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  1. Article ; Online: RNA modifications and the link to human disease.

    Yanas, Amber / Liu, Kathy Fange

    Methods in enzymology

    2019  Volume 626, Page(s) 133–146

    Abstract: Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). ...

    Abstract Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.
    MeSH term(s) 5-Methylcytosine/analysis ; 5-Methylcytosine/metabolism ; Adenosine/analogs & derivatives ; Adenosine/analysis ; Adenosine/metabolism ; Animals ; Guanosine/analogs & derivatives ; Guanosine/analysis ; Guanosine/metabolism ; Humans ; Methylation ; Nucleic Acid Conformation ; Pseudouridine/analysis ; Pseudouridine/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; Uridine/analogs & derivatives ; Uridine/analysis ; Uridine/metabolism
    Chemical Substances 8-methylguanosine ; RNA, Messenger ; RNA, Ribosomal ; Guanosine (12133JR80S) ; Pseudouridine (1445-07-4) ; 1-methyladenosine (15763-06-1) ; 5,6-dihydrouridine (5627-05-4) ; 5-Methylcytosine (6R795CQT4H) ; RNA, Transfer (9014-25-9) ; Adenosine (K72T3FS567) ; Uridine (WHI7HQ7H85)
    Language English
    Publishing date 2019-09-03
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2019.08.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity.

    Yanas, Amber / Shweta, Him / Owens, Michael C / Liu, Kathy Fange / Goldman, Yale E

    bioRxiv : the preprint server for biology

    2023  

    Abstract: DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous ... ...

    Abstract DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nano-sized RNA-protein clusters (RPCs) that foster their catalytic activities
    Language English
    Publishing date 2023-11-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.29.569239
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation

    Shen, Hui / Yanas, Amber / Owens, Michael C. / Zhang, Celia / Fritsch, Clark / Fare, Charlotte M. / Copley, Katie E. / Shorter, James / Goldman, Yale E. / Liu, Kathy Fange

    Molecular cell. 2022 July 21, v. 82, no. 14

    2022  

    Abstract: Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs ... ...

    Abstract Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
    Keywords RNA helicases ; Y chromosome ; adenosinetriphosphatase ; human diseases ; human health ; metabolism ; separation ; sexual dimorphism
    Language English
    Dates of publication 2022-0721
    Size p. 2588-2603.e9.
    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.2022.04.022
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2005/501: Show issues

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  4. Article: Mutant forms of DDX3X with diminished catalysis form hollow condensates that exhibit sex-specific regulation.

    Owens, Michael C / Shen, Hui / Yanas, Amber / Mendoza-Figueroa, Maria Saraí / Lavorando, Ellen / Wei, Xiaoyu / Shweta, Him / Tang, Hsin-Yao / Goldman, Yale E / Liu, Kathy Fange

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mutations in the RNA helicase DDX3X, implicated in various cancers and neurodevelopmental disorders, often impair RNA unwinding and translation. However, the mechanisms underlying this impairment and the differential interactions of DDX3X mutants with ... ...

    Abstract Mutations in the RNA helicase DDX3X, implicated in various cancers and neurodevelopmental disorders, often impair RNA unwinding and translation. However, the mechanisms underlying this impairment and the differential interactions of DDX3X mutants with wild-type (WT) X-linked DDX3X and Y-linked homolog DDX3Y remain elusive. This study reveals that specific DDX3X mutants more frequently found in disease form distinct hollow condensates in cells. Using a combined structural, biochemical, and single-molecule microscopy study, we show that reduced ATPase and RNA release activities contribute to condensate formation and the catalytic deficits result from inhibiting the catalytic cycle at multiple steps. Proteomic investigations further demonstrate that these hollow condensates sequester WT DDX3X/DDX3Y and other proteins crucial for diverse signaling pathways. WT DDX3X enhances the dynamics of heterogeneous mutant/WT hollow condensates more effectively than DDX3Y. These findings offer valuable insights into the catalytic defects of specific DDX3X mutants and their differential interactions with wild-type DDX3X and DDX3Y, potentially explaining sex biases in disease.
    Language English
    Publishing date 2023-11-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.19.533240
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation.

    Shen, Hui / Yanas, Amber / Owens, Michael C / Zhang, Celia / Fritsch, Clark / Fare, Charlotte M / Copley, Katie E / Shorter, James / Goldman, Yale E / Liu, Kathy Fange

    Molecular cell

    2022  Volume 82, Issue 14, Page(s) 2588–2603.e9

    Abstract: Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs ... ...

    Abstract Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
    MeSH term(s) DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Female ; Humans ; Male ; Minor Histocompatibility Antigens/metabolism ; Protein Biosynthesis ; Proteins/metabolism ; RNA/metabolism ; RNA Helicases/genetics ; RNA Helicases/metabolism
    Chemical Substances Minor Histocompatibility Antigens ; Proteins ; RNA (63231-63-0) ; DDX3X protein, human (EC 3.6.1.-) ; DDX3Y protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2022-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2022.04.022
    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:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Coordination of mRNA and tRNA methylations by TRMT10A.

    Ontiveros, R Jordan / Shen, Hui / Stoute, Julian / Yanas, Amber / Cui, Yixiao / Zhang, Yuyu / Liu, Kathy Fange

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 14, Page(s) 7782–7791

    Abstract: The posttranscriptional modification of messenger RNA (mRNA) and transfer RNA (tRNA) provides an additional layer of regulatory complexity during gene expression. Here, we show that a tRNA methyltransferase, TRMT10A, interacts with an mRNA demethylase ... ...

    Abstract The posttranscriptional modification of messenger RNA (mRNA) and transfer RNA (tRNA) provides an additional layer of regulatory complexity during gene expression. Here, we show that a tRNA methyltransferase, TRMT10A, interacts with an mRNA demethylase FTO (ALKBH9), both in vitro and inside cells. TRMT10A installs
    MeSH term(s) Adenosine/genetics ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics ; Gene Expression Regulation/genetics ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Methylation ; Methyltransferases/genetics ; RNA, Messenger/genetics ; RNA, Transfer/genetics ; RNA-Binding Proteins/genetics ; tRNA Methyltransferases/genetics
    Chemical Substances RNA, Messenger ; RNA-Binding Proteins ; YTHDF2 protein, human ; RNA, Transfer (9014-25-9) ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO (EC 1.14.11.33) ; FTO protein, human (EC 1.14.11.33) ; Methyltransferases (EC 2.1.1.-) ; TRMT10A protein, human (EC 2.1.1.-) ; tRNA Methyltransferases (EC 2.1.1.-) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2020-03-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1913448117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

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