Non-coding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription interfaces with Polycomb Repressive Complex 2 silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C ( FLC ). Through genetic, chromatin, and computational analyses, we show that FLC is silenced through pathways that function with different dynamics: an antisense transcription-mediated pathway capable of fast response; and in parallel a slow Polycomb Repressive Complex 2 (PRC2) switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the antisense and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates slowly due to reduced growth at low temperatures. The parallel activities of the regulatory steps, which we encapsulate in a mathematical model, creates a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC . Significance The role of non-coding transcription in establishing and maintaining chromatin states is controversial, mainly because of extensive feedbacks complicating analysis of the relationship between co-transcriptional processing, chromatin state and transcription. This controversy has extended to the role of antisense transcription in the Polycomb-mediated epigenetic silencing of Arabidopsis FLC , a key step in the process of vernalization. Here, we show that antisense transcription and PRC2 silence FLC in parallel pathways that are affected by growth dynamics and temperature fluctuations. These features explain the varied importance of antisense transcription in cold-induced FLC epigenetic silencing seen in various studies using different environmental and growth conditions. The parallel repressive inputs and extensive feedbacks make the mechanism counter-intuitive but provide great flexibility to the plant.

Antisense transcription and PRC2 repression function in parallel during vernalization