Mutation in <scp>THO2</scp> , a component of <scp>THO</scp> / <scp>TREX</scp> complex, causes transcriptional gene silencing and genome‐wide <scp>DNA</scp> methylation changes

<jats:title>SUMMARY</jats:title> <jats:p> DNA methylation plays important roles in silencing of transgenes, endogenous genes, and transposable elements (TEs). To identify genes involved in antagonizing transcriptional or DNA hypermethylation‐induced gene silencing, a genetic screening was conducted and thus a <jats:italic>tho2‐8</jats:italic> mutant was recovered. THO2 is a major component of the THO/TREX (Transcription‐Export) complex, which plays essential roles in mRNA export. The <jats:italic>tho2‐8</jats:italic> mutation caused overaccumulation of DNA methylation on a <jats:italic>d35S</jats:italic> promoter ahead of <jats:italic>LUC</jats:italic> , suggesting its roles in antisilencing of transgenes. This mutation also resulted in significant genome‐wide alterations in DNA methylation in a locus‐specific manner, including 2513 hyper‐DMRs and 1717 hypo‐DMRs. The hyper‐DMRs in the <jats:italic>tho2‐8</jats:italic> mutant not only exhibited a considerable overlap with those in DNA demethylation mutants (like <jats:italic>ros1‐7</jats:italic> ), but also with hypo‐DMRs from <jats:italic>nrpd1‐3</jats:italic> and <jats:italic>nrpe1‐11</jats:italic> mutants, demonstrating that THO2 is able to protect those loci targeted by DNA demethylation and/or RdDM pathways from hypermethylation. The <jats:italic>tho2‐8</jats:italic> mutant also contained a plethora of CHH hypo‐DMRs, which overlapped in large numbers with those from the <jats:italic>nrpd1‐3</jats:italic> and <jats:italic>nrpe1‐11</jats:italic> mutants, indicating that THO2 is required for the establishment/maintenance of DNA methylation at many loci. Additionally, the <jats:italic>tho2‐8</jats:italic> mutation caused an increase in overall 24‐nt siRNA levels and many upregulated and downregulated DEGs/DETEs. The effects of THO2 on DNA methylation patterns appeared to be associated with the functioning of Pol IV and Pol V because THO2 physically interacted with NRPD7 and was necessary for normal accumulation levels of several Pol V‐dependent <jats:italic>IGN</jats:italic> s' transcripts. Thus, this study provided valuable insights into new roles of THO2 in DNA methylation patterning. </jats:p>