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  1. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A quantitative map of human primary microRNA processing sites

    Kim, Kijun / Baek, S. Chan / Lee, Young-Yoon / Bastiaanssen, Carolien / Kim, Jeesoo / Kim, Haedong / Kim, V. Narry

    Molecular cell. 2021 Aug. 19, v. 81, no. 16

    2021  

    Abstract: Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by ... ...

    Abstract Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.
    Keywords cells ; exhibitions ; humans ; loci ; microRNA ; wills
    Language English
    Dates of publication 2021-0819
    Size p. 3422-3439.e11.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.07.002
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Genomic Clustering Facilitates Nuclear Processing of Suboptimal Pri-miRNA Loci.

    Shang, Renfu / Baek, S Chan / Kim, Kijun / Kim, Boseon / Kim, V Narry / Lai, Eric C

    Molecular cell

    2020  Volume 78, Issue 2, Page(s) 303–316.e4

    Abstract: Nuclear processing of most miRNAs is mediated by Microprocessor, comprised of RNase III enzyme Drosha and its cofactor DGCR8. Here, we uncover a hidden layer of Microprocessor regulation via studies of Dicer-independent mir-451, which is clustered with ... ...

    Abstract Nuclear processing of most miRNAs is mediated by Microprocessor, comprised of RNase III enzyme Drosha and its cofactor DGCR8. Here, we uncover a hidden layer of Microprocessor regulation via studies of Dicer-independent mir-451, which is clustered with canonical mir-144. Although mir-451 is fully dependent on Drosha/DGCR8, its short stem and small terminal loop render it an intrinsically weak Microprocessor substrate. Thus, it must reside within a cluster for normal biogenesis, although the identity and orientation of its neighbor are flexible. We use DGCR8 tethering assays and operon structure-function assays to demonstrate that local recruitment and transfer of Microprocessor enhances suboptimal substrate processing. This principle applies more broadly since genomic analysis indicates suboptimal canonical miRNAs are enriched in operons, and we validate several of these experimentally. Proximity-based enhancement of suboptimal hairpin processing provides a rationale for genomic retention of certain miRNA operons and may explain preferential evolutionary emergence of miRNA operons.
    MeSH term(s) Cell Nucleus/genetics ; Genomics ; Humans ; MicroRNAs/genetics ; RNA Processing, Post-Transcriptional/genetics ; RNA-Binding Proteins/genetics ; Ribonuclease III/genetics
    Chemical Substances DGCR8 protein, human ; MicroRNAs ; RNA-Binding Proteins ; DROSHA protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2020-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2020.02.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: A quantitative map of human primary microRNA processing sites.

    Kim, Kijun / Baek, S Chan / Lee, Young-Yoon / Bastiaanssen, Carolien / Kim, Jeesoo / Kim, Haedong / Kim, V Narry

    Molecular cell

    2021  Volume 81, Issue 16, Page(s) 3422–3439.e11

    Abstract: Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by ... ...

    Abstract Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as "nick" or "inverse" processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.
    MeSH term(s) Binding Sites/genetics ; Genome, Human/genetics ; HEK293 Cells ; Humans ; MicroRNAs/genetics ; RNA Interference ; RNA Processing, Post-Transcriptional/genetics ; Ribonuclease III/genetics ; Serine-Arginine Splicing Factors/genetics
    Chemical Substances MicroRNAs ; SRSF3 protein, human ; Serine-Arginine Splicing Factors (170974-22-8) ; DROSHA protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2021-07-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.07.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Molecular Basis for the Single-Nucleotide Precision of Primary microRNA Processing.

    Kwon, S Chul / Baek, S Chan / Choi, Yeon-Gil / Yang, Jihye / Lee, Young-Suk / Woo, Jae-Sung / Kim, V Narry

    Molecular cell

    2018  Volume 73, Issue 3, Page(s) 505–518.e5

    Abstract: Microprocessor, composed of DROSHA and its cofactor DGCR8, initiates microRNA (miRNA) biogenesis by processing the primary transcripts of miRNA (pri-miRNAs). Here we investigate the mechanism by which Microprocessor selects the cleavage site with single- ... ...

