A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization

Abstract

Gene activation in eukaryotes frequently involves interactions between chromosomal regions. We have investigated whether higher-order chromatin structures are involved in the regulation of the Arabidopsis floral repressor gene FLC, a target of several chromatin regulatory pathways. Here, we identify a gene loop involving the physical interaction of the 5 0 and 3 0 flanking regions of the FLC locus using chromosome conformation capture. The FLC loop is unaffected by mutations disrupting conserved chromatin regulatory pathways leading to very different expression states. However, the loop is disrupted during vernalization, the cold-induced, Polycomb-dependent epigenetic silencing of FLC. Loop disruption parallels timing of the cold-induced FLC transcriptional shut-down and upregulation of FLC antisense transcripts, but does not need a cold-induced PHD protein required for the epigenetic silencing. We suggest that gene loop disruption is an early step in the switch from an expressed to a Polycomb-silenced state.

The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis

“…As reported previously, loop formation was reduced by vernalization in the wild type (Crevillén et al, 2013). Interestingly, we observed that the FLC loop was more stable after vernalization in both RNAi lines ( Figure 8D), and these observations were in agreement with the expression data and the phenotype observed.…”

“…Surprisingly, the FLC loop was not disturbed by mutations that affect several chromatin regulatory pathways and lead to different expression levels (Crevillén et al, 2013), indicating that expression of FLC can be modulated independently of the spatial organization at this locus. However, the formation of this loop may mediate the vernalization pathway for FLC regulation, since its formation was disrupted during vernalization, concomitant with the downregulation of FLC.…”

“…Recently, Crevillén et al (2013) demonstrated that the FLC locus could make a loop that plays a role in its transcriptional regulation. Since histone depletion facilitates chromatin loops (Diesinger et al, 2010), we performed 3C experiments to explore whether BAF60 could regulate the maintenance of this highorder chromatin structure.…”

“…Since a major conclusion from Crevillén et al (2013) was that the FLC gene loop could be disrupted by vernalization, we analyzed the flowering phenotype of both RNAi lines after vernalization. The vernalization treatment efficiently reduced flowering time in the wild type: as expected, plants displayed a significant reduction of the rosette leaf number at flowering (Student's t test, P = 0.05) and of the number of days to bolting (Student's t test, P = 0.05; Figures 8A and 8B).…”

“…More recently, Crevillén et al (2013) have used quantitative chromosome conformation capture (3C) in a range of Arabidopsis genotypes and showed that higher order chromatin structure is probably involved in FLC regulation. They detected a gene loop at the FLC locus, reflecting interaction between sequences in the FLC 59 flanking region with sequences in the 39 flanking region, and clearly demonstrated that this loop structure could be efficiently disrupted during vernalization.…”