A Paragenetic Perspective on Integration of RNA Silencing into the Epigenome and Its Role in the Biology of Higher Plants

Abstract

We describe features of RNA silencing and associated epigenetic imprints that illustrate potential roles for RNA interference(RNAi) in maintenance and transmission of epigenetic states between cells, throughout a plant, and perhaps even acrosssexual generations. Three types of transgenes can trigger RNAi of homologous endogenous plant genes: (1) "sense" transgenesthat overexpress translatable transcripts, (2) inverted repeat (IR) transgenes that produce double-stranded RNA(dsRNA), and (3) antisense transgenes. Each mode of RNAi produces a different characteristic developmental silencing pattern.Single-copy transgenes are sufficient for sense-RNAi and antisense-RNAi, but not inverted repeat-RNAi. A single prematuretermination codon dramatically attenuates sense-RNAi, but it has no effect on antisense or inverted repeat-RNAi. Wereport here that antisense transgenes altered by removal of nonsense codons generate silencing patterns characteristic ofsense-RNAi. Duplication of a sense overexpression transgene results in two types of epigenetic events: (1) complete loss ofsilencing and (2) altered developmental pattern of silencing. We also report that duplicating only the transgene promoterresults in complete loss of silencing, whereas duplicating only transcribed sequences produces the second class, which arevein-based patterns. We infer that the latter class is due to systemic RNA silencing signals that interact with certain epigeneticstates of the transgene to imprint it with information generated at a distance elsewhere in the plant.