REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.

In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, Pol IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. These findings establish a direct connection between sequence-specific transcription factors and the spatial regulation of siRNAs production and DNA methylation, offering new insights into the genetic control of epigenetic patterning. For ChIP-seq experiments, 1~2 g of unopen flower buds from the T2 lines were collected. For sRNA-seq and WGBS, ovule or anther tissues (stage 9 or earlier) from 5- to 6-week-old plants were harvested.