RTEL1 is involved in transcriptional gene silencing and inhibition of heterochromatic DNA methylation

Transcriptional gene silencing is an essential mechanism for controlling the expression of genes and transposable elements (TEs) and is commonly associated with high levels of DNA methylation. Thus, release of silencing is frequently observed in mutants for genes involved in DNA methylation maintenance. However, studies in Arabidopsis thaliana have revealed that transcriptional repression of some DNA-methylated genes and TEs also relies on repressors that operate through pathways largely independent of DNA methylation. One such pathway appears linked to DNA replication and DNA repair and mutations in factors involved in these processes such as the polymerases alpha, delta and epsilon destabilize silencing. Here, we isolate a new mutant allele of the helicase REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) gene from a genetic screen for TGS-deficient mutants. RTEL1 is highly conserved among eukaryotes and plays an important role in the resolution of DNA secondary structures during DNA replication. We show that rtel1 causes release of TGS without loss of DNA methylation or global changes in chromatin accessibility. However, many heterochromatic loci show increased levels of DNA methylation and chromatin accessibility in rtel1 mutants. Our findings reveal a function for RTEL1 in maintaining silencing and in preventing DNA hypermethylation of heterochromatin. Overall design: RNA-seq of wild-type, rtel1, mom1 and rtel1 mom1 mutant plants; ATAC-seq of wild-type and rtel1 seedlings; ChIP-seq for H3K27me3 in wild-type and rtel1 seedlings.