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  1. 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: 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 ... ...

    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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  2. Article ; Online: Photoactivatable ribonucleosides mark base-specific RNA-binding sites

    Jong Woo Bae / Sangtae Kim / V. Narry Kim / Jong-Seo Kim

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: RNA-protein interactions play critical roles in post-transcriptional gene regulation. Here the authors demonstrate pRBS-ID, an updated MS/MS-based method that combines the benefits of photoactivatable ribonucleosides and the chemical cleavage of RNA. ...

    Abstract RNA-protein interactions play critical roles in post-transcriptional gene regulation. Here the authors demonstrate pRBS-ID, an updated MS/MS-based method that combines the benefits of photoactivatable ribonucleosides and the chemical cleavage of RNA.
    Keywords Science ; Q
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: PARN and TOE1 Constitute a 3′ End Maturation Module for Nuclear Non-coding RNAs

    Ahyeon Son / Jong-Eun Park / V. Narry Kim

    Cell Reports, Vol 23, Iss 3, Pp 888-

    2018  Volume 898

    Abstract: Summary: Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to ... ...

    Abstract Summary: Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable. : By analyzing the 3′ termini of transcriptome, Son et al. reveal the targets of PARN and TOE1, two nuclear deadenylases with disease associations. Both deadenylases are involved in nuclear small non-coding RNA maturation, but not in mRNA deadenylation. Their combined activity is particularly important for biogenesis of scaRNAs and TERC. Keywords: PARN, TOE1, CAF1Z, deadenylase, 3′ end maturation, adenylation, deadenylation, scaRNA, TERC
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates

    Kim, Baekgyu / Kyowon Jeong / V. Narry Kim

    Molecular cell. 2017 Apr. 20, v. 66, no. 2

    2017  

    Abstract: MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective ... ...

    Abstract MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed “formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq),” which allows identification of DROSHA cleavage sites at single-nucleotide resolution. fCLIP identifies numerous processing sites, suggesting widespread end modifications during miRNA maturation. fCLIP also finds many pri-miRNAs that undergo alternative processing, yielding multiple miRNA isoforms. Moreover, we discovered dozens of DROSHA substrates on non-miRNA loci, which may serve as cis-elements for DROSHA-mediated gene regulation. We anticipate that fCLIP-seq could be a general tool for investigating interactions between dsRNA-binding proteins and structured RNAs.
    Keywords crosslinking ; double-stranded RNA ; formaldehyde ; genes ; loci ; microRNA ; precipitin tests ; proteins ; ribonucleases
    Language English
    Dates of publication 2017-0420
    Size p. 258-269.e5.
    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.2017.03.013
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Functional and molecular dissection of HCMV long non-coding RNAs

    Sungwon Lee / Hyewon Kim / Ari Hong / Jaewon Song / Sungyul Lee / Myeonghwan Kim / Sung-yeon Hwang / Dongjoon Jeong / Jeesoo Kim / Ahyeon Son / Young-suk Lee / V. Narry Kim / Jong-seo Kim / Hyeshik Chang / Kwangseog Ahn

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 20

    Abstract: Abstract Small, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus ... ...

    Abstract Abstract Small, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus life cycle. Here, we dissected the functional and molecular landscape of HCMV lncRNAs. We found that HCMV lncRNAs occupy ~ 30% and 50–60% of total and poly(A)+viral transcriptome, respectively, throughout virus life cycle. RNA1.2, RNA2.7, and RNA4.9, the three abundantly expressed lncRNAs, appear to be essential in all infection states. Among these three lncRNAs, depletion of RNA2.7 and RNA4.9 results in the greatest defect in maintaining latent reservoir and promoting lytic replication, respectively. Moreover, we delineated the global post-transcriptional nature of HCMV lncRNAs by nanopore direct RNA sequencing and interactome analysis. We revealed that the lncRNAs are modified with N6-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth analysis demonstrated that m6A machineries stabilize HCMV lncRNAs, which could account for the overwhelming abundance of viral lncRNAs. Our study lays the groundwork for understanding the viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells

