Promiscuous CRE-CRE interaction that acts as a causative force driving de novel methylation in cis-regulatory elements in plants [AGeRdDM BSseq]

Cis-regulatory elements (CREs) control gene expression amplitude, tissue specificity and timing, whereby they directly impact phenotypic variation. However, in plants, CREs frequently become prone to RNA-directed DNA methylation (RdDM) when in a transgenic state (particularly in a tandem-repeat configuration), and the mechanism driving this phenomenon is currently unknown. In this study, we demonstrate that three of six flower-specific CREs, including the AGAMOUS enhancer (AGe), undergo transcriptional silencing when in a transgenic state, leading to the production of mutant flowers in 28-44% of transgenic lines. This silencing is dependent on the transgene self-transcribed non-coding RNAs (ncRNAs) that feed into biogenesis of 24-nt small interfering RNAs (siRNAs) and the canonical RdDM pathway, but not RNAs transcribed by the RNA polymerase II promoter. Strikingly, this ncRNA-dependent, siRNA-driven RdDM is prone to the enhancing action of an adjacent CaMV35S enhancer (35Se), which was shown to promiscuously interact with, and ectopically activate, numerous CREs including the AGe. This enhancement corresponded with an increase in ncRNAs specifically transcribed from the antisense strand of the transgene. We further demonstrate that the same 35Se inserted approximately 3.5 kb upstream of the native AGe within a genome promiscuously interacts with and activating de novo RdDM activity in the AGe, resulting in a mutant flower. These findings provide the first evidence that promiscuous CRE-CRE interactions serve as a causative force driving RdDM/silencing, and novel insight into the mechanism underlying the methylation-vulnerablity of the CRE transgenes, duplicated genes and repetitive genomic regions rich in transposon elements, where promiscuous CRE-CRE interactions are common. Overall design: Comparison of DNA methylation profile among different lines