The plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution

Maintenance and dynamic reprogramming of chromatin organization during development

Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.

The Histone Variant H3.3 Is Required for Plant Growth and Fertility in Arabidopsis

Histones are the core components of the eukaryote chromosome, and have been implicated in transcriptional gene regulation. There are three major isoforms of histone H3 in Arabidopsis. Studies have shown that the H3.3 variant is pivotal in modulating nucleosome structure and gene transcription. However, the function of H3.3 during development remains to be further investigated in plants. In this study, we disrupted all three H3.3 genes in Arabidopsis. Two triple mutants, h3.3cr-4 and h3.3cr-5, were created by the CRISPR/Cas9 system. The mutant plants displayed smaller rosettes and decreased fertility. The stunted growth of h3.3cr-4 may result from reduced expression of cell cycle regulators. The shorter stamen filaments, but not the fertile ability of the gametophytes, resulted in reduced fertility of h3.3cr-4. The transcriptome analysis suggested that the reduced filament elongation of h3.3cr-4 was probably caused by the ectopic expression of several JASMONATE-ZIM DOMAIN (JAZ) genes, which are the key repressors of the signaling pathway of the phytohormone jasmonic acid (JA). These observations suggest that the histone variant H3.3 promotes plant growth, including rosette growth and filament elongation.

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.

Mitotic inheritance of genetic and epigenetic information via the histone H3.1 variant

The replication-dependent histone H3.1 variant, ubiquitous in multicellular eukaryotes, has been proposed to play key roles during chromatin replication due to its unique expression pattern restricted to the S phase of the cell cycle. Here, we describe recent discoveries in plants regarding molecular mechanisms and cellular pathways involving H3.1 that contribute to the maintenance of genomic and epigenomic information. First, we highlight new advances concerning the contribution of the histone chaperone CAF-1 and the TSK-H3.1 DNA repair pathway in preventing genomic instability during replication. We then summarize the evidence connecting H3.1 to specific roles required for the mitotic inheritance of epigenetic states. Finally, we discuss the recent identification of a specific interaction between H3.1 and DNA polymerase epsilon and its functional implications.

Advances in biological functions and mechanisms of histone variants in plants

Nucleosome is the basic subunit of chromatin, consisting of approximately 147bp DNA wrapped around a histone octamer, containing two copies of H2A, H2B, H3 and H4. A linker histone H1 can bind nucleosomes through its conserved GH1 domain, which may promote chromatin folding into higher-order structures. Therefore, the complexity of histones act importantly for specifying chromatin and gene activities. Histone variants, encoded by separate genes and characterized by only a few amino acids differences, can affect nucleosome packaging and stability, and then modify the chromatin properties. Serving as carriers of pivotal genetic and epigenetic information, histone variants have profound significance in regulating plant growth and development, response to both biotic and abiotic stresses. At present, the biological functions of histone variants in plant have become a research hotspot. Here, we summarize recent researches on the biological functions, molecular chaperons and regulatory mechanisms of histone variants in plant, and propose some novel research directions for further study of plant histone variants research field. Our study will provide some enlightens for studying and understanding the epigenetic regulation and chromatin specialization mediated by histone variant in plant.

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

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), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is 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. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3^K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3^K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are 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.

Histone variants and modifications during abiotic stress response

Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.

Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis

The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in endowing seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5' gene end distribution and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3' gene end, correlating with gene body DNA methylation and the restriction of chromatin accessibility and cryptic transcription at this region. Our results suggest a fundamental role of H3.3 in initiating chromatin accessibility at regulatory regions in seed and licensing the embryonic to post-embryonic transition.

Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii

Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α-linolenic acid (ALA). Here, we report chromosome-level genome assembly (12.28 Gb) of P. ostii. In contrast to monocots with giant genomes, tree peony does not appear to have undergone lineage-specific whole-genome duplication. Instead, explosive LTR expansion in the intergenic regions within a short period (~ two million years) may have contributed to the formation of its giga-genome. In addition, expansion of five types of histone encoding genes may have helped maintain the giga-chromosomes. Further, we conduct genome-wide association studies (GWAS) on 448 accessions and show expansion and high expression of several genes in the key nodes of fatty acid biosynthetic pathway, including SAD, FAD2 and FAD3, may function in high level of ALAs synthesis in tree peony seeds. Moreover, by comparing with cultivated tree peony (P. suffruticosa), we show that ectopic expression of class A gene AP1 and reduced expression of class C gene AG may contribute to the formation of petaloid stamens. Genomic resources reported in this study will be valuable for studying chromosome/genome evolution and tree peony breeding.

Mutation of histone H3 serine 28 to alanine influences H3K27me3-mediated gene silencing in Arabidopsis thaliana

Histone modifications are essential for chromatin activity and play an important role in many biological processes. Trimethylation of histone H3K27 (H3K27me3) is a repressive modification established by Polycomb Repressive Complex 2 (PRC2). Although the presence of the histone H3 serine 28 phosphorylation (H3S28ph) modification at adjacent amino acid residues has both positive and negative effects on Polycomb silencing in mammals, little is known about the effect of H3S28ph on H3K27me3-mediated gene silencing in plants. In this study, we show that mutating H3S28A in Arabidopsis (Arabidopsis thaliana) causes a dominant-negative effect that leads to an early-flowering phenotype by promoting the expression of flowering-promoting genes independently of abnormal cell division. While H3S28ph levels decreased due to the H3S28A mutation, H3K27me3 levels at the same loci did not increase. Moreover, we observed decreased H3K27me3 levels at some known PRC2 target genes in H3.3S28A transgenic lines, rather than the expected enhanced H3K27me3-mediated silencing. In line with the reduced H3K27me3 levels, the expression of the PRC2 catalytic subunits CURLY LEAF and SWINGER decreased. Taken together, these data demonstrate that H3.3S28 is required for PRC2-dependent H3K27me3-mediated silencing in Arabidopsis, suggesting that H3S28 has a noncanonical function in H3K27me3-mediated gene silencing.

