Arabidopsis Chromatin Remodeler Brahma: Its Functional Interplay with Polycomb Proteins and The REF6 Histone Demethylase

BRAHMA (BRM) is a SWI/SNF-type chromatin remodeling ATPase that plays an important role in regulation of gene expression. Tri-methylation of lysine 27 on histone H3 (H3K27me3) is a histone modification that is associated with transcriptionally repressed genes and catalyzed by Polycomb Group (PcG) proteins. BRM has been proposed to antagonize the function of PcG proteins but the underlying molecular mechanism is unclear. To understand how BRM regulates the function of PcG proteins during plant development, a genome-wide analysis of H3K27me3 in brm mutant was performed using chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Loss of BRM leads to increased H3K27me3 deposition at many Arabidopsis thaliana genes. It is shown that physical presence of BRM reduces the association of PcG proteins with genes. For example, without BRM, an elevated PcG occupancy at the flowering repressor gene SHORT VEGETATIVE PHASE (SVP) is accompanied by increased frequency of the H3K27me3 level and a concomitant reduction of the SVP transcription. Finally, genetic studies using gain- and loss-of-function mutants have established that BRM represses flowering transition by activating SVP transcription. This work highlights a crucial role of BRM in counter-balancing the activity of PcG proteins during plant development. In Arabidopsis, H3K27me3 can be removed by H3K27 demethylase, called RELATIVE OF EARLY FLOWERING 6 (REF6). Even though both REF6 and BRM are thought to activate gene expression at the chromatin level, how their activities are coordinated remains unclear. It is shown here that BRM and REF6 share common DNA binding motifs, and co-localize on more than 1,000 Arabidopsis genes, many of which are involved in responses to various stimuli, including plant hormones. Furthermore, depletion of REF6 reduces the occupancy of BRM at hundreds of BRM-REF6 co-targets, indicating that REF6 facilitates the recruitment of BRM. Consistent with these observations, BRM and REF6 form a protein complex in vivo and co-activate the expression of a set of common genes. Together, these results demonstrate an unanticipated genome-wide coordination between an H3K27 demethylase and the BRM chromatin remodeling protein