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The exosome complex functions in RNA metabolism and transcriptional gene silencing. Here, we report that mutations of two  Arabidopsis  genes encoding nuclear exosome components  AtRRP6L1  and  AtRRP6L2 , cause de-repression of the main flowering repressor  FLOWERING LOCUS C  ( FLC ) and thus delay flowering in early-flowering  Arabidopsis  ecotypes.  AtRRP6L  mutations affect the expression of known  FLC  regulatory antisense (AS) RNAs AS I and II, and cause an increase in Histone3 K4 trimethylation (H3K4me3) at  FLC . AtRRP6L1 and AtRRP6L2 function redundantly in regulation of  FLC  and also act independently of the exosome core complex. Moreover, we discovered a novel, long non-coding, non-polyadenylated antisense transcript (ASL, for Antisense Long) originating from the  FLC  locus in wild type plants. The AtRRP6L proteins function as the main regulators of ASL synthesis, as these mutants show little or no ASL transcript. Unlike ASI/II, ASL associates with H3K27me3 regions of  FLC , suggesting that it could function in the maintenance of H3K27 trimethylation during vegetative growth. AtRRP6L mutations also affect H3K27me3 levels and nucleosome density at the  FLC  locus. Furthermore, AtRRP6L1 physically associates with the ASL transcript and directly interacts with the  FLC  locus. We propose that AtRRP6L proteins participate in the maintenance of H3K27me3 at  FLC via  regulating ASL. Furthermore, AtRRP6Ls might participate in multiple  FLC  silencing pathways by regulating diverse antisense RNAs derived from the  FLC  locus.

Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis