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

Area of Science:

• Genomics
• Developmental Biology
• Molecular Biology

Background:

• RNA-sequencing (RNA-seq) is a common method to study gene expression changes in response to genetic mutations in model organisms.
• Standard analysis assumes differential gene expression between genotypes reveals mutation-specific pathway effects.

Purpose of the Study:

• To investigate the impact of allele-specific expression on RNA-seq interpretation in zebrafish.
• To determine if genes on the same chromosome as a mutation are spuriously identified as differentially expressed.

Main Methods:

• Incross of haplotype-resolved wild-type zebrafish.
• Analysis of allele-specific expression patterns.
• Comparison of gene expression profiles between mutant and sibling embryos.

Main Results:

• Widespread allele-specific expression was observed in zebrafish, even in wild-type incrosses.
• Differential gene expression on the same chromosome as a mutation can arise from allele-specific expression, not the mutation itself.
• Genomic location is often overlooked in RNA-seq data interpretation, leading to potential misinterpretation.

Conclusions:

• Allele-specific expression can create false positives in RNA-seq studies of genetic mutations.
• The genomic location of differentially expressed genes must be considered to avoid erroneous pathway attribution.
• Findings impact RNA-seq experiment interpretation in outbred and non-inbred model organisms.