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

Franziska Turck,Nicolas Buisine,George Coupland,Séverine Gagnot,Marie-Laure Martin-Magniette,Robert A Martienssen,Elodie Guillaume,Sara Farrona,François Roudier,Vincent Colot

doi:10.1371/journal.pgen.0030086.eor

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.

Highlights

Spatial and temporal patterns of gene transcription are central to the developmental programs of plants and animals
We present highly detailed ‘‘epigenomic’’ maps that establish that TFL2/LHP1 associates with a subset of Arabidopsis genes that are marked by tri-methylation of Lysine 27 of histone H3
PCR analysis of chromatin immunoprecipitation (ChIP) DNA recovered from seedlings indicated a clear association of TFL2/LHP1 with the putative target gene FLOWERING LOCUS T (FT), but not with the WRKY33 gene taken as a negative control (Figure 1A)

Summary

Introduction

Spatial and temporal patterns of gene transcription are central to the developmental programs of plants and animals. Proteins that repress transcription of genes that promote flowering or confer floral organ identity were identified by analysis of early-flowering mutants, and several of these proteins were predicted to play roles in chromatin regulation [1,2,3,4,5,6,7]. In Drosophila and mammals, PRC2 catalyzes the tri-methylation of lysine 27 of histone H3 (H3K27me3) of nucleosomes widely located across target developmental genes [11,12]. This tri-methylation is proposed to be recognized by the chromodomain of Polycomb, a central component of PRC1 [13], which maintains the stable transcriptional repression of target genes, precisely how PRC1 operates is unclear. Despite the importance of PRC2 in the regulation of gene expression in plants, plant genomes do not appear to encode homologues of the metazoan PRC1 complex [8]

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