim 1 ,
V. N. Kim ✉︎ (corresponding author) S. H. Roh ✉︎ (corresponding author) Nature
(2023), 615(7951):331-338
Cite: Structure of the human DICER–pre-miRNA complex in a dicing state
High-throughput in vitro processing of human primary microRNA by the recombinant Microprocessor K. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) STAR Protocols
(2022), 3(1):101042
Cite: High-throughput in vitro processing of human primary microRNA by the recombinant Microprocessor
A quantitative map of human primary microRNA processing sites K. Kim 1 ,
S. Baek 1 ,
Y. Lee ,
C. Bastiaanssen ,
J. Kim ,
H. Kim , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2021), 81(16):3422-3439.e11
Cite: A quantitative map of human primary microRNA processing sites
ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8 S. C. Kwon 1 ,
H. Jang 1 ,
S. Shen 1 ,
S. C. Baek ,
K. Kim ,
J. Yang ,
J. Kim ,
J.-S. Kim ,
S. Wang ,
Y. Shi ,
F. Li ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2020), 48(19):11097-11112
Cite: ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8
Genomic clustering facilitates nuclear processing of suboptimal pri-miRNA loci R. Shang 1 ✉︎ (corresponding author) S. C. Baek 1 ,
K. Kim ,
B. Kim ,
V. N. Kim , and
E. C. Lai ✉︎ (corresponding author) Molecular Cell
(2020), 78(2):303-316.e4
Cite: Genomic clustering facilitates nuclear processing of suboptimal pri-miRNA loci
A mechanism for microRNA arm switching regulated by uridylation H. Kim 1 ,
J. Kim 1 ,
S. Yu ,
Y.-Y. Lee ,
J. Park ,
R. J. Choi ,
S.-J. Yoon ,
S.-G. Kang , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2020), 78(6):1224-1236.e5
Cite: A mechanism for microRNA arm switching regulated by uridylation
Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification H. Kim 1 ,
J. Kim 1 ,
K. Kim ,
H. Chang ,
K. You , and
V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2019), 47(5):2630-2640
Cite: Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification
Molecular basis for the single-nucleotide precision of primary microRNA processing S. C. Kwon ,
S. C. Baek ,
Y. G. Choi ,
J. Yang ,
Y. Lee ,
J.-S. Woo ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2019), 73(3):505-518.e5
Cite: Molecular basis for the single-nucleotide precision of primary microRNA processing
fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA B. Kim and
V. N. Kim ✉︎ (corresponding author) Methods
(2018), 152:3-11
Cite: fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA
Microprocessor depends on hemin to recognize the apical loop of primary microRNA T. A. Nguyen 1 ✉︎ (corresponding author) J. Park 1 ,
T. L. Dang ,
Y. G. Choi , and
V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2018), 46(11):5726-5736
Cite: Microprocessor depends on hemin to recognize the apical loop of primary microRNA
SRSF3 recruits DROSHA to the basal junction of primary microRNAs K. Kim 1 ,
T. D. Nguyen 1 ,
S. Li , and
T. A. Nguyen ✉︎ (corresponding author) RNA
(2018), 24(7):892-898
Cite: SRSF3 recruits DROSHA to the basal junction of primary microRNAs
Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and noncanonical substrates B. Kim 1 ,
K. Jeong 1 , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2017), 66(2):258-269.e5
Cite: Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and noncanonical substrates
Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis Y.-K. Kim ✉︎ (corresponding author) B. Kim , and
