Chromatin-Dependent Repression of theArabidopsisFloral Integrator Genes Involves Plant Specific PHD-Containing Proteins  

Abstract

The interplay among histone modifications modulates the expression of master regulatory genes in development. Chromatin effector proteins bind histone modifications and translate the epigenetic status into gene expression patterns that control development. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific proteins with a plant homeodomain (PHD) motif, SHORT LIFE (SHL) and EARLY BOLTING IN SHORT DAYS (EBS), function in the chromatin-mediated repression of floral initiation and play independent roles in the control of genes regulating flowering. Previous results showed that repression of the floral integrator FLOWERING LOCUS T (FT) requires EBS. We establish that SHL is necessary to negatively regulate the expression of SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), another floral integrator. SHL and EBS recognize di-and trimethylated histone H3 at lysine 4 and bind regulatory regions of SOC1 and FT, respectively. These PHD proteins maintain an inactive chromatin conformation in SOC1 and FT by preventing high levels of H3 acetylation, bind HISTONE DEACETYLASE6, and play a central role in regulating flowering time. SHL and EBS are widely conserved in plants but are absent in other eukaryotes, suggesting that the regulatory module mediated by these proteins could represent a distinct mechanism for gene expression control in plants.

A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence

“…The abundance of H3K4me3 and H3K9ac histone modifications changes at specific loci during numerous developmental transitions in plants (Kim et al, 2008(Kim et al, , 2009a(Kim et al, , 2012Charron et al, 2009;Adrian et al, 2010;Anzola et al, 2010;van Dijk et al, 2010;Brusslan et al, 2012;Malapeira et al, 2012;López-González et al, 2014;Molitor et al, 2014;Schenke et al, 2014), and thus, it is likely that the final stage of leaf development, leaf senescence, would be accompanied by changes in these two well-characterized histone modifications that positively correlate with gene expression. Leaves were harvested from progressively more senescent plants and subject to RNA-seq and ChIP-seq, so that a direct correlation between gene expression and Table II.…”

HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing

“…In yeast, RPD3, the ortholog of Arabidopsis HDA6, has been shown to be part of a large protein complex that includes transcriptional repressors such as Switch Independent3 and Unscheduled Meiotic gene Expression1 (Grzenda et al, 2009). And there is evidence that plant HDAs also operate in multiprotein complexes containing histone-binding proteins, corepressors, and associated proteins (Gu et al, 2011;Perrella et al, 2013;López-González et al, 2014). It is thus possible that the hda6-8 mutation in the E-R motif affects the interaction of HDA6 with the complex.…”

Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

“…S6). We selected histone marks that are usually located within genes and that were previously analyzed for florigen genes of other plant species (Jiang et al, 2008;Adrian et al, 2010;He, 2012;Sun et al, 2012;Gu et al, 2013;Mascheretti et al, 2013;López-González et al, 2014). Four histone marks usually associated with active transcription were selected for chromatin analysis.…”

“…FT, a phosphatidylethanolamine-binding protein, then moves from leaves through the phloem to the shoot apical meristem (Corbesier et al, 2007;Jaeger and Wigge, 2007), where it interacts with a basic Leu zipper domain transcription factor encoded by FLOWERING LOCUS D (FD) to induce the expression of floral identity genes, such as APETALA1 (Abe et al, 2005;Wigge et al, 2005). Recently, it was shown that chromatin-related mechanisms play an important role in regulating FT expression (He, 2012;Gu et al, 2013;Bu et al, 2014;López-González et al, 2014;Wang et al, 2014).…”