ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis

RNA silencing negatively regulates gene expression at either transcriptional or post-transcriptional levels through DNA methylation, histone modification, mRNA cleavage or translational inhibition. 21- to 24-nucleotide (nt) small interfering RNAs (siRNAs), which are processed from double-stranded RNAs (dsRNAs) by different Dicer-like enzymes, play essential roles in RNA silencing in plants. Genetic screens based on inverted-repeat (IR) triggers expressed specifically in the phloem have long been used to identify regulators required for transgene-induced RNA silencing. Here, using the SUC-SUL IR reporter system, we revealed that ALTERED MERISTEM PROGRAM1 (AMP1) and its paralog LIKE AMP1 (LAMP1) impair RNA silencing through repressing the biogenesis of IR-derived siRNAs. In the amp1 lamp1 background, the transcription of the IR transgene SUC:SUL is enhanced due to elevated ARGONAUTE 1 (AGO1) protein levels. The ago1-27 mutation rescues the elevated transcription of SUC:SUL in SUC-SUL amp1 lamp1 by decreasing the occupancy of RNA polymerase II (Pol II). Genetic analysis indicates that AMP1 acts upstream of RNA polymerase IV subunit 1 (NRPD1), RNA-dependent RNA polymerase 2 (RDR2) and Dicer-Like 4 (DCL4), which are required for IR-induced RNA silencing. We also show that AMP1 reduces the abundance of endogenous IR-derived siRNAs, which implies a broad role of AMP1 on IR silencing. Together, these results uncover two previously unknown players in siRNA biogenesis from IRs-AGO1 that promotes IR transcription and AMP1 that inhibits this effect of AGO1.