Mind the gap: Epigenetic regulation of chromatin accessibility in plants

Abstract

Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.

Advances Box.

Technological advances have enabled the precise study of chromatin accessibility and 3D structure.

Both the Polycomb complexes PRC1 and PRC2 jointly and independently regulate gene expression and chromatin architecture.

Significant progress in understanding the role of histone variants in plants highlights their importance in chromatin regulation.

Recent characterization of the composition of several chromatin regulators confirms their conservation but also brings to light new plant-specific subunits and complexes.

Phase separation adds a new layer of regulation to consider in chromatin organization.

Outstanding Questions Box.

How are chromatin regulators assembled in plant cells?

What is the direct impact of internal and external inputs on the function of these regulators?

What is the impact of histone variants, histone PTMs, and DNA methylation on their functionality?

What is the contribution of these regulators to the cell type–specific chromatin accessibility landscape?

What is the degree of cooperation among various chromatin regulators over single loci?

What are the functions of the plant-specific complexes and subunits?

Addressing the correlation vs causation question. How do epigenetic marks directly impact on processes like chromatin accessibility control?

Regulation of chromatin accessibility

In eukaryotic cells, DNA and histones tightly associate to form chromatin, a structure that plays an essential role in compacting the DNA molecule within the reduced space of the nucleus and that regulates various nuclear processes, including transcription, replication, repair, and recombination. These roles are strongly influenced by the presence and organization of nucleosomes, the basic unit of chromatin, which consists of a protein octamer made up of one histone H3-H4 tetramer and two H2A-H2B dimers wrapped by 147 bp of DNA (Kornberg 1974; Luger et al. 1997) (Fig. 1). Besides representing the first layer of compaction in the genome, nucleosomes significantly contribute to chromatin accessibility because nucleosome-bound DNA is less accessible to most DNA-binding proteins. Moreover, linker DNA, the DNA between nucleosomes, can associate with the H1 linker histone, further promoting chromatin compaction (Hergeth and Schneider 2015). Importantly, nucleosomes not merely act as repressors of chromatin accessibility but also serve as central signaling hubs in the nucleus. This occurs through their diverse histone variants and tail modifications, which act as platforms for the recruitment of histone readers that mediate downstream signaling events (Klemm et al. 2019). The density, composition, and modifications of nucleosomes vary across the genome, defining distinct functional regions. For instance, constitutive heterochromatin is densely packed with nucleosomes that incorporate specific histone variants and post-translational modifications (PTMs). In contrast, regulatory elements within euchromatin, such as insulators, enhancers, and promoters, are nucleosome depleted or have fewer nucleosomes, reflecting the necessity for these regions to remain accessible to DNA readers like the transcription machinery, among others (Klemm et al. 2019) (Fig. 1).

Figure 1.

Chromatin accessibility and compaction across multiple levels. The fundamental unit of chromatin is the nucleosome, which results from the interaction between DNA and histones. Both of these components can undergo epigenetic modifications, such as histone variants and PTMs, in addition to DNA methylation. In euchromatic regions, chromatin organization facilitates access to the transcriptional machinery, aided by the actions of chromatin remodelers and modifiers that establish specific configurations and modifications to promote transcription. In contrast, facultative and constitutive heterochromatic regions, characterized by marks like H3K27me3 and H3K9me2, among others, adopt a condensed conformation that restricts access to DNA and transcription. Chromatin also forms higher-order structures organized by structural proteins, including loops, topologically associated domains (TADs) that bring functionally related regions in close proximity, and compartments A and B, which are formed by large clusters of euchromatin and heterochromatin, respectively. Lastly, chromosomes occupy distinct and exclusive territories within the nucleus. The circles connecting the chromatin loops represent structural proteins involved in higher-order chromatin associations. Created with BioRender.com.

Numerous factors influence the DNA-histone and histone-histone interactions, impacting nucleosome stability and positioning (Mansisidor and Risca 2022). One such factor is the DNA sequence composition, which determines the bendability of DNA around the nucleosome. Genomic studies using naked DNA and purified histones have demonstrated that DNA alone can partially dictate nucleosome positioning, although this is not sufficient to recapitulate the in vivo nucleosome landscape (Zhang et al. 2009, 2011; Krietenstein et al. 2016). Epigenetic marks, such as DNA methylation, histone variants, and histone modifications, directly or indirectly affect nucleosome stability and positioning (see following sections). Additionally, histone chaperones and ATP-dependent remodelers play crucial roles in nucleosome assembly, disassembly, positioning, stability, and composition (see Box 1 and section "Function of Snf2 chromatin remodelers"). Furthermore, DNA binding proteins like transcription factors (TFs) can influence the presence and positioning of nucleosomes because they may compete for DNA binding or recruit chromatin remodelers and other complexes that further modulate chromatin accessibility. Although presence of a nucleosome normally prevents TF binding, certain types of TFs known as pioneering factors are able to associate with nucleosomal DNA and carry out their function (Lai et al. 2018). For example, two recent studies reported the pioneering function of the flowering master regulator LEAFY, which associates with nucleosomes to promote chromatin opening at key floral regulatory targets (Jin et al. 2021; Lai et al. 2021).

BOX 1. Factors Involved in Nucleosome Assembly and Deposition.

Histone chaperones play an essential role in histone storage, transport, modification, assembly, and turnover by interacting with pairs of canonical H3-H4 and H2A-H2B histones or pairs that specifically incorporate histone variants. Additionally, some ATP-dependent chromatin remodelers can also participate in the nucleosome assembly and deposition.

In this box, we briefly summarize the current knowledge about chaperones and remodelers in plants and highlight areas that require further study.

H3.1-H4, H3.3-H4, and cenH3-H4 Assembly and Deposition

The assembly and deposition of H3.1-H4 are replication-dependent and are mediated by the Chromatin assembly factor 1 (CAF1) chaperone complex. In contrast, H3.3 is deposited in a replication-independent manner, either by the Histone regulator A complex (HIRA) (assisted by Anti-Silencing Function 1 chaperones) (Zhong et al. 2022) or by the ALPHA-THALASSEMIA MENTAL RETARDATION SYNDