RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [sRNA_seq libraries]

Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. thaliana endosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict Overall design: Sequencing of three replicates of sRNA from mat nrpd1+/- (Ler nrpd1-/- x Col-0 F1) and nrpd1-/- (Ler nrpd1-/- x Col-0 nrpd1-/- F1) and two replicates from pat nrpd1+/- (Ler x Col nrpd1-/- F1)