The frequency natural antisense transcript first increases, then decreases frequency gene expression by changing flexible gene-silencing regions

Induction of the frq antisense transcript qrf significantly altered heterochromatin formation and DNA methylation at frq.

• Replacing the endogenous qrf promoter impacted the regulation of chromatin structure.
• Low-level induction of qrf dramatically affected the endogenous circadian rhythm and increased circadian output.
• Initial expression of qrf enhanced frq gene expression by creating a more accessible chromatin environment.
• The effect of antisense transcript expression initially promoting sense gene expression before silencing was also observed with a NAT to a hygromycin resistance gene.
• Facultative heterochromatin silencing at frq operates in a parallel pathway to VVD-dependent silencing.
• Dicer-independent siRNA-mediated facultative heterochromatin repression occurs alongside other feedback processes.

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