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  1. Article ; Online: High-throughput

    Kim, Kijun / Kim, V Narry

    STAR protocols

    2022  Volume 3, Issue 1, Page(s) 101042

    Abstract: We describe a protocol to conduct a high- ... ...

    Abstract We describe a protocol to conduct a high-throughput
    MeSH term(s) Humans ; MicroRNAs/genetics ; Microcomputers ; Ribonuclease III/genetics
    Chemical Substances MicroRNAs ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2022-01-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2021.101042
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  2. Article ; Online: High-throughput in vitro processing of human primary microRNA by the recombinant microprocessor

    Kijun Kim / V. Narry Kim

    STAR Protocols, Vol 3, Iss 1, Pp 101042- (2022)

    2022  

    Abstract: ... of this profile, please refer to Kim et al. (2021). ...

    Abstract Summary: We describe a protocol to conduct a high-throughput in vitro processing assay, using 1,881 human primary microRNAs (pri-miRNAs) and recombinant Microprocessor complex, followed by deep sequencing library generation. This comprehensive approach allows the mapping of cleavage sites and the measurement of processing efficiency of a large number of substrates simultaneously. Our protocol is readily modifiable to investigate the effects of chemicals and regulatory proteins. Moreover, cis-acting elements can be examined by replacing the wild-type pri-miRNAs with mutant variants.For complete details on the use and execution of this profile, please refer to Kim et al. (2021).
    Keywords Bioinformatics ; Sequencing ; Molecular Biology ; Protein Biochemistry ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Sequence determinant of small RNA production by DICER.

    Lee, Young-Yoon / Kim, Haedong / Kim, V Narry

    Nature

    2023  Volume 615, Issue 7951, Page(s) 323–330

    Abstract: RNA silencing relies on specific and efficient processing of double-stranded RNA by Dicer, which yields microRNAs (miRNAs) and small interfering RNAs (siRNAs) ...

    Abstract RNA silencing relies on specific and efficient processing of double-stranded RNA by Dicer, which yields microRNAs (miRNAs) and small interfering RNAs (siRNAs)
    MeSH term(s) Humans ; Base Pairing ; DEAD-box RNA Helicases/metabolism ; MicroRNAs/biosynthesis ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Ribonuclease III/metabolism ; RNA Interference ; RNA, Double-Stranded/chemistry ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; RNA, Small Interfering/biosynthesis ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA Precursors/biosynthesis ; RNA Precursors/chemistry ; RNA Precursors/genetics ; RNA Precursors/metabolism ; Base Sequence ; Nucleic Acid Conformation
    Chemical Substances DEAD-box RNA Helicases (EC 3.6.4.13) ; DICER1 protein, human (EC 3.1.26.3) ; MicroRNAs ; Ribonuclease III (EC 3.1.26.3) ; RNA, Double-Stranded ; RNA, Small Interfering ; RNA Precursors
    Language English
    Publishing date 2023-02-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-05722-4
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  4. Article ; Online: RNA-targeting CRISPR comes of age.

    Kim, V Narry

    Nature biotechnology

    2018  Volume 36, Issue 1, Page(s) 44–45

    MeSH term(s) Clustered Regularly Interspaced Short Palindromic Repeats ; RNA ; RNA Editing
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2018-03-09
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/nbt.4054
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  5. Article ; Online: Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle.

    Choi, Yeon / Um, Buyeon / Na, Yongwoo / Kim, Jeesoo / Kim, Jong-Seo / Kim, V Narry

    Molecular cell

    2024  

    Abstract: mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse ... ...

    Abstract mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.
    Language English
    Publishing date 2024-04-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.03.012
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  6. Article ; Online: Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution.

    Lee, Young-Suk / Levdansky, Yevgen / Jung, Yoonseok / Kim, V Narry / Valkov, Eugene

    Nature structural & molecular biology

    2024  

    Abstract: Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression. The incorporation of non-adenosines in poly(A) tails, or 'mixed tailing', has been observed in vertebrates ... ...

