A Generalized Linear Model for Decomposing Cis -regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

G3 : Genes - Genomes - Genetics
Yasuaki TakadaNaoki Osada

Abstract

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, where...Continue Reading

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Citations

Apr 11, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Carmen Emborski, Alexander S Mikheyev
Apr 17, 2021·Genome Research·Bryan A Ramirez-CoronaZeba Wunderlich

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Datasets Mentioned

BETA
PRJDB5381
E-MTAB-1091

Methods Mentioned

BETA
RNA-seq

Software Mentioned

GATK
ENSEMBL
R script
ASE
R package
R
DAVID
TIGER
EdgeR
bowtie2

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