Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in <i>Arabidopsis</i>.

Abstract

<i>Arabidopsis</i> seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the <i>NRPD1</i>-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with an <i>nrpd1</i> mutant. We also monitored the spatial-temporal activity of the <i>NRPD1</i>-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternal <i>NRPD1</i> allele in the endosperm or seed coat. A group of maternally expressed <i>NRPD1</i>-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by the <i>NRPD1</i>-mediated pathway irrespective of complete silencing (<i>AGL91</i>) or incomplete silencing (<i>AGL40</i>) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.