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  1. Book: The eukaryotic RNA exosome

    Vaňáčová, Štěpánka / LaCava, John

    methods and protocols

    (Methods in molecular biology ; 2062 ; Springer protocols)

    2020  

    Author's details edited by John LaCava, Štěpánka Vaňáčová
    Series title Methods in molecular biology ; 2062
    Springer protocols
    Collection
    Language English
    Size xiii, 517 Seiten, Illustrationen
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT020312543
    ISBN 978-1-4939-9821-0 ; 9781493998227 ; 1-4939-9821-8 ; 1493998226
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    Zs A 7042 -2062- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Correction to: The Eukaryotic RNA Exosome.

    LaCava, John / Vaňáčová, Štěpánka

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2062, Page(s) C1–C4

    Abstract: The original version of this book was inadvertently published with the hyperlinks deleted from the reference section in the Chapters 1,5,8,11,13,15,16 and 24. These are corrected now. ...

    Abstract The original version of this book was inadvertently published with the hyperlinks deleted from the reference section in the Chapters 1,5,8,11,13,15,16 and 24. These are corrected now.
    Language English
    Publishing date 2020-11-30
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9822-7_25
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  3. Article ; Online: Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation.

    Hejret, Vaclav / Varadarajan, Nandan Mysore / Klimentova, Eva / Gresova, Katarina / Giassa, Ilektra-Chara / Vanacova, Stepanka / Alexiou, Panagiotis

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 22895

    Abstract: Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily ... ...

    Abstract Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily via a 'seed' mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 'guide'-'target' interactions remains elusive. Our study employs two experimental methods-AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA 'guide' and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 'guides' derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each 'guide' class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its 'guide' repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/ .
    MeSH term(s) Animals ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; RNA, Ribosomal ; RNA, Transfer ; Mammals/metabolism
    Chemical Substances MicroRNAs ; Argonaute Proteins ; RNA, Ribosomal ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2023-12-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-49757-z
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  4. Article ; Online: The role of 3' end uridylation in RNA metabolism and cellular physiology.

    Zigáčková, Dagmar / Vaňáčová, Štěpánka

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2018  Volume 373, Issue 1762

    Abstract: Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular ...

    Abstract Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection. Defects in uridylation have been linked to several diseases. This review summarizes the current knowledge about the role of the 3' terminal oligo(U)-tailing in biology of various RNAs in eukaryotes and describes key factors involved in these pathways.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
    MeSH term(s) Eukaryota ; Eukaryotic Cells/physiology ; Humans ; RNA/metabolism ; RNA 3' End Processing ; Uridine/metabolism
    Chemical Substances RNA (63231-63-0) ; Uridine (WHI7HQ7H85)
    Language English
    Publishing date 2018-11-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2018.0171
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Einzelsignatur: Show issues

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  5. Article ; Online: DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs.

    Roithová, Adriana / Feketová, Zuzana / Vaňáčová, Štěpánka / Staněk, David

    Nucleic acids research

    2020  Volume 48, Issue 11, Page(s) 6184–6197

    Abstract: Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed ... ...

    Abstract Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed along the pathway. Here, we analyzed the fate of small nuclear RNAs (snRNAs) that are unable to acquire a ring of Sm proteins. We showed that snRNAs lacking the Sm ring are unstable and accumulate in P-bodies in an LSm1-dependent manner. We further provide evidence that defective snRNAs without the Sm binding site are uridylated at the 3' end and associate with DIS3L2 3'→5' exoribonuclease and LSm proteins. Finally, inhibition of 5'→3' exoribonuclease XRN1 increases association of ΔSm snRNAs with DIS3L2, which indicates competition and compensation between these two degradation enzymes. Together, we provide evidence that defective snRNAs without the Sm ring are uridylated and degraded by alternative pathways involving either DIS3L2 or LSm proteins and XRN1.
    MeSH term(s) Base Sequence ; Binding Sites ; Exoribonucleases/metabolism ; HeLa Cells ; Humans ; Nucleic Acid Conformation ; Organelles/metabolism ; Protein Binding ; Proto-Oncogene Proteins/metabolism ; RNA Stability ; RNA Transport ; RNA, Small Nuclear/chemistry ; RNA, Small Nuclear/metabolism ; RNA-Binding Proteins/metabolism ; SMN Complex Proteins/metabolism
    Chemical Substances GEMIN5 protein, human ; LSM1 protein, human ; Proto-Oncogene Proteins ; RNA, Small Nuclear ; RNA-Binding Proteins ; SMN Complex Proteins ; DIS3L2 protein, human (EC 3.1.-) ; Exoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2020-05-22
    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/gkaa301
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    Zs.A 1067: Show issues Location:
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  6. Article ; Online: HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs.

    Cavallin, Ivana / Bartosovic, Marek / Skalicky, Tomas / Rengaraj, Praveenkumar / Demko, Martin / Schmidt-Dengler, Martina Christina / Drino, Aleksej / Helm, Mark / Vanacova, Stepanka

    RNA (New York, N.Y.)

    2022  Volume 28, Issue 12, Page(s) 1568–1581

    Abstract: Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5- ... ...

    Abstract Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm
    MeSH term(s) Humans ; Chromatin Immunoprecipitation Sequencing ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Anticodon ; RNA, Untranslated/genetics ; AlkB Homolog 8, tRNA Methyltransferase/genetics
    Chemical Substances RNA, Transfer (9014-25-9) ; Anticodon ; RNA, Untranslated ; ALKBH8 protein, human (EC 1.14.11.-) ; AlkB Homolog 8, tRNA Methyltransferase (EC 1.14.11.-)
    Language English
    Publishing date 2022-10-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079421.122
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    Zs.A 4777: Show issues Location:
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  7. Article ; Online: The role of RNA adenosine demethylases in the control of gene expression.

