Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis

Abstract

Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is Lysine 27 of H3 (H3K27), which trimethylation by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatio-temporal patterns of key developmental genes. H3K27 is also subjected to acetylation, found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. In order to decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3K27A variant causes severe developmental defects, part of them reminiscent of PRC2 mutants, part of them new. They include early flowering, increased callus formation, and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.

Manipulating plant development by editing histone methylation with the dCas9 tool: theCUC3boundary gene as a case study

“…Manipulation of histone residues allowed revealing the key role of H3 methylations in animal and plant cell differentiation and specific developmental programs [12][13][14][15] . In a prior study involving the editing of the H3K27 residue in Arabidopsis thaliana, we not only confirmed expected functions for the H3K27me3 mark but also discovered novel roles in cell fates, critical for tissue regeneration and plant architecture through stem tissue differentiation 16 . While such global approaches have provided valuable insights, they affect the entire epigenome simultaneously, making it challenging to pinpoint the direct effect of a specific mark on a target gene 11 .…”

Maintenance and dynamic reprogramming of chromatin organization during development

“…Instead, in euchromatin that comprises most of the genes, transcriptional activity correlates with enrichment in H3K4me3, H3K9ac and/or H2Bubiquitination (Leng et al, 2020), while gene repression is achieved by H3K27me3 deposition by the Polycomb Repressive complex 2 (PRC2; Mozgova & Hennig, 2015; Figure 1). The importance of these histone modifications, especially the Polycomb mark H3K27me3, for plant development has been revealed by genetic approaches either removing histone modifiers (Goodrich et al, 1997), or more recently expressing histone proteins that cannot be post-translationally modified at specific sites (Corcoran et al, 2022;Fal et al, 2022;Xu et al, 2022). Corcoran et al (2022) probed systematically the importance of modifiable histone H4 residues by replacing endogenous H4 genes by transgenes carrying different point mutations, revealing many residues critical for plant survival or development, including correct flowering time.…”

“…(2022) probed systematically the importance of modifiable histone H4 residues by replacing endogenous H4 genes by transgenes carrying different point mutations, revealing many residues critical for plant survival or development, including correct flowering time. Interfering specifically with modifications set on H3K27 by replacing lysine 27 by alanine in a transgene‐encoded H3 resulted in a substantially altered transcriptome when assessed in calli and strong developmental abnormalities partly reminiscent of those found in mutants of histone methyltransferases of the PRC2 complex (Fal et al., 2022). While interpretation of these observations is complicated by the fact that lysine residues can undergo several modifications, these phenotypes confirm the critical role for H3K27me3 in plant development.…”

“…Subtle changes in H3K27me3 levels were also observed, even though they are likely the indirect consequence of altered expression of CURLY LEAF ( CLF ) and SWINGER ( SWN ) coding for histone methyltransferase subunits of the PRC2 complex. Interestingly, whether the K27A mutation was introduced in the H3.1 or the H3.3 variant affected gene expression and plant development in a different manner (Fal et al., 2022; Xu et al., 2022). In both studies, the expression of a mutated version of H3.3 caused more severe developmental defects.…”

Histone variants and modifications during abiotic stress response

“…This mark specifically controls transcriptional repression by a group of genes silenced by PRC1, suggesting the possible function that the K129Ub might have in the dual role of H2A.Z ( Gómez-Zambrano et al., 2019 ). Moreover, a recent preprint suggest that the K27 residue in the histone variant H3.3 is indispensable for many developmental processes that ranges from flowering to callus formation ( Fal et al., 2022 ). Additionally, it has been reported that the SQ motif present in H2A.W.7 prevents the phosphorylation of the KSPK motif, a mark associated with DNA damage response ( Schmücker et al., 2021 ), which indicates that the differences in the variants’ sequences result in diversity in transcriptional regulation.…”