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Joint quantification of genetic and epigenetic effects on gene expression isimportant for understanding the establishment of complex gene regulationsystems in living organisms. In particular, genomic imprinting and maternaleffects play important roles in the developmental process of mammals andflowering plants. However, the influence of these effects on gene expressionare difficult to quantify because they act simultaneously with cis-regulatorymutations. Here we propose a simple method to decompose cis-regulatory (i.e.,allelic genotype, AG), genomic imprinting (i.e., parent-of-origin, PO), andmaternal (i.e., maternal genotype, MG) effects on allele-specific geneexpression using RNA-seq data obtained from reciprocal crosses. We evaluatedthe efficiency of method using a simulated dataset and applied the method towhole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seqdata. Consistent with previous studies, we found little evidence of PO and MGeffects in adult Drosophila samples. In contrast, we identified dozens andhundreds of mouse genes with significant PO and MG effects, respectively.Interestingly, a similar number of genes with significant PO effect were detectin mouse TSCs and livers, whereas more genes with significant MG effect wereobserved in livers. Further application of this method will clarify how thesethree effects influence gene expression levels in different tissues anddevelopmental stages, and provide novel insight into the evolution of geneexpression regulation.

A generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression