Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27

Abstract

TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) is the only Arabidopsis protein with overall sequence similarity to the HETEROCHROMATIN PROTEIN 1 (HP1) family of metazoans and S. pombe. TFL2/LHP1 represses transcription of numerous genes, including the flowering-time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC), as well as the floral organ identity genes AGAMOUS (AG) and APETALA 3 (AP3). These genes are also regulated by proteins of the Polycomb repressive complex 2 (PRC2), and it has been proposed that TFL2/LHP1 represents a potential stabilizing factor of PRC2 activity. Here we show by chromatin immunoprecipitation and hybridization to an Arabidopsis Chromosome 4 tiling array (ChIP-chip) that TFL2/LHP1 associates with hundreds of small domains, almost all of which correspond to genes located within euchromatin. We investigated the chromatin marks to which TFL2/LHP1 binds and show that, in vitro, TFL2/LHP1 binds to histone H3 di- or tri-methylated at lysine 9 (H3K9me2 or H3K9me3), the marks recognized by HP1, and to histone H3 trimethylated at lysine 27 (H3K27me3), the mark deposited by PRC2. However, in vivo TFL2/LHP1 association with chromatin occurs almost exclusively and co-extensively with domains marked by H3K27me3, but not H3K9me2 or -3. Moreover, the distribution of H3K27me3 is unaffected in lhp1 mutant plants, indicating that unlike PRC2 components, TFL2/LHP1 is not involved in the deposition of this mark. Rather, our data suggest that TFL2/LHP1 recognizes specifically H3K27me3 in vivo as part of a mechanism that represses the expression of many genes targeted by PRC2.

Epigenetic Natural Variation in Arabidopsis thaliana

“…Methylation of genes, however, is independent of DDM1, DRM1, DRM2, and CMT3, which are requisite components of the siRNA-mediated silencing pathway [26,27,53], and heterochromatic histone modifications such as H3K9me2 do not associate with regions of genic methylation [17]. Recently, profiles of H3K27me3, H3K27me2, H3K9me2, and H3K9me3 have been obtained using the same microarray platform, and none of these profiles overlapped significantly with genic methylation [54]. The primary basis for this model is a weak correlation between siRNAs and gene methylation (Table 2) [28], but this is probably due to unidentified TE fragments or repeat structure within some methylated genes that can directly recruit the heterochromatic silencing apparatus (Protocol S1).…”

A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem

“…In tfl2 mutants, the main inflorescence shoots are terminated after three to four flowers are created, and lateral shoots are often terminated as a single flower ( Fig. 6D; Takada and Goto 2003;Turck et al 2007;Zhang et al 2007b). In tfl2 mutants (n = 20), KNU-GUS was strongly expressed in flowers, and occasionally the strong ectopic expression was detected in the vasculature of inflorescence stems ( Fig.…”

“…6D-G). TFL2 encodes A. thaliana LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), which epigenetically represses FLOWERING LOCUS C (FLC), AG, and AP3 through the H3K27me3 repressive mark (Sung et al 2006;Turck et al 2007). Genome-wide analysis of LHP1-binding sites showed that the KNU locus is bound by LHP1 in seedlings (Zhang et al 2007b).…”

Regulation of flowering time: all roads lead to Rome

“…Several studies have demonstrated that trimethylation of lysine 27 in the amino terminus of histone H3 (H3K27me3) provides an assembly platform for repressive complexes. In this context it is interesting to note that recent genome-wide surveys indicate that all flowering time genes but CO are H3K27me3 targets [56][57][58]. H3K27 trimethylation is carried out by the polycomb repressive complex 2 (PRC2) and mutants in a number of PRC2 genes [i.e.…”