The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis

Abstract

The histone H3 family in animals and plants includes replicative H3 and non-replicative H3.3 variants. H3.3 preferentially associates with active transcription, yet its function in development and transcription regulation remains elusive. The floral transition in Arabidopsis (Arabidopsis thaliana) involves complex chromatin regulation at a central flowering repressor FLOWERING LOCUS C (FLC). Here we show that H3.3 upregulates FLC expression and promotes active histone modifications Histone H3 lysine 4 trimethylation (H3K4me3) and Histone H3 lysine 36 trimethylation (H3K36me3) at the FLC locus. The FLC activator FRIGIDA (FRI) directly mediates H3.3 enrichment at FLC, leading to chromatin conformation changes and further induction of active histone modifications at FLC. Moreover, the antagonistic H3.3 and H2A.Z act in concert to activate FLC expression, likely by forming unstable nucleosomes ideal for transcription processing. We also show that H3.3 knockdown leads to H3K4me3 reduction at a subset of particularly short genes, suggesting the general role of H3.3 in promoting H3K4me3. The finding that H3.3 stably accumulates at FLC in the absence of H3K36me3 indicates that the H3.3 deposition may serve as a prerequisite for active histone modifications. Our results reveal the important function of H3.3 in mediating the active chromatin state for flowering repression.

Recent advances in the chromatin-based mechanism of FLOWERING LOCUS C repression through autonomous pathway genes

“…In contrast to the GH1-HMGA family proteins, the histone variant H3.3 appears to stabilize FLC looping by binding at both ends of FLC gene (Zhao F. et al, 2021). Importantly, h3.3 knock-down mutants (h3.3kd) consistently show reduced FLC looping and decreased FLC level (Zhao F. et al, 2021). Therefore, it is likely that the opposite effects of GH1-HMGA family proteins and H3.3 for the FLC looping may be associated with their antagonistic function on FLC expression.…”

“…However, the causal relationship between the chromatin looping and the repression of FLC by GH1-HMGA family proteins should be validated in the future study. In contrast to the GH1-HMGA family proteins, the histone variant H3.3 appears to stabilize FLC looping by binding at both ends of FLC gene (Zhao F. et al, 2021). Importantly, h3.3 knock-down mutants (h3.3kd) consistently show reduced FLC looping and decreased FLC level (Zhao F. et al, 2021).…”

Cap‐binding complex assists RNA polymerase II transcription in plant salt stress response

“…Plant materials were fixed with 1% formaldehyde and ChIP experiments were performed with sonicated chromatin as previously described (Zhao et al, 2021). Immunoprecipitation was carried out with anti-Myc (Easybio, BE2011), anti-H3K4me3 (Abcam; ab8580) or anti-Pol II Ser2P (Abcam; ab5095) antibody.…”

Deposition and eviction of histone variants define functional chromatin states in plants

“…Instead, reduction in H3.3 reduces gene body methylation and increases H2A.Z and linker histone H1 occupancy over gene bodies. Notwithstanding the modest changes in gene expression, diverse developmental defects are observed in H3.3 KD plants including late flowering due to a role of H3.3 in regulating expression of FLOWERING LOCUS C (FLC) [41]*. Indeed, FLC expression and H3.3 deposition is enhanced in the presence of functional FRIGIDA (FRI), a component of the transcription activator complex FRI-C, which directly recruits the H3.3 chaperone HIRA to FLC [41]*.…”

“…This could be a compensatory mechanism to ensure nucleosome occupancy or their assembly at specific loci may directly affect gene expression. Even though most of the atypical H3 variants are expressed in specific cells, it will be interesting to investigate whether they are incorporated genome-wide like H3.10 or whether they could be deposited at specific sets of genes, as shown for the deposition of H3.3 at the FLC locus by recruitment of HIRA via FRI [41]*. To understand where and how histone variants will exert their function, it is important to consider the different modes and machineries of deposition and exchange.…”