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

In model organisms, RNA-sequencing (RNA-seq) 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 co...

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Autores principales: White, Richard J, Mackay, Eirinn, Wilson, Stephen W, Busch-Nentwich, Elisabeth M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8884726/
https://www.ncbi.nlm.nih.gov/pubmed/35175196
http://dx.doi.org/10.7554/eLife.72825
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author White, Richard J
Mackay, Eirinn
Wilson, Stephen W
Busch-Nentwich, Elisabeth M
author_facet White, Richard J
Mackay, Eirinn
Wilson, Stephen W
Busch-Nentwich, Elisabeth M
author_sort White, Richard J
collection PubMed
description In model organisms, RNA-sequencing (RNA-seq) 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 over-represented 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.
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spelling pubmed-88847262022-03-01 Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants White, Richard J Mackay, Eirinn Wilson, Stephen W Busch-Nentwich, Elisabeth M eLife Chromosomes and Gene Expression In model organisms, RNA-sequencing (RNA-seq) 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 over-represented 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. eLife Sciences Publications, Ltd 2022-02-17 /pmc/articles/PMC8884726/ /pubmed/35175196 http://dx.doi.org/10.7554/eLife.72825 Text en © 2022, White et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
White, Richard J
Mackay, Eirinn
Wilson, Stephen W
Busch-Nentwich, Elisabeth M
Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title_full Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title_fullStr Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title_full_unstemmed Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title_short Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
title_sort allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8884726/
https://www.ncbi.nlm.nih.gov/pubmed/35175196
http://dx.doi.org/10.7554/eLife.72825
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