V. N. Kim ✉︎ (corresponding author) Proceedings of the National Academy of Sciences of the U.S.A.
(2016), 113(13):E1881-E1889
Cite: Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis
Structure of human DROSHA S. C. Kwon 1 ,
T. A. Nguyen 1 ,
Y.-G. Choi 1 ,
M. H. Jo ,
S. Hohng ,
V. N. Kim ✉︎ (corresponding author) J.-S. Woo ✉︎ (corresponding author) Cell
(2016), 164(1-2):81-90
Cite: Structure of human DROSHA
Functional anatomy of the human Microprocessor T. A. Nguyen ,
M. H. Jo ,
Y.-G. Choi ,
J. Park ,
S. C. Kwon ,
S. Hohng ,
V. N. Kim ✉︎ (corresponding author) J.-S. Woo ✉︎ (corresponding author) Cell
(2015), 161(6):1374-1387
Cite: Functional anatomy of the human Microprocessor
TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms B. Kim 1 ,
M. Ha 1 ,
L. Loeff 1 ,
H. Chang ,
D. K. Simanshu ,
S. Li ,
M. Fareh ,
D. J. Patel ,
C. Joo ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) EMBO Journal
(2015), 34(13):1801-1815
Cite: TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms Supplementary data
Adenylation of maternally inherited microRNAs by Wispy 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 ✉︎ (corresponding author) Molecular Cell
(2014), 56(5):696-707
Cite: Adenylation of maternally inherited microRNAs by Wispy
Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP Y. Kim 1 ,
J. Yeo 1 ,
J. H. Lee 1 ,
J. Cho ,
D. Seo ,
J. Kim , and
V. N. Kim ✉︎ (corresponding author) Cell Reports
(2014), 9(3):1061-1074
Cite: Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP
Regulation of microRNA biogenesis M. Ha and
V. N. Kim Nature Reviews Molecular Cell Biology
(2014), 15(8):509-524
Cite: Regulation of microRNA biogenesis
MeCP2 caught moonlighting as a suppressor of microRNA processing J.-S. Woo and
V. N. Kim ✉︎ (corresponding author) Developmental Cell
(2014), 28(5):477-478
Cite: MeCP2 caught moonlighting as a suppressor of microRNA processing
A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer Y. Tian 1 ,
D. K. Simanshu 1 ,
J.-B. Ma ,
J.-E. Park ,
I. Heo ,
V. N. Kim , and
D. J. Patel ✉︎ (corresponding author) Molecular Cell
(2014), 53(4):606-616
Cite: A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer
Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs I. Heo 1 ,
M. Ha 1 ,
J. Lim ,
M.-J. Yoon ,
J.-E. Park ,
S. C. Kwon ,
H. Chang , and
V. N. Kim Cell
(2012), 151(3):521-532
Cite: Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs
MicroRNA factory: RISC assembly from precursor microRNAs Y. Kim and
V. N. Kim Molecular Cell
(2012), 46(4):384-386
Cite: MicroRNA factory: RISC assembly from precursor microRNAs
Dicer recognizes the 5′ end of RNA for efficient and accurate processing J.-E. Park 1 ,
I. Heo 1 ,
Y. Tian ,
D. K. Simanshu ,
H. Chang ,
D. Jee ,
D. J. Patel , and
V. N. Kim ✉︎ (corresponding author) Nature
(2011), 475(7355):201-205
Cite: Dicer recognizes the 5′ end of RNA for efficient and accurate processing
Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation K.-H. Yeom ,
I. Heo ,
J. Lee ,
S. Hohng ,
V. N. Kim ✉︎ (corresponding author) C. Joo ✉︎ (corresponding author) EMBO Reports
(2011), 12(7):690-696
Cite: Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation
Modifications of small RNAs and their associated proteins Y.-K. Kim ,
I. Heo , and
V. N. Kim Cell
(2010), 143(5):703-709
Cite: Modifications of small RNAs and their associated proteins
Regulating the regulators: posttranslational modifications of RNA silencing factors I. Heo and
V. N. Kim Cell
(2009), 139(1):28-31
Cite: Regulating the regulators: posttranslational modifications of RNA silencing factors
TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation I. Heo 1 ,
C. Joo 1 ,
Y.-K. Kim 1 ,
M. Ha ,
M.-J. Yoon ,
J. Cho ,
K.-H. Yeom ,
J. Han , and
V. N. Kim Cell
(2009), 138(4):696-708
Cite: TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation
Biogenesis of small RNAs in animals V. N. Kim ✉︎ (corresponding author) J. Han , and
M. C. Siomi ✉︎ (corresponding author) Nature Reviews Molecular Cell Biology
(2009), 10(2):126-139
Cite: Biogenesis of small RNAs in animals
Posttranscriptional crossregulation between Drosha and DGCR8 J. Han ,
J. S. Pedersen ,
S. C. Kwon ,
C. D. Belair ,
Y.-K. Kim ,
K. H. Yeom ,
W. Y. Yang ,
D. Haussler ,
R. Blelloch , and
V. N. Kim ✉︎ (corresponding author) Cell
(2009), 136(1):75-84
Cite: Posttranscriptional crossregulation between Drosha and DGCR8
Lin28 mediates the terminal uridylation of let-7 precursor microRNA I. Heo 1 ,
C. Joo 1 ,
J. Cho ,
M. Ha ,
J. Han , and
V. N. Kim Molecular Cell
(2008), 32(2):276-284
Cite: Lin28 mediates the terminal uridylation of let-7 precursor microRNA
Sorting out small RNAs V. N. Kim ✉︎ (corresponding author) Cell
(2008), 133(1):25-26
Cite: Sorting out small RNAs
Crystal structure of human DGCR8 core S. Y. Sohn 1 ,
W. J. Bae 1 ,
J. J. Kim ,
K. H. Yeom ,
V. N. Kim , and
Y. Cho Nature Structural & Molecular Biology
(2007), 14(9):847-853
Cite: Crystal structure of human DGCR8 core
Processing of intronic microRNAs Y.-K. Kim and
V. N. Kim ✉︎ (corresponding author) EMBO Journal
(2007), 26(3):775-783
Cite: Processing of intronic microRNAs
Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes V. N. Kim ✉︎ (corresponding author) Genes & Development
(2006), 20(15):1993-1997
Cite: Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes
Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing K. H. Yeom ,
Y. Lee ,
J. Han ,
M. R. Suh , and
V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2006), 34(16):4622-4629
Cite: Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex J. Han 1 ,
Y. Lee 1 ,
K. H. Yeom 1 ,
J. W. Nam ,
I. Heo ,
J. K. Rhee ,
S. Y. Sohn ,
Y. Cho ,
B. T. Zhang , and
V. N. Kim Cell
(2006), 125(5):887-901
Cite: Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
The role of PACT in the RNA silencing pathway Y. Lee 1 ,
I. Hur 1 ,
S. Y. Park 1 ,
Y.-K. Kim ,
M. R. Suh , and
V. N. Kim ✉︎ (corresponding author) EMBO Journal
(2006), 25(3):522-532
Cite: The role of PACT in the RNA silencing pathway
Human microRNA prediction through a probabilistic co-learning model of sequence and structure J. W. Nam ,
K. R. Shin ,
J. Han ,
Y. Lee ,
V. N. Kim , and
B. T. Zhang ✉︎ (corresponding author) Nucleic Acids Research
(2005), 33(11):3570-3581
Cite: Human microRNA prediction through a probabilistic co-learning model of sequence and structure
MicroRNA biogenesis: coordinated cropping and dicing V. N. Kim ✉︎ (corresponding author) Nature Reviews Molecular Cell Biology
(2005), 6(5):376-385
Cite: MicroRNA biogenesis: coordinated cropping and dicing
Small RNAs: classification, biogenesis, and function V. N. Kim ✉︎ (corresponding author) Molecules and Cells
(2005), 19(1):1-15
Cite: Small RNAs: classification, biogenesis, and function
The Drosha-DGCR8 complex in primary microRNA processing J. Han 1 ,
Y. Lee 1 ,
K. H. Yeom ,
Y.-K. Kim ,
H. Jin , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2004), 18(24):3016-3027
Cite: The Drosha-DGCR8 complex in primary microRNA processing
MicroRNA genes are transcribed by RNA polymerase II Y. Lee ,
M. Kim ,
J. Han ,
K. H. Yeom ,
S. Lee ,
S. H. Baek , and
V. N. Kim ✉︎ (corresponding author) EMBO Journal
(2004), 23(20):4051-4060
Cite: MicroRNA genes are transcribed by RNA polymerase II
MicroRNA precursors in motion: exportin-5 mediates their nuclear export V. N. Kim ✉︎ (corresponding author) Trends in Cell Biology
(2004), 14(4):156-159
Cite: MicroRNA precursors in motion: exportin-5 mediates their nuclear export
The nuclear RNase III Drosha initiates microRNA processing Y. Lee ,
C. Ahn ,
J. Han ,
H. Choi ,
J. Kim ,
J. Yim ,
J. Lee ,
P. Provost ,
O. Radmark ,
S. Kim , and
V. N. Kim Nature
(2003), 425(6956):415-419
Cite: The nuclear RNase III Drosha initiates microRNA processing
MicroRNA maturation: stepwise processing and subcellular localization Y. Lee ,
K. Jeon ,
J. T. Lee ,
S. Kim , and
V. N. Kim ✉︎ (corresponding author) EMBO Journal
(2002), 21(17):4663-4670
Cite: MicroRNA maturation: stepwise processing and subcellular localization
microRNA Function and Disease
Small and long non-coding RNAs: past, present, and future L.-L. Chen ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Cell
(2024), 187(23):6451-6485
Cite: Small and long non-coding RNAs: past, present, and future
The regulatory impact of RNA-binding proteins on microRNA targeting S. Kim 1 ,
S. Kim 1 ,
H. R. Chang 1 ,
D. Kim 1 ,
J. Park ,
N. Son ,
J. Park ,
M. Yoon ,
G. Chae ,
Y.-K. Kim ,
V. N. Kim ,
Y. K. Kim ,
J.-W. Nam ,
