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

Abstract

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.

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

“…At1g54440 encodes AtRRP6L1, a nuclear subunit that associates with the exosome core complex. AtRRP6L1 has been reported to function in the processing of long non-coding RNAs (lncRNAs) involved in epigenetic silencing (Shin and Chekanova, 2014). It also participates in the retention of Pol V transcribed scaffold lncRNAs through a pathway independent of exosome-mediated RNA degradation (Zhang et al, 2014a).…”

Functions of plants long non-coding RNAs

“…Probably, the repression of distal COOLAIR transcription, the degradation products of distal forms of COOLAIR, or the degradation process itself, is the signal for recruiting FLD to FLC chromatin and decreases H3K4 dimethylation levels. Interestingly, recent data showed that exosome components RRP6L-1 and -2 are essential for repression of FLC through modulating different COOLAIR expression [56].…”

Analysis of Rice Genome Long Non-Coding RNA Sequences

“…In Arabidopsis, lncRNAs such as COLDAIR (cold-assisted intronic non-coding RNA) and COOLAIR (cold induced long antisense intragenic RNA) have been demonstrated to mediate chromatin modifying activities in transcriptional silencing of FLC during veRNAlization [10,11]. Another antisense lncRNA, ASL, a nonpolyadenylated transcript, has been discovered and is implicated in epigenetic silencing of FLC [12]. LincRNAs such as AT4 and IPS1 (INDUCED BY PHOSPHATE STARVATION1) act as decoys of miRNAs by a target mimicry mechanism.…”