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

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 5' end sequencing of endosperm mRNAs from two replicates of wild-type (Ler x Col-0 F1) and three replicates of nrpd1-/- (Ler nrpd1-/- x Col-0 nrpd1-/-).

胚乳（endosperm）——一种介导母本资源向子代转运的种子组织——其基因表达受到复杂的表观遗传调控。本研究证实，植物特异性RNA聚合酶IV（RNA Polymerase IV，Pol IV）介导亲本对胚乳基因表达的调控。该酶是生成通常指导DNA甲基化的小干扰RNA（small interfering RNA，siRNA）所必需的。我们对野生型植株与Pol IV突变体杂交获得的正反交杂合子的拟南芥（Arabidopsis thaliana，A. thaliana）胚乳中的小RNA、DNA甲基化以及信使RNA（messenger RNA，mRNA）进行了比较分析。研究发现，母本来源与父本来源的Pol IV对胚乳的调控作用存在差异：母本与父本Pol IV的缺失会在不同的基因组位点上影响小RNA（sRNAs）丰度与DNA甲基化水平。值得注意的是，在部分基因座（locus的复数形式为loci）上，母本与父本来源的Pol IV对基因表达存在拮抗效应，二者分别促进或抑制胚乳的基因表达。此类亲本起源特异性的拮抗效应此前鲜有报道，其与亲本冲突演化下的基因调控系统相符。本研究对两类样本的胚乳mRNA开展了5'端测序：一类为野生型（Ler × Col-0 F1）的两个生物学重复样本，另一类为nrpd1-/-突变体（Ler nrpd1-/- × Col-0 nrpd1-/-）的三个生物学重复样本。