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Research article

Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation

Patrycja Sosińska-Zawierucha, Piotr Zawierucha, Andrzej Bręborowicz, Jan Barciszewski
Biochemical Journal Sep 05, 2018, 475 (17) 2727-2748; DOI: 10.1042/BCJ20180239
Patrycja Sosińska-Zawierucha
Department of Pathophysiology, Poznan University of Medical Sciences, Poznań, PolandInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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  • For correspondence: psosinska@ump.edu.pl
Piotr Zawierucha
Department of Anatomy, Poznan University of Medical Sciences, Poznań, PolandComputer Sciences Unit, Poznan University of Medical Sciences, Poznań, Poland
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Andrzej Bręborowicz
Department of Pathophysiology, Poznan University of Medical Sciences, Poznań, Poland
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Jan Barciszewski
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Abstract

Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.

  • BCYRN1
  • BC200 RNA
  • computational modelling
  • enzymatic probing
  • structure prediction
  • Abbreviations

    BC200 RNA,
    brain cytoplasmic 200 RNA;
    RNPCs,
    ribonucleoprotein complexes
    • © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society
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    September 2018

    Volume: 475 Issue: 17

    Biochemical Journal: 475 (17)
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    Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation
    Patrycja Sosińska-Zawierucha, Piotr Zawierucha, Andrzej Bręborowicz, Jan Barciszewski
    Biochemical Journal Sep 2018, 475 (17) 2727-2748; DOI: 10.1042/BCJ20180239
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    Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation
    Patrycja Sosińska-Zawierucha, Piotr Zawierucha, Andrzej Bręborowicz, Jan Barciszewski
    Biochemical Journal Sep 2018, 475 (17) 2727-2748; DOI: 10.1042/BCJ20180239

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    Keywords

    BCYRN1
    BC200 RNA
    computational modelling
    enzymatic probing
    structure prediction

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