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Inference of Allele-Specific Expression from RNA-seq Data

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Book cover Plant Epigenetics and Epigenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1112))

Abstract

The differential abundance of transcripts from alternative alleles of a gene, for example in a hybrid plant or an outbred natural population, can provide information about the nature of interindividual or interstrain variation in gene expression. Allele-specific expression (ASE) can result from epigenetic phenomena, such as imprinting (when the overexpressed allele is inherited consistently from one parent) or allele-specific chromatin modifications. Alternatively, DNA sequence variants in the promoter or within the transcribed region of a gene can affect the rate of transcription or the rate of decay of the transcript, respectively. The existence of this allelic variation and the insights it provides into the nature of the gene regulation are of significant interest. With the recent widespread availability of sequencing based transcriptomics, the power to detect ASE has increased; however, inference of ASE from transcriptome sequencing data is subject to several caveats and potential biases and the results need to be interpreted with care.

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Author information

Authors and Affiliations

  1. School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway (NUI Galway), Ireland

    Paul K. Korir & Cathal Seoighe

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  1. Paul K. Korir
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  2. Cathal Seoighe
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Editors and Affiliations

  1. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

    Charles Spillane

  2. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

    Peter C. McKeown

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Korir, P.K., Seoighe, C. (2014). Inference of Allele-Specific Expression from RNA-seq Data. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 1112. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-773-0_4

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  • DOI: https://doi.org/10.1007/978-1-62703-773-0_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-772-3

  • Online ISBN: 978-1-62703-773-0

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