DNA polymerase epsilon binds histone H3.1-H4 and recruits MORC1 to mediate meiotic heterochromatin condensation

Heterochromatin is essential for genomic integrity and stability in eukaryotes. The mechanisms that regulate meiotic heterochromatin formation remain largely undefined. Here, we show that the catalytic subunit (POL2A) of Arabidopsis DNA polymerase epsilon (POL ε) is required for proper formation of meiotic heterochromatin. The POL2A N terminus interacts with the GHKL adenosine triphosphatase (ATPase) MORC1 (Microrchidia 1), and POL2A is required for MORC1's localization on meiotic heterochromatin. Mutations affecting the POL2A N terminus cause aberrant morphology of meiotic heterochromatin, which is also observed in morc1. Moreover, the POL2A C-terminal zinc finger domain (ZF1) specifically binds to histone H3.1-H4 dimer or tetramer and is important for meiotic heterochromatin condensation. Interestingly, we also found similar H3.1-binding specificity for the mouse counterpart. Together, our results show that two distinct domains of POL2A, ZF1 and N terminus bind H3.1-H4 and recruit MORC1, respectively, to induce a continuous process of meiotic heterochromatin organization. These activities expand the functional repertoire of POL ε beyond its classic role in DNA replication and appear to be conserved in animals and plants.

The Role of the TSK/TONSL-H3.1 Pathway in Maintaining Genome Stability in Multicellular Eukaryotes

Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with H3.3, the H3.1 variant has been hypothesized to play unique roles in cells, as it is specifically expressed and inserted into chromatin during DNA replication. However, identifying a function that is unique to H3.1 during replication has remained elusive. In this review, we discuss recent findings regarding the involvement of the H3.1 variant in regulating the TSK/TONSL-mediated resolution of stalled or broken replication forks. Uncovering this new function for the H3.1 variant has been made possible by the identification of the first proteins containing domains that can selectively bind or modify the H3.1 variant. The functional characterization of H3-variant-specific readers and writers reveals another layer of chromatin-based information regulating transcription, DNA replication, and DNA repair.

Histone Variants in the Specialization of Plant Chromatin

The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.

The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication

The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. We found that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed histone H3 lysine 27 monomethylation in plants depends on H3.1, TSK, and DNA polymerase theta (Pol θ). This work reveals an H3.1-specific function during replication and a common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone monomethyltransferases and reading of the H3.1 variant.

Histone variants take center stage in shaping the epigenome

The dynamic properties of the nucleosome are central to genomic activity. Variants of the core histones that form the nucleosome play a pivotal role in modulating nucleosome structure and function. Despite often small differences in sequence, histone variants display remarkable diversity in genomic deposition and post-translational modification. Here, we summarize the roles played by histone variants in the establishment, maintenance and reprogramming of plant chromatin landscapes, with a focus on histone H3 variants. Deposition of replicative H3.1 during DNA replication controls epigenetic inheritance, while local replacement of H3.1 with H3.3 marks cells undergoing terminal differentiation. Deposition of specialized H3 variants in specific cell types is emerging as a novel mechanism of selective epigenetic reprogramming during the plant life cycle.

Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory

Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.

Similar yet critically different: the distribution, dynamics and function of histone variants

Organization of the genetic information into chromatin plays an important role in the regulation of all DNA template-based reactions. The incorporation of different variant versions of the core histones H3, H2A, and H2B, or the linker histone H1 results in nucleosomes with unique properties. Histone variants can differ by only a few amino acids or larger protein domains and their incorporation may directly affect nucleosome stability and higher order chromatin organization or indirectly influence chromatin function through histone variant-specific binding partners. Histone variants employ dedicated histone deposition machinery for their timely and locus-specific incorporation into chromatin. Plants have evolved specific histone variants with unique expression patterns and features. In this review, we discuss our current knowledge on histone variants in Arabidopsis, their mode of deposition, variant-specific post-translational modifications, and genome-wide distribution, as well as their role in defining different chromatin states.

A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.

The evolution and functional divergence of the histone H2B family in plants

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.

In addition to well-studied variants from core histones families H2A and H3, we report that land plants diversified their H2B family, leading to specialized H2B variants with specific patterns of expression, genomic distributions and properties.

The atypical histone variant H3.15 promotes callus formation in Arabidopsis thaliana

Plants are capable of regenerating new organs after mechanical injury. The regeneration process involves genome-wide reprogramming of transcription, which usually requires dynamic changes in the chromatin landscape. We show that the histone 3 variant HISTONE THREE RELATED 15 (H3.15) plays an important role in cell fate reprogramming during plant regeneration in Arabidopsis H3.15 expression is rapidly induced upon wounding. Ectopic overexpression of H3.15 promotes cell proliferation to form a larger callus at the wound site, whereas htr15 mutation compromises callus formation. H3.15 is distinguished from other Arabidopsis histones by the absence of the lysine residue 27 that is trimethylated by the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) in constitutively expressed H3 variants. Overexpression of H3.15 promotes the removal of the transcriptional repressive mark H3K27me3 from chromatin, which results in transcriptional de-repression of downstream genes, such as WUSCHEL RELATED HOMEOBOX 11 (WOX11). Our results reveal a new mechanism for a release from PRC2-mediated gene repression through H3.15 deposition into chromatin, which is involved in reprogramming cell fate to produce pluripotent callus cells.

H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity

The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis

The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes^1-5. In plants, timely transition to a flowering state is crucial for successful reproduction^6-9. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana^10,11. We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.