Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana.

Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process.

Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis.

The floral transition marks the switch from vegetative to reproductive growth, and is controlled by different pathways responsive to endogenous and exogenous cues. The developmental switch is accompanied by local changes in chromatin such as histone modifications. In this study we demonstrate large-scale reorganization of chromatin in rosette leaves during the floral transition. An extensive reduction in chromocenters prior to bolting is followed by a recovery of the heterochromatin domains after elongation of the floral stem. The transient reduction in chromocenters is a result of relocation away from chromocenters of methylated DNA sequences, 5S rDNA and interspersed pericentromeric repeats, but not of 45S rDNA or the 180-bp centromere tandem repeats. Moreover, fluorescence in situ hybridization analysis revealed decondensation of chromatin in gene-rich regions. A mutant analysis indicated that the blue-light photoreceptor CRYPTOCHROME 2 is involved in triggering chromatin decondensation, suggesting a light-signaling pathway towards large-scale chromatin modulation.