C. Shin ✉︎ (corresponding author) D. Baek ✉︎ (corresponding author) Nature Communications
(2021), 12(1):5057
Cite: The regulatory impact of RNA-binding proteins on microRNA targeting
microRNA-30a arbitrates intestinal-type early gastric carcinogenesis by directly targeting ITGA2 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 ✉︎ (corresponding author) J. R. Goldenring ✉︎ (corresponding author) H. K. Yang ✉︎ (corresponding author) Gastric Cancer
(2020), 23(4):600-613
Cite: microRNA-30a arbitrates intestinal-type early gastric carcinogenesis by directly targeting ITGA2
Quantification of purified endogenous miRNAs with high sensitivity and specificity S. Shin 1 ,
Y. Jung 1 ,
H. Uhm ,
M. Song ,
S. Son ,
J. Goo ,
C. Jeong ,
J.-J. Song ,
V. N. Kim , and
S. Hohng ✉︎ (corresponding author) Nature Communications
(2020), 11(1):6033
Cite: Quantification of purified endogenous miRNAs with high sensitivity and specificity
Stress-activated miR-204 governs senescent phenotypes of chondrocytes to promote osteoarthritis development D. Kang 1 ,
J. Shin 1 ,
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 , and
J. H. Kim ✉︎ (corresponding author) Science Translational Medicine
(2019), 11(486):eaar6659
Cite: Stress-activated miR-204 governs senescent phenotypes of chondrocytes to promote osteoarthritis development
miR-30a-5p as a tumor suppressor gene in gastric cancer J. Min ,
T.-S. Han ,
B. Choi ,
K. Hur ,
K. Yanagihara ,
V. N. Kim ✉︎ (corresponding author) H.-J. Lee ✉︎ (corresponding author) H.-K. Yang ✉︎ (corresponding author) Journal of Clinical Oncology
(2018), 36(4_suppl):84
Cite: miR-30a-5p as a tumor suppressor gene in gastric cancer
MicroRNA-139-5p regulates proliferation of hematopoietic progenitors and is repressed during BCR-ABL-mediated leukemogenesis J. Choi ,
Y.-K. Kim ,
K. Park ,
J. Nah ,
S. S. Yoon ,
D. W. Kim ,
V. N. Kim , and
R. H. Seong Blood
(2016), 128(17):2117-2129
Cite: MicroRNA-139-5p regulates proliferation of hematopoietic progenitors and is repressed during BCR-ABL-mediated leukemogenesis
Gastric carcinogenesis in the miR-222/221 transgenic mouse model B. Choi 1 ,
J. Yu 1 ,
T.-S. Han ,
Y.-K. Kim ,
K. Hur ,
B.-C. Kang ,
W. H. Kim ,
D.-Y. Kim ,
H.-J. Lee ,
V. N. Kim , and
H.-K. Yang ✉︎ (corresponding author) Cancer Research and Treatment
(2016), 49(1):150-160
Cite: Gastric carcinogenesis in the miR-222/221 transgenic mouse model
Temporal landscape of microRNA-mediated host-virus crosstalk during productive human cytomegalovirus infection S. Kim 1 ,
D. Seo 1 ,
D. Kim ,
Y. Hong ,
H. Chang ,
D. Baek ,
V. N. Kim ,
S. Lee , and
K. Ahn ✉︎ (corresponding author) Cell Host & Microbe
(2015), 17(6):838-851
Cite: Temporal landscape of microRNA-mediated host-virus crosstalk during productive human cytomegalovirus infection
MicroRNA-29c mediates initiation of gastric carcinogenesis by directly targeting ITGB1 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 ✉︎ (corresponding author) H.-K. Yang ✉︎ (corresponding author) Gut
(2015), 64(2):203-214
Cite: MicroRNA-29c mediates initiation of gastric carcinogenesis by directly targeting ITGB1
miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data I. Jang 1 ,
H. Chang 1 ,
Y. Jun ,
S. Park ,
J. O. Yang ,
B. Lee ,
W. Kim ,
V. N. Kim , and
S. Lee Bioinformatics
(2015), 31(4):596-598
Cite: miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data
Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP Y. Kim 1 ,
J. Yeo 1 ,
J. H. Lee 1 ,
J. Cho ,
D. Seo ,
J. Kim , and
V. N. Kim ✉︎ (corresponding author) Cell Reports
(2014), 9(3):1061-1074
Cite: Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP
TALEN-based knockout library for human microRNAs Y.-K. Kim 1 ,
G. Wee 1 ,
J. Park ,
J. Kim ,
D. Baek ,
J.-S. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2013), 20(12):1458-1464
Cite: TALEN-based knockout library for human microRNAs
Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO) 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 ACS Nano
(2013), 7(7):5882-5891
Cite: Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO)
miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting 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 ✉︎ (corresponding author) S. Lee ✉︎ (corresponding author) Nucleic Acids Research
