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A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants

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Abstract

In an attempt both to catalogue 3′ regulatory region (3′ RR)-mediated disease and to improve our understanding of the structure and function of the 3′ RR, we have performed a systematic analysis of disease-associated variants in the 3′ RRs of human protein-coding genes. We have previously analysed the variants that have occurred in two specific domains/motifs of the 3′ untranslated region (3′ UTR) as well as in the 3′ flanking region. Here we have focused upon 83 known variants within the upstream sequence (USS; between the translational termination codon and the upstream core polyadenylation signal sequence) of the 3′ UTR. To place these variants in their proper context, we first performed a comprehensive survey of known cis-regulatory elements within the USS and the mechanisms by which they effect post-transcriptional gene regulation. Although this survey supports the view that RNA regulatory elements function within the context of specific secondary structures, there are no general rules governing how secondary structure might exert its influence. We have therefore addressed this question by systematically evaluating both functional and non-functional (based upon in vitro reporter gene and/or electrophoretic mobility shift assay data) USS variant-containing sequences against known cis-regulatory motifs within the context of predicted RNA secondary structures. This has allowed us not only to establish a reliable and objective means to perform secondary structure prediction but also to identify consistent patterns of secondary structural change that could potentiate the discrimination of functional USS variants from their non-functional counterparts. The resulting rules were then used to infer potential functionality in the case of some of the remaining functionally uncharacterised USS variants, from their predicted secondary structures. This not only led us to identify further patterns of secondary structural change but also several potential novel cis-regulatory motifs within the 3′ UTRs studied.

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Acknowledgements

JMC is a visiting Professor of Genetics supported by the Ministère de la Jeunesse, de l’Éducation Nationale et de la Recherche, France. This work was supported by the INSERM (Institut National de la Santé et de la Recherche Médicale), France. The authors are most grateful to Peter Stenson for provision of HGMD data.

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Authors and Affiliations

  1. INSERM, U613, 29220, Brest, France

    Jian-Min Chen & Claude Férec

  2. Etablissement Français du Sang – Bretagne, 46 rue Félix Le Dantec, 29220, Brest, France

    Jian-Min Chen & Claude Férec

  3. Faculté de Médecine de Brest et des Sciences de la Santé, Université de Bretagne Occidentale, 29238, Brest, France

    Jian-Min Chen & Claude Férec

  4. Laboratoire de Génétique Moléculaire et d’Histocompatibilité, CHRU Brest, Hôpital Morvan, 29220, Brest, France

    Claude Férec

  5. Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK

    David N. Cooper

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  1. Jian-Min Chen
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Chen, JM., Férec, C. & Cooper, D.N. A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants . Hum Genet 120, 301–333 (2006). https://doi.org/10.1007/s00439-006-0218-x

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