MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and helitrons

Abstract

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type endosperm. Consistent with the role of DNA methylation in gene silencing, we find 96 gene and 86 TE differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed EM-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately [2/3] of all MEGs show evidence of regulation by DNA glycosylases. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation. Significance StatementThis work investigates the transcriptome changes resulting from the loss of function of DNA glycosylase MDR1, revealing that, in wild-type endosperm, targets of MDR1 are expressed predominantly from the maternal allele and this expression is suppressed in mutants. Furthermore, by combining expression data, DNA methylation data, and developmental expression data, we are able to categorize all maternally expressed, imprinted genes based on DNA glycosylase dependent or independent regulatory methods.