(2012), 41(D1):D252-D257
Cite: miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting
Conserved microRNA miR-8 controls body size in response to steroid signaling in Drosophila H. Jin ,
V. N. Kim ✉︎ (corresponding author) S. Hyun ✉︎ (corresponding author) Genes & Development
(2012), 26(13):1427-1432
Cite: Conserved microRNA miR-8 controls body size in response to steroid signaling in Drosophila
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells Y.-K. Kim ,
J. Yeo ,
B. Kim ,
M. Ha , and
V. N. Kim Molecular Cell
(2012), 46(6):893-895
Cite: Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells
Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1 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 ✉︎ (corresponding author) Nature Immunology
(2011), 12(10):984-991
Cite: Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1
Conserved microRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K S. Hyun 1 ,
J. H. Lee 1 ,
H. Jin 1 ,
J. Nam ,
B. Namkoong ,
Gina Lee ,
J. Chung , and
V. N. Kim Cell
(2009), 139(6):1096-1108
Cite: Conserved microRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K
Human UPF1 participates in small RNA-induced mRNA downregulation H. Jin 1 ,
M. R. Suh 1 ,
J. Han ,
K.-H. Yeom ,
Y. Lee ,
I. Heo ,
M. Ha ,
S. Hyun , and
V. N. Kim ✉︎ (corresponding author) Molecular and Cellular Biology
(2009), 29(21):5789-5799
Cite: Human UPF1 participates in small RNA-induced mRNA downregulation
Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer 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 ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2009), 37(5):1672-1681
Cite: Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer
miR-29 miRNAs activate p53 by targeting p85a and CDC42 S. Y. Park 1 ,
J. H. Lee 1 ,
M. Ha ,
J. W. Nam , and
V. N. Kim Nature Structural & Molecular Biology
(2009), 16(1):23-29
Cite: miR-29 miRNAs activate p53 by targeting p85a and CDC42
Cell cycle micromanagement in embryonic stem cells V. N. Kim ✉︎ (corresponding author) Nature Genetics
(2008), 40(12):1391-1392
Cite: Cell cycle micromanagement in embryonic stem cells
Genomics of microRNA V. N. Kim and
J. W. Nam Trends in Genetics
(2006), 22(3):165-173
Cite: Genomics of microRNA
Small RNAs: classification, biogenesis, and function V. N. Kim ✉︎ (corresponding author) Molecules and Cells
(2005), 19(1):1-15
Cite: Small RNAs: classification, biogenesis, and function
Human embryonic stem cells express a unique set of microRNAs 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 ✉︎ (corresponding author) K. S. Kim ✉︎ (corresponding author) Developmental Biology
(2004), 270(2):488-498
Cite: Human embryonic stem cells express a unique set of microRNAs
RNA-Binding Proteins
Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle Y. Choi 1 ,
B. Um 1 ,
Y. Na ,
J. Kim ,
J.-S. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2024), 84(9):1764-1782.e10
Cite: Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle
Photoactivatable ribonucleosides mark base-specific RNA-binding sites J. W. Bae ,
S. Kim ,
V. N. Kim ✉︎ (corresponding author) J.-S. Kim ✉︎ (corresponding author) Nature Communications
(2021), 12(1):6026
Cite: Photoactivatable ribonucleosides mark base-specific RNA-binding sites
The regulatory impact of RNA-binding proteins on microRNA targeting S. Kim 1 ,
S. Kim 1 ,
H. R. Chang 1 ,
D. Kim 1 ,
J. Park ,
N. Son ,
J. Park ,
M. Yoon ,
G. Chae ,
Y.-K. Kim ,
V. N. Kim ,
Y. K. Kim ,
J.-W. Nam ,
C. Shin ✉︎ (corresponding author) D. Baek ✉︎ (corresponding author) Nature Communications
(2021), 12(1):5057
Cite: The regulatory impact of RNA-binding proteins on microRNA targeting
The SARS-CoV-2 RNA interactome S. Lee 1 ,
Y. Lee 1 ,
Y. Choi ,
A. Son ,
Y. Park ,
K.-M. Lee ,
J. Kim ,
J.-S. Kim , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2021), 81(13):2838-2850.e6
Cite: The SARS-CoV-2 RNA interactome
FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo Y. Na ,
H. Kim ,
Y. Choi ,
S. Shin ,
J. H. Jung ,
S. C. Kwon ,
V. N. Kim ✉︎ (corresponding author) J. S. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2021), 49(5):e28
Cite: FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo
Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution J. W. Bae ,
S. C. Kwon ,
Y. Na ,
V. N. Kim ✉︎ (corresponding author) J. S. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2020), 27(7):678-682
Cite: Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution
fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA B. Kim and
V. N. Kim ✉︎ (corresponding author) Methods
(2018), 152:3-11
Cite: fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA
The RNA-binding protein repertoire of embryonic stem cells 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 Nature Structural & Molecular Biology
(2013), 20(9):1122-1130
Cite: The RNA-binding protein repertoire of embryonic stem cells
LIN28A is a suppressor of ER-associated translation in embryonic stem cells J. Cho 1 ,
H. Chang 1 ,
S. C. Kwon ,
B. Kim ,
Y. Kim ,
J. Choe ,
M. Ha ,
Y. K. Kim , and
V. N. Kim ✉︎ (corresponding author) Cell
(2012), 151(4):765-777
Cite: LIN28A is a suppressor of ER-associated translation in embryonic stem cells
Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation S. J. Yim 1 ,
Y. S. Lee 1 ,
J. A. Lee ,
D. J. Chang ,
J. H. Han ,
H. Kim ,
H. Park ,
H. Jun ,
V. N. Kim , and
B. K. Kaang Journal of Neurochemistry
(2006), 98(2):420-429
Cite: Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation
Methods and Resources
Analyzing viral epitranscriptomes using nanopore direct RNA sequencing A. Hong 1 ,
D. Kim 1 ,
V. N. Kim , and
H. Chang ✉︎ (corresponding author) Journal of Microbiology
(2022), 60(9):867-876
Cite: Analyzing viral epitranscriptomes using nanopore direct RNA sequencing
High-throughput in vitro processing of human primary microRNA by the recombinant Microprocessor K. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) STAR Protocols
(2022), 3(1):101042
Cite: High-throughput in vitro processing of human primary microRNA by the recombinant Microprocessor
Photoactivatable ribonucleosides mark base-specific RNA-binding sites J. W. Bae ,
S. Kim ,
V. N. Kim ✉︎ (corresponding author) J.-S. Kim ✉︎ (corresponding author) Nature Communications
(2021), 12(1):6026
Cite: Photoactivatable ribonucleosides mark base-specific RNA-binding sites
FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo Y. Na ,
H. Kim ,
Y. Choi ,
S. Shin ,
J. H. Jung ,
S. C. Kwon ,
V. N. Kim ✉︎ (corresponding author) J. S. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2021), 49(5):e28
Cite: FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo
Development of multiplexed immuno-N-terminomics to reveal the landscape of proteolytic processing in early embryogenesis of Drosophila melanogaster S. Shin ,
J. H. Hong ,
Y. Na ,
M. Lee ,
W.-J. Qian ,
V. N. Kim , and
J.-S. Kim ✉︎ (corresponding author) Analytical Chemistry
(2020), 92(7):4926-4934
Cite: Development of multiplexed immuno-N-terminomics to reveal the landscape of proteolytic processing in early embryogenesis of Drosophila melanogaster
Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution J. W. Bae ,
S. C. Kwon ,
Y. Na ,
V. N. Kim ✉︎ (corresponding author) J. S. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2020), 27(7):678-682
Cite: Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution
Development of a laboratory-safe and low-cost detection protocol for SARS-CoV-2 of the coronavirus disease 2019 (COVID-19) J. Won ,
S. Lee ,
M. Park ,
T. Y. Kim ,
M. G. Park ,
B. Y. Choi ,
D. Kim ,
H. Chang ,
V. N. Kim , and
C. Justin Lee ✉︎ (corresponding author) Experimental Neurobiology
(2020), 29(2):107-119
Cite: Development of a laboratory-safe and low-cost detection protocol for SARS-CoV-2 of the coronavirus disease 2019 (COVID-19)
MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and in vitro chemical labeling Y. Choi 1 ,
K. Jeong 1 ,
S. Shin 1 ,
J. W. Lee 1 ,
Y. Lee ,
S. Kim ,
S. A. Kim ,
J. Jung ,
K. P. Kim ,
V. N. Kim ✉︎ (corresponding author) J. S. Kim ✉︎ (corresponding author) Analytical Chemistry
(2020), 92(7):4980-4989
Cite: MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and in vitro chemical labeling
Quantification of purified endogenous miRNAs with high sensitivity and specificity S. Shin 1 ,
Y. Jung 1 ,
H. Uhm ,
M. Song ,
S. Son ,
J. Goo ,
C. Jeong ,
J.-J. Song ,
V. N. Kim , and
S. Hohng ✉︎ (corresponding author) Nature Communications
