Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants.
Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants.
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DOI：
10.7554/elife.72825
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发表时间：
2022-02-17
期刊：
影响因子：
7.7
通讯作者：
Busch-Nentwich EM
中科院分区：
文献类型：
--
作者：
White RJ;Mackay E;Wilson SW;Busch-Nentwich EM
在模式生物中，rna测序（RNA-seq）经常用于评估基因突变对细胞和发育过程的影响。通常情况下，一种突变的杂合动物通过杂交产生具有不同基因型的后代。所得胚胎按基因型分组，以比较纯合子突变胚胎与杂合子和野生型兄弟姐妹。人们认为，两组之间表达差异的基因可以揭示受突变影响的途径。在斑马鱼中，由于来自不同遗传背景的等位基因的表达水平不同，差异表达的基因通常在与突变相同的染色体上过度表达。通过对单倍型分离的野生型鱼进行杂交，我们发现了广泛的等位基因特异性表达的证据，当将基因组某一区域纯合的胚胎与其兄弟姐妹进行比较时，这种表达表现为差异表达。当分析突变的转录组时，这意味着同一染色体上基因的差异表达可能不是由该突变引起的。通常，差异表达基因的基因组位置在解释其相对于表型的重要性时不被考虑。这可能会导致通路被错误地牵连或忽视，因为在与突变相同的染色体上存在虚假的差异表达基因的噪音。这些观察结果对涉及近亲繁殖动物和非近亲繁殖模式生物的RNA-seq实验的解释具有启示意义。
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.