    Abstract Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression. The incorporation of non-adenosines in poly(A) tails, or 'mixed tailing', has been observed in vertebrates and viruses. Here, to quantitate the effect of mixed tails, we mathematically modeled deadenylation reactions at single-nucleotide resolution using an in vitro deadenylation system reconstituted with the complete human CCR4-NOT complex. Applying this model, we assessed the disrupting impact of single guanosine, uridine or cytosine to be equivalent to approximately 6, 8 or 11 adenosines, respectively. CCR4-NOT stalls at the 0, -1 and -2 positions relative to the non-adenosine residue. CAF1 and CCR4 enzyme subunits commonly prefer adenosine but exhibit distinct sequence selectivities and stalling positions. Our study provides an analytical framework to monitor deadenylation and reveals the molecular basis of tail sequence-dependent regulation of mRNA stability.
    Language English
    Publishing date 2024-02-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-023-01187-1
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  7. Article ; Online: Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing.

    Son, Soomin / Kim, Baekgyu / Yang, Jihye / Kim, V Narry

    Genes & development

    2023  Volume 37, Issue 9-10, Page(s) 383–397

    Abstract: DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well documented, the contribution of N-terminal proline-rich disordered domain ( ... ...

    Abstract DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well documented, the contribution of N-terminal proline-rich disordered domain (PRD) remains elusive. Here we show that the PRD promotes the processing of miRNA hairpins located within introns. We identified a DROSHA isoform (p140) lacking the PRD, which is produced by proteolytic cleavage. Small RNA sequencing revealed that p140 is significantly impaired in the maturation of intronic miRNAs. Consistently, our minigene constructs demonstrated that PRD enhances the processing of intronic hairpins, but not those in exons. Splice site mutations did not affect the PRD's enhancing effect on intronic constructs, suggesting that the PRD acts independently of splicing reaction by interacting with sequences residing within introns. The N-terminal regions from zebrafish and
    MeSH term(s) Animals ; Humans ; Introns/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Proline/genetics ; Proline/metabolism ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; RNA Processing, Post-Transcriptional ; Zebrafish
    Chemical Substances DROSHA protein, human (EC 3.1.26.3) ; MicroRNAs ; Proline (9DLQ4CIU6V) ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2023-05-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.350275.122
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  8. Article ; Online: Analyzing viral epitranscriptomes using nanopore direct RNA sequencing.

    Hong, Ari / Kim, Dongwan / Kim, V Narry / Chang, Hyeshik

    Journal of microbiology (Seoul, Korea)

    2022  Volume 60, Issue 9, Page(s) 867–876

    Abstract: RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including ... ...

    Abstract RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N
    MeSH term(s) High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing ; Nanopores ; RNA, Viral/genetics ; Sequence Analysis, RNA/methods ; Transcriptome
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2022-08-24
    Publishing country Korea (South)
    Document type Journal Article
    ZDB-ID 2012399-1
    ISSN 1976-3794 ; 1225-8873
    ISSN (online) 1976-3794
    ISSN 1225-8873
    DOI 10.1007/s12275-022-2324-4
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  9. Article ; Online: Correction to 'Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification'.

    Kim, Haedong / Kim, Jimi / Kim, Kijun / Chang, Hyeshik / You, Kwontae / Kim, V Narry

    Nucleic acids research

    2022  Volume 50, Issue 3, Page(s) 1799–1800

    Language English
    Publishing date 2022-01-25
    Publishing country England
    Document type Published Erratum
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac078
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  10. Article ; Online: Structural atlas of human primary microRNAs generated by SHAPE-MaP.

    Baek, S Chan / Kim, Boseon / Jang, Harim / Kim, Kijun / Park, Il-Soo / Min, Dal-Hee / Kim, V Narry

    Molecular cell

    2024  Volume 84, Issue 6, Page(s) 1158–1172.e6

    Abstract: MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'- ... ...

    Abstract MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3' bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.
    MeSH term(s) Humans ; RNA Processing, Post-Transcriptional ; MicroRNAs/metabolism ; RNA, Small Interfering ; Ribonuclease III/genetics
    Chemical Substances MicroRNAs ; RNA, Small Interfering ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2024-03-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.02.005
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