(2020), 11(1):6033
Cite: Quantification of purified endogenous miRNAs with high sensitivity and specificity
Deuterium-free, three-plexed peptide diethylation for highly accurate quantitative proteomics J. Jung ,
K. Jeong ,
Y. Choi ,
S. A. Kim ,
H. Kim ,
J. W. Lee ,
V. N. Kim ,
K. P. Kim , and
J. S. Kim Journal of Proteome Research
(2019), 18(3):1078-1087
Cite: Deuterium-free, three-plexed peptide diethylation for highly accurate quantitative proteomics
Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification H. Kim 1 ,
J. Kim 1 ,
K. Kim ,
H. Chang ,
K. You , and
V. N. Kim ✉︎ (corresponding author) Nucleic Acids Research
(2019), 47(5):2630-2640
Cite: Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification
fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA B. Kim and
V. N. Kim ✉︎ (corresponding author) Methods
(2018), 152:3-11
Cite: fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: lessons from DROSHA
RNA-targeting CRISPR comes of age V. N. Kim ✉︎ (corresponding author) Nature Biotechnology
(2018), 36(1):44-45
Cite: RNA-targeting CRISPR comes of age
mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development J. Lim 1 ,
M. Lee 1 ,
A. Son ,
H. Chang , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2016), 30(14):1671-1682
Cite: mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development
Next-generation libraries for robust RNA interference-based genome-wide screens M. Kampmann ✉︎ (corresponding author) M. A. Horlbeck ,
Y. Chen ,
J. C. Tsai ,
M. C. Bassik ,
L. A. Gilbert ,
J. E. Villalta ,
S. C. Kwon ,
H. Chang ,
V. N. Kim , and
J. S. Weissman ✉︎ (corresponding author) Proceedings of the National Academy of Sciences of the U.S.A.
(2015), 112(26):E3384-E3391
Cite: Next-generation libraries for robust RNA interference-based genome-wide screens
miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data I. Jang 1 ,
H. Chang 1 ,
Y. Jun ,
S. Park ,
J. O. Yang ,
B. Lee ,
W. Kim ,
V. N. Kim , and
S. Lee Bioinformatics
(2015), 31(4):596-598
Cite: miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data
TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications H. Chang 1 ,
J. Lim 1 ,
M. Ha , and
V. N. Kim ✉︎ (corresponding author) Molecular Cell
(2014), 53(6):1044-1052
Cite: TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications
TALEN-based knockout library for human microRNAs Y.-K. Kim 1 ,
G. Wee 1 ,
J. Park ,
J. Kim ,
D. Baek ,
J.-S. Kim ✉︎ (corresponding author) V. N. Kim ✉︎ (corresponding author) Nature Structural & Molecular Biology
(2013), 20(12):1458-1464
Cite: TALEN-based knockout library for human microRNAs
Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO) 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 ACS Nano
(2013), 7(7):5882-5891
Cite: Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO)
Bringing single-molecule spectroscopy to macromolecular protein complexes C. Joo ✉︎ (corresponding author) M. Fareh , and
V. N. Kim Trends in Biochemical Sciences
(2013), 38(1):30-37
Cite: Bringing single-molecule spectroscopy to macromolecular protein complexes
miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting 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 ✉︎ (corresponding author) S. Lee ✉︎ (corresponding author) Nucleic Acids Research
(2012), 41(D1):D252-D257
Cite: miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells Y.-K. Kim ,
J. Yeo ,
B. Kim ,
M. Ha , and
V. N. Kim Molecular Cell
(2012), 46(6):893-895
Cite: Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells
Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation K.-H. Yeom ,
I. Heo ,
J. Lee ,
S. Hohng ,
V. N. Kim ✉︎ (corresponding author) C. Joo ✉︎ (corresponding author) EMBO Reports
(2011), 12(7):690-696
Cite: Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation
Human microRNA prediction through a probabilistic co-learning model of sequence and structure J. W. Nam ,
K. R. Shin ,
J. Han ,
Y. Lee ,
V. N. Kim , and
B. T. Zhang ✉︎ (corresponding author) Nucleic Acids Research
(2005), 33(11):3570-3581
Cite: Human microRNA prediction through a probabilistic co-learning model of sequence and structure
Other Topics
STING facilitates nuclear import of herpesvirus genome during infection Y. Hong ,
H. Jeong ,
K. Park ,
S. Lee ,
J. Y. Shim ,
H. Kim ,
Y. Song ,
S. Park ,
H. Y. Park ,
V. N. Kim , and
K. Ahn ✉︎ (corresponding author) Proceedings of the National Academy of Sciences of the U.S.A.
(2021), 118(33):e2108631118
Cite: STING facilitates nuclear import of herpesvirus genome during infection
Coordinate regulation of the senescent state by selective autophagy Y. Lee 1 ,
J. Kim 1 ,
M. Kim 1 ,
Y. Kwon ,
S. Shin ,
H. Yi ,
H. Kim ,
M. Chang ,
C. Chang ,
S. Kang ,
V. N. Kim ,
J. Kim ,
J. Kim ,
S. J. Elledge , and
C. Kang ✉︎ (corresponding author) Developmental Cell
(2021), 56(10):1512-1525.e7
Cite: Coordinate regulation of the senescent state by selective autophagy
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells C. Kim 1 ,
S. Sung 1 ,
J.-S. Kim 1 ,
H. Lee ,
Y. Jung ,
S. Shin ,
E. Kim ,
J. J. Seo ,
J. Kim ,
D. Kim ,
H. Niida ,
V. N. Kim ,
D. Park ✉︎ (corresponding author) J. Lee ✉︎ (corresponding author) Nature Communications
(2021), 12(1):1097
Cite: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells
Brain somatic mutations in MTOR reveal translational dysregulations underlying intractable focal epilepsy J. K. Kim ,
J. Cho ,
S. H. Kim ,
H. C. Kang ,
D. S. Kim ,
V. N. Kim , and
J. H. Lee ✉︎ (corresponding author) Journal of Clinical Investigation
(2019), 129(10):4207-4223
Cite: Brain somatic mutations in MTOR reveal translational dysregulations underlying intractable focal epilepsy
Response to comment on “Multiple repressive mechanisms in the hippocampus during memory formation” J. Cho ,
N.-K. Yu ,
V. N. Kim ✉︎ (corresponding author) B.-K. Kaang ✉︎ (corresponding author) Science
(2016), 353(6298):453
Cite: Response to comment on “Multiple repressive mechanisms in the hippocampus during memory formation”
Role of the small subunit processome in the maintenance of pluripotent stem cells K. T. You ,
J. Park , and
V. N. Kim ✉︎ (corresponding author) Genes & Development
(2015), 29(19):2004-2009
Cite: Role of the small subunit processome in the maintenance of pluripotent stem cells
Multiple repressive mechanisms in the hippocampus during memory formation J. Cho 1 ,
N.-K. Yu 1 ,
J.-H. Choi ,
S.-E. Sim ,
S. J. Kang ,
C. Kwak ,
S.-W. Lee ,
J. Kim ,
D. I. Choi ,
V. N. Kim ✉︎ (corresponding author) B.-K. Kaang ✉︎ (corresponding author) Science
(2015), 350(6256):82-87
Cite: Multiple repressive mechanisms in the hippocampus during memory formation
Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells K. Boo 1 ,
J. Bhin 1 ,
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 ✉︎ (corresponding author) H. Lee ✉︎ (corresponding author) S. H. Baek ✉︎ (corresponding author) Nature Communications
(2015), 6(1):6810
Cite: Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells
The co-regulation mechanism of transcription factors in the human gene regulatory network J. Kim ,
M. Choi ,
J. R. Kim ,
H. Jin ,
V. N. Kim , and
K. H. Cho ✉︎ (corresponding author) Nucleic Acids Research
(2012), 40(18):8849-8861
Cite: The co-regulation mechanism of transcription factors in the human gene regulatory network
Control of splicing efficiency by the mouse histone H2a element in a murine leukemia virus-based retroviral vector J. T. Lee ,
S. S. Yu ,
V. N. Kim , and
S. Kim Molecular Therapy
(2007), 15(1):167-172
Cite: Control of splicing efficiency by the mouse histone H2a element in a murine leukemia virus-based retroviral vector
Downregulation of GFAP, TSP-1, and p53 in human glioblastoma cell line, U373MG, by IE1 protein from human cytomegalovirus K. Lee ,
K. Jeon ,
J. M. Kim ,
V. N. Kim ,
D. H. Choi ,
S. U. Kim , and
S. Kim Glia
(2005), 51(1):1-12
Cite: Downregulation of GFAP, TSP-1, and p53 in human glioblastoma cell line, U373MG, by IE1 protein from human cytomegalovirus
Book chapters