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

Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants

Although histone modifications are linked with chromatin activities such as transcription, proofs of their causal importance remain limited. Sequence variants within each histone family expand chromatin diversity and may carry specific modifications, further raising questions about their coordination. Here, we investigate the role of lysine 4 (K4) in two Arabidopsis H3 variants, H3.1 and H3.3. K4 is essential for H3.3 function but not H3.1 in plant development. Mutating K4 in H3.3 drastically reduced H3K4 methylation levels and mimicked the transcriptomic effects of losing SDG2, the major H3K4 trimethylation (H3K4me3) methyltransferase. Moreover, H3.3K4 and SDG2 are required for de novo gene activation and RNA Pol II elongation. H3K4 methylation is preferentially enriched on H3.3, likely due to the coordinated activity of H3.3 deposition and H3K4 methylation. Furthermore, we reveal the diverse impacts of K4 nearby residue mutations on H3K4 methylation and H3.3 function. These findings highlight H3.3 as a critical substrate for H3K4 methylation, which is important for gene expression regulation.

Whirly Transcription Factor NtWHY1 Positively Regulates the Biosynthesis of Cembranoid Diterpenoids by Directly Targeting NtCBTS in Tobacco

Cembranoid diterpenoids, as crucial secondary metabolites in tobacco, play significant physiological roles and exhibit notable biological activities, while the transcriptional regulators governing their biosynthesis remain largely unexplored. A whirly transcription factor NtWHY1 is screened out by DNA pull down using the promoter of NtCBTS (cembratrien-ol synthase), a known key gene in the pathway of cembranoid diterpenoid biosynthesis. Further experiments revealed that NtWHY1 encodes a protein with dual localization in chloroplasts and the nucleus, and it is highly transcriptionally active in tobacco's glandular trichomes and leaves. The expression level of NtWHY1 is positively correlated with the expression level of NtCBTS, as well as the products of α-cembrenediol (α-CBD) and β-cembrenediol (β-CBD), two main cembranoid diterpenoids in tobacco. We also proved that NtWHY1 can directly bind to the promoter region of NtCBTS, with evidence from chromatin immunoprecipitation (ChIP), dual-Luciferase (Dual-LUC) and electrophoretic mobility shift (EMSA) assays. Furthermore, ChIP assays have revealed that NtWHY1 silencing is correlated with reduced H3K9 acetylation and increased H3K27 methylation levels within the promoter region of NtCBTS. Collectively, our results elucidate a novel regulatory role of NtWHY1 in the biosynthesis of cembranoid diterpenoids, thereby advancing our understanding of plant secondary metabolism.

Using Callus as an Ex Vivo System for Chromatin Analysis

Next-generation sequencing has revolutionized epigenetics research, enabling a comprehensive analysis of DNA methylation and histone modification profiles to explore complex biological systems at unprecedented depth. Deciphering the intricate epigenetic mechanisms that regulate gene activity presents significant challenges, including the issue of analyzing heterogeneous cell populations in bulk. Bulk analysis introduces bias and can obscure crucial information by averaging readouts from distinct cells. Various approaches have been developed to address this issue, such as cell-type-specific enrichment or single-cell sequencing techniques. However, the need for transgenic lines with fluorescent markers, along with technical challenges such as efficient protoplast isolation and low yield, limits their widespread adoption and use in multi-omic studies. This review discusses the pros and cons of these approaches, providing a valuable basis for selecting the most suitable strategy to minimize heterogeneity. We will also highlight the use of cotyledon-derived callus as an ex vivo system as a simple, accessible, and robust platform for enabling high-throughput multi-omic analyses.

The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions

Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.

Plant histone variants at the nexus of chromatin readouts, stress and development

Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.