    Rajecka, Veronika / Skalicky, Tomas / Vanacova, Stepanka

    Biochimica et biophysica acta. Gene regulatory mechanisms

    2018  Volume 1862, Issue 3, Page(s) 343–355

    Abstract: RNA modifications are being recognized as an essential factor in gene expression regulation. They play essential roles in germ line development, differentiation and disease. In eukaryotic mRNAs, ... ...

    Abstract RNA modifications are being recognized as an essential factor in gene expression regulation. They play essential roles in germ line development, differentiation and disease. In eukaryotic mRNAs, N
    MeSH term(s) Adenine/analogs & derivatives ; Adenine/metabolism ; AlkB Homolog 5, RNA Demethylase/metabolism ; Animals ; Humans ; RNA/genetics ; RNA/metabolism ; RNA Processing, Post-Transcriptional
    Chemical Substances RNA (63231-63-0) ; AlkB Homolog 5, RNA Demethylase (EC 1.14.11.-) ; Adenine (JAC85A2161) ; 6-methyladenine (W7IBY2BGAX)
    Language English
    Publishing date 2018-12-11
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2918786-2
    ISSN 1876-4320 ; 1874-9399
    ISSN (online) 1876-4320
    ISSN 1874-9399
    DOI 10.1016/j.bbagrm.2018.12.001
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    Zs.A 7156: Show issues Location:
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  8. Article ; Online: Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays.

    Zigáčková, Dagmar / Rájecká, Veronika / Vaňáčová, Štěpánka

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 2062, Page(s) 237–253

    Abstract: The RNA exosome processes a wide variety of RNA and mediates RNA maturation, quality control and decay. In marked contrast to its high processivity in vivo, the purified exosome exhibits only weak activity on RNA substrates in vitro. Its activity is ... ...

    Abstract The RNA exosome processes a wide variety of RNA and mediates RNA maturation, quality control and decay. In marked contrast to its high processivity in vivo, the purified exosome exhibits only weak activity on RNA substrates in vitro. Its activity is regulated by several auxiliary proteins, and protein complexes. In budding yeast, the activity of exosome is enhanced by the polyadenylation complex referred to as TRAMP. TRAMP oligoadenylates precursors and aberrant forms of RNAs to promote their trimming or complete degradation by exosomes. This chapter provides protocols for the purification of TRAMP and exosome complexes from yeast and the in vitro evaluation of exosome activation by the TRAMP complex. The protocols can be used for different purposes, such as the assessment of the role of individual subunits, protein domains or particular mutations in TRAMP-exosome RNA processing in vitro.
    MeSH term(s) Cell Nucleus/metabolism ; Exosome Multienzyme Ribonuclease Complex/metabolism ; Exosomes/metabolism ; Polyadenylation/physiology ; RNA/metabolism ; RNA Stability/physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Serine Endopeptidases/metabolism
    Chemical Substances Saccharomyces cerevisiae Proteins ; RNA (63231-63-0) ; Exosome Multienzyme Ribonuclease Complex (EC 3.1.-) ; Serine Endopeptidases (EC 3.4.21.-) ; tunicate retinoic acid-inducible modular protease (EC 3.4.21.-)
    Language English
    Publishing date 2019-11-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9822-7_12
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  9. Article ; Online: RNA methylation in nuclear pre-mRNA processing.

    Covelo-Molares, Helena / Bartosovic, Marek / Vanacova, Stepanka

    Wiley interdisciplinary reviews. RNA

    2018  Volume 9, Issue 6, Page(s) e1489

    Abstract: Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also ...

    Abstract Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also study messenger RNA (mRNA). Subsequently, mRNA modifications, namely methylation, have emerged as key players in eukaryotic gene expression regulation. The most abundant and widely studied internal mRNA modification is N
    MeSH term(s) Animals ; Cell Nucleus/metabolism ; Epigenesis, Genetic ; Humans ; Methylation ; RNA Precursors/metabolism ; RNA, Messenger/metabolism ; Transcriptome
    Chemical Substances RNA Precursors ; RNA, Messenger
    Language English
    Publishing date 2018-06-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2634714-3
    ISSN 1757-7012 ; 1757-7004
    ISSN (online) 1757-7012
    ISSN 1757-7004
    DOI 10.1002/wrna.1489
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    Zs.A 6953: Show issues Location:
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  10. Article ; Online: Interplays of different types of epitranscriptomic mRNA modifications.

    Rengaraj, Praveenkumar / Obrdlík, Aleš / Vukić, Dragana / Varadarajan, Nandan Mysore / Keegan, Liam P / Vaňáčová, Štěpánka / O'Connell, Mary A

    RNA biology

    2021  Volume 18, Issue sup1, Page(s) 19–30

    Abstract: Eukaryotic mRNAs are modified by several chemical marks which have significant impacts on mRNA biology, gene expression, and cellular metabolism as well as on the survival and development of the whole organism. The most abundant and well-studied mRNA ... ...

    Abstract Eukaryotic mRNAs are modified by several chemical marks which have significant impacts on mRNA biology, gene expression, and cellular metabolism as well as on the survival and development of the whole organism. The most abundant and well-studied mRNA base modifications are m
    MeSH term(s) Animals ; Epigenesis, Genetic ; Epigenomics/methods ; Humans ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcriptome
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2021-08-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1555-8584
    ISSN (online) 1555-8584
    DOI 10.1080/15476286.2021.1969113
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