Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis

The methylation of histone 3 lysine 4 (H3K4) is essential for gene activation. Flowering Locus C (FLC), an important flowering repressor, quantitatively regulates flowering time in Arabidopsis and its expression level is coincident with H3K4 trimethylation (H3K4me3) dynamics. The methylation state of FLC chromatin is determined by the balance between methylation and demethylation, which is mediated by histone methyltransferases and demethylases, respectively. However, little is known about the role of histone demethylase(s) in FLC regulation. Here, we characterized the biochemical activity and biological function of a novel JmjC domain-containing H3K4 demethylase, JMJ15, in Arabidopsis. JMJ15, which is a member of the H3K4 demethylase JARID1 family, displayed H3K4me3 demethylase activity both in vitro and in vivo. The mutation of JMJ15 did not produce an obvious phenotype; however, overexpression JMJ15 resulted in an obvious early flowering phenotype, which was associated with the repression of FLC level and reduction in H3K4me3 at the FLC locus, resulting in increased FT expression. Our results suggest that JMJ15 is a novel H3K4 demethylase, involved in the control of flowering time by demethylating H3K4me3 at FLC chromatin when it was overexpressed in Arabidopsis. KEY MESSAGE: Overexpression of a histone H3K4 demethylase, JMJ15, represses FLC expression by decreasing its chromatin H3K4me3 level, thereby controlling flowering time in Arabidopsis.     

The downregulation of FLOWERING LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms

FLOWERING LOCUS C (FLC), a repressor of flowering, is a major determinant of flowering time in Arabidopsis. FLC expression is repressed by vernalization and in plants with low levels of DNA methylation, resulting in early flowering. This repression is not associated with changes of DNA methylation within the FLC locus in either vernalized plants or plants with low levels of DNA methylation. In both cases, there is a reduction of histone H3 trimethyl-lysine 4 (K4) and acetylation of both histones H3 and H4 around the promoter-translation start of FLC. The expression of the two genes flanking FLC is also repressed in both conditions and repression is associated with decreased histone H3 acetylation. The changes in histone modifications at the FLC gene cluster, which are similar in vernalized plants and in plants with reduced DNA methylation, must arise by different mechanisms. VERNALIZATION 1, VERNALIZATION 2 and VERNALIZATION INSENSITIVE 3 modulate FLC expression in vernalized plants; these proteins play no role in the downregulation of FLC in plants with low levels of DNA methylation. Chimeric FLC::GUS transgenes respond to vernalization but these same transgenes show a position-dependent response to low levels of DNA methylation. In plants with reduced DNA methylation, expression of the five MADS AFFECTING FLOWERING (MAF) genes is repressed, suggesting that DNA methylation alters the expression of a trans-acting regulator common to FLC and members of the related MAF gene family. Our observations suggest that DNA methylation is not part of the vernalization pathway.     

Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells

Vernalization promotes flowering in Arabidopsis through epigenetic repression of the floral repressor, FLOWERING LOCUS C (FLC). Vernalization, like other polycomb-mediated repression events, occurs in two stages; FLC repression is established at low temperatures, then maintained during subsequent growth at 22 degrees C. Low temperatures induce VIN3 activity, which is required for changes in histone modifications and the associated FLC repression. Plant polycomb proteins FIE, VRN2, CLF, and SWN, together with VIN3, form a complex that adds histone H3 lysine 27 methylation at FLC in vernalized plants. VRN1 and LHP1 are required for maintenance of FLC repression. Tissue must be undergoing cell division during low-temperature treatments for acceleration of flowering to occur. We show that low-temperature treatments repress FLC in cells that are not mitotically active, but this repression is not fully maintained. Trimethyl-lysine 27 (K27me3), is enriched at the start of the FLC gene during the cold, before spreading across the locus after vernalization. In the absence of DNA replication, K27me3 is added to chromatin at the start of FLC but is removed on return to 22 degrees C. This suggests that DNA replication is essential for maintenance of vernalization-induced repression of FLC.     

Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition

The timing of the developmental transition to flowering is critical to reproductive success in plants. Here, we show that Arabidopsis thaliana homologs of human Lysine-Specific Demethylase1 (LSD1; a histone H3-Lys 4 demethylase) reduce the levels of histone H3-Lys 4 methylation in chromatin of the floral repressor FLOWERING LOCUS C (FLC) and the sporophytically silenced floral repressor FWA. Two of the homologs, LSD1-LIKE1 (LDL1) and LSD1-LIKE2 (LDL2), act in partial redundancy with FLOWERING LOCUS D (FLD; an additional homolog of LSD1) to repress FLC expression. However, LDL1 and LDL2 appear to act independently of FLD in the silencing of FWA, indicating that there is target gene specialization within this histone demethylase family. Loss of function of LDL1 and LDL2 affects DNA methylation on FWA, whereas FLC repression does not appear to involve DNA methylation; thus, members of the LDL family can participate in a range of silencing mechanisms.     

A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression

Flowering time relies on the integration of intrinsic developmental cues and environmental signals. FLC and its downstream target FT are key players in the floral transition in Arabidopsis. Here, we characterized the expression pattern and function of JMJ18, a novel JmjC domain-containing histone H3K4 demethylase gene in Arabidopsis. JMJ18 was dominantly expressed in companion cells; its temporal expression pattern was negatively and positively correlated with that of FLC and FT, respectively, during vegetative development. Mutations in JMJ18 resulted in a weak late-flowering phenotype, while JMJ18 overexpressors exhibited an obvious early-flowering phenotype. JMJ18 displayed demethylase activity toward H3K4me3 and H3K4me2, and bound FLC chromatin directly. The levels of H3K4me3 and H3K4me2 in chromatins of FLC clade genes and the expression of FLC clade genes were reduced, whereas FT expression was induced and the protein expression of FT increased in JMJ18 overexpressor lines. The early-flowering phenotype caused by the overexpression of JMJ18 was mainly dependent on the functional FT. Our findings suggest that the companion cell-dominant and developmentally regulated JMJ18 binds directly to the FLC locus, reducing the level of H3K4 methylation in FLC chromatin and repressing the expression of FLC, thereby promoting the expression of FT in companion cells to stimulate flowering.