    Abstract Microprocessor, composed of DROSHA and its cofactor DGCR8, initiates microRNA (miRNA) biogenesis by processing the primary transcripts of miRNA (pri-miRNAs). Here we investigate the mechanism by which Microprocessor selects the cleavage site with single-nucleotide precision, which is crucial for the specificity and functionality of miRNAs. By testing ∼40,000 pri-miRNA variants, we find that for some pri-miRNAs the cleavage site is dictated mainly by the mGHG motif embedded in the lower stem region of pri-miRNA. Structural modeling and deep-sequencing-based complementation experiments show that the double-stranded RNA-binding domain (dsRBD) of DROSHA recognizes mGHG to place the catalytic center in the appropriate position. The mGHG motif as well as the mGHG-recognizing residues in DROSHA dsRBD are conserved across eumetazoans, suggesting that this mechanism emerged in an early ancestor of the animal lineage. Our findings provide a basis for the understanding of miRNA biogenesis and rational design of accurate small-RNA-based gene silencing.
    MeSH term(s) HCT116 Cells ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleotide Motifs ; Protein Interaction Domains and Motifs ; RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; Structure-Activity Relationship ; Substrate Specificity
    Chemical Substances DGCR8 protein, human ; MicroRNAs ; RNA-Binding Proteins ; DROSHA protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3)
    Language English
    Publishing date 2018-12-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2018.11.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8.

    Kwon, S Chul / Jang, Harim / Shen, Siyuan / Baek, S Chan / Kim, Kijun / Yang, Jihye / Kim, Jeesoo / Kim, Jong-Seo / Wang, Suman / Shi, Yunyu / Li, Fudong / Kim, V Narry

    Nucleic acids research

    2020  Volume 48, Issue 19, Page(s) 11097–11112

    Abstract: The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a ... ...

    Abstract The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a new component of Microprocessor. Through a crystal structure and biochemical experiments, we reveal that ERH uses its hydrophobic groove to bind to a conserved region in the N-terminus of DGCR8, in a 2:2 stoichiometry. Knock-down of ERH or deletion of the DGCR8 N-terminus results in a reduced processing of suboptimal pri-miRNAs in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate 'cluster assistance' in which Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA biogenesis pathway.
    MeSH term(s) Cell Cycle Proteins/metabolism ; HCT116 Cells ; HEK293 Cells ; Humans ; K562 Cells ; MicroRNAs/metabolism ; Protein Binding ; Protein Conformation ; RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/metabolism ; Transcription Factors/metabolism
    Chemical Substances Cell Cycle Proteins ; DGCR8 protein, human ; ERH protein, human ; MIRN144 microRNA, human ; MIRN451 microRNA, human ; MicroRNAs ; RNA-Binding Proteins ; Transcription Factors
    Language English
    Publishing date 2020-11-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    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/gkaa827
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Show issues Location:
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  7. Article ; Online: L1 retrotransposons exploit RNA m

    Hwang, Sung-Yeon / Jung, Hyunchul / Mun, Seyoung / Lee, Sungwon / Park, Kiwon / Baek, S Chan / Moon, Hyungseok C / Kim, Hyewon / Kim, Baekgyu / Choi, Yongkuk / Go, Young-Hyun / Tang, Wanxiangfu / Choi, Jongsu / Choi, Jung Kyoon / Cha, Hyuk-Jin / Park, Hye Yoon / Liang, Ping / Kim, V Narry / Han, Kyudong /
    Ahn, Kwangseog

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 880

    Abstract: L1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of ... ...

    Abstract L1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of L1, which exploits RNA m
    MeSH term(s) 5' Untranslated Regions ; Adenosine/analogs & derivatives ; Adenosine/genetics ; Adenosine/metabolism ; AlkB Homolog 5, RNA Demethylase/metabolism ; Animals ; Evolution, Molecular ; HeLa Cells ; Humans ; Long Interspersed Nucleotide Elements/genetics ; Methylation ; Methyltransferases/metabolism ; Primates/classification ; Primates/genetics ; Protein Biosynthesis ; RNA/chemistry ; RNA/metabolism ; Ribonucleoproteins/metabolism
    Chemical Substances 5' Untranslated Regions ; Ribonucleoproteins ; RNA (63231-63-0) ; N-methyladenosine (CLE6G00625) ; ALKBH5 protein, human (EC 1.14.11.-) ; AlkB Homolog 5, RNA Demethylase (EC 1.14.11.-) ; Methyltransferases (EC 2.1.1.-) ; METTL3 protein, human (EC 2.1.1.62) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2021-02-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-21197-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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