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Approaches to Link RNA Secondary Structures with Splicing Regulation

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Spliceosomal Pre-mRNA Splicing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1126))

Abstract

In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This chapter describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3′ splice site (3′ss).

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Author information

Authors and Affiliations

  1. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Mireya Plass

  2. Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain

    Eduardo Eyras

  3. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

    Eduardo Eyras

Authors
  1. Mireya Plass
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  2. Eduardo Eyras
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Editor information

Editors and Affiliations

  1. University of California, Irvine, California, USA

    Klemens J. Hertel

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Plass, M., Eyras, E. (2014). Approaches to Link RNA Secondary Structures with Splicing Regulation. In: Hertel, K. (eds) Spliceosomal Pre-mRNA Splicing. Methods in Molecular Biology, vol 1126. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-980-2_25

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  • DOI: https://doi.org/10.1007/978-1-62703-980-2_25

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-979-6

  • Online ISBN: 978-1-62703-980-2

  • eBook Packages: Springer Protocols

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