1. Chromosomes and Gene Expression
  2. Developmental Biology

Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

  1. Richard J White
  2. Eirinn Mackay
  3. Stephen W Wilson
  4. Elisabeth M Busch-Nentwich  Is a corresponding author
  1. University of Cambridge, United Kingdom
  2. University College London, United Kingdom
https://doi.org/10.7554/eLife.72825
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  1. Richard J White
  2. Eirinn Mackay
  3. Stephen W Wilson
  4. Elisabeth M Busch-Nentwich
(2022)
Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
eLife 11:e72825.
https://doi.org/10.7554/eLife.72825
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Abstract

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that the differential expression of genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

Data availability

Sequencing data have been deposited in ENA under the accessions shown in the Materials and Methods. Differentially expressed gene lists for all the experiments are available at doi.org/10.6084/m9.figshare.15082239.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Richard J White

    Department of Medicine, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  2. Eirinn Mackay

    Department of Cell and Developmental Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  3. Stephen W Wilson

    Department of Cell and Developmental Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8557-5940

  4. Elisabeth M Busch-Nentwich

    Department of Medicine, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    e.busch-nentwich@qmul.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6450-744X

Funding

Medical Research Council (MR/L003775/1)

  • Stephen W Wilson

Medical Research Council (MR/T020164/1)

  • Stephen W Wilson

Wellcome Trust (095722/Z/11/Z)

  • Stephen W Wilson

Wellcome Trust (206194)

  • Richard J White
  • Elisabeth M Busch-Nentwich

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Ferenc Muller

Version history

  1. Received: August 5, 2021
  2. Preprint posted: August 6, 2021 (view preprint)
  3. Accepted: February 16, 2022
  4. Accepted Manuscript published: February 17, 2022 (version 1)
  5. Version of Record published: February 28, 2022 (version 2)

Copyright

© 2022, White et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Richard J White
  2. Eirinn Mackay
  3. Stephen W Wilson
  4. Elisabeth M Busch-Nentwich
(2022)
Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
eLife 11:e72825.
https://doi.org/10.7554/eLife.72825

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