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Chimeric RNA pp 27–40Cite as

Identification of Chimeric RNAs Using RNA-Seq Reads and Protein–Protein Interactions of Translated Chimeras

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2079))

Abstract

Chimeric RNA moieties typically consist of exons from two genes expressed from different genomic locations and produced by chromosomal translocations, trans-splicing or transcription errors. Recent advances in next-generation sequencing procedures have opened new horizons for identification of novel chimeric transcripts in various diseases in a personalized manner. Here we describe the detailed computational procedures to identify chimeric transcripts using RNA-seq reads. Moreover, we elaborate on the domain–domain co-occurrence method to detect alterations in chimeric protein–protein interaction (ChiPPI) networks produced by chimeric RNA that are translated to chimeric proteins.

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Authors and Affiliations

  1. Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel

    Milana Frenkel-Morgenstern

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  1. Milana Frenkel-Morgenstern
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Correspondence to Milana Frenkel-Morgenstern .

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  1. Department of Paathology, School of Medicine, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA

    Hui Li

  2. Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA

    Justin Elfman

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Frenkel-Morgenstern, M. (2020). Identification of Chimeric RNAs Using RNA-Seq Reads and Protein–Protein Interactions of Translated Chimeras. In: Li, H., Elfman, J. (eds) Chimeric RNA. Methods in Molecular Biology, vol 2079. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9904-0_3

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  • DOI: https://doi.org/10.1007/978-1-4939-9904-0_3

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