Long-range control of gene expression via RNA-directed DNA methylation

Rna-mediated transcriptional silencing,in plants known as rna-directed dna methylation (rddm),is a conserved process where small interfering rna (sirna) and long non-coding rna (lncrna) help establish repressive chromatin modifications. this process represses transposons and affects the expression of protein-coding genes. we found that in arabidopsis thaliana ago4 binding sites are often located distant from genes differentially expressed in ago4. using hi-c to compare interactions between genotypes,we show that rddm-targeted loci have the potential to engage in chromosomal interactions,but these interactions are inhibited in wild-type conditions. in mutants defective in rddm,the frequency of chromosomal interactions at rddm targets is increased. this includes increased frequency of interactions between pol v methylated sites and distal genes that are repressed by rddm. we propose a model,where rddm prevents the formation of chromosomal interactions between genes and their distant regulatory elements. © 2017 rowley et al.