    Chuna Kim / Sanghyun Sung / Jong-Seo Kim / Hyunji Lee / Yoonseok Jung / Sanghee Shin / Eunkyeong Kim / Jenny J. Seo / Jun Kim / Daeun Kim / Hiroyuki Niida / V. Narry Kim / Daechan Park / Junho Lee

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: Telomeres can be maintained by a telomerase-independent mechanism called an alternative lengthening of telomeres (ALT). Here the authors use mouse Terc (telomerase RNA) knockout embryonic cells and provide longitudinal analysis of ALT telomeres ... ...

    Abstract Telomeres can be maintained by a telomerase-independent mechanism called an alternative lengthening of telomeres (ALT). Here the authors use mouse Terc (telomerase RNA) knockout embryonic cells and provide longitudinal analysis of ALT telomeres maintained with non-telomeric sequences.
    Keywords Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Quantification of purified endogenous miRNAs with high sensitivity and specificity

    Soochul Shin / Yoonseok Jung / Heesoo Uhm / Minseok Song / Soomin Son / Jiyoung Goo / Cherlhyun Jeong / Ji-Joon Song / V. Narry Kim / Sungchul Hohng

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 8

    Abstract: MicroRNAs are potentially powerful biomarkers, though clinical use requires rapid and reliable profiling. Here the authors report amplification-free multicolour single-molecule imaging with single base mismatch sensitivity. ...

    Abstract MicroRNAs are potentially powerful biomarkers, though clinical use requires rapid and reliable profiling. Here the authors report amplification-free multicolour single-molecule imaging with single base mismatch sensitivity.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: The regulatory impact of RNA-binding proteins on microRNA targeting

    Sukjun Kim / Soyoung Kim / Hee Ryung Chang / Doyeon Kim / Junehee Park / Narae Son / Joori Park / Minhyuk Yoon / Gwangung Chae / Young-Kook Kim / V. Narry Kim / Yoon Ki Kim / Jin-Wu Nam / Chanseok Shin / Daehyun Baek

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: miRNAs are loaded into Argonaute protein and repress complementary mRNA targets. Here the authors show the unappreciated role of RNA binding proteins for efficient miRNA targeting and expand the current understanding of miRNA targeting. ...

    Abstract miRNAs are loaded into Argonaute protein and repress complementary mRNA targets. Here the authors show the unappreciated role of RNA binding proteins for efficient miRNA targeting and expand the current understanding of miRNA targeting.
    Keywords Science ; Q
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

    Park, Jong-Eun / Hyerim Yi / Hyeshik Chang / V. Narry Kim / Yoosik Kim

    Molecular cell. 2016 May 05, v. 62, no. 3

    2016  

    Abstract: Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we ... ...

    Abstract Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell-cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. We also find that poly(A) tail length is coupled to translation when the poly(A) tail is <20 nucleotides. However, as most genes have >20 nucleotide poly(A) tails, their translation is regulated mainly via poly(A) tail length-independent mechanisms during the cell cycle. Specifically, we find that terminal oligopyrimidine (TOP) tract-containing transcripts escape global translational suppression in M phase and are actively translated. Our quantitative and comprehensive data provide a revised view of translational control in the somatic cell cycle.
    Keywords messenger RNA ; mitosis ; nucleotides ; regulator genes ; ribosomes ; somatic cells ; translation (genetics)
    Language English
    Dates of publication 2016-0505
    Size p. 462-471.
    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.2016.04.007
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  10. Article ; Online: L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

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

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: L1 is a group of active retrotransposons in humans. Here the authors show that m6A modifications on L1 RNA increase translation efficiency and retrotransposition in human cells. M6A motifs are more enriched in evolutionary young L1s. ...

    Abstract L1 is a group of active retrotransposons in humans. Here the authors show that m6A modifications on L1 RNA increase translation efficiency and retrotransposition in human cells. M6A motifs are more enriched in evolutionary young L1s.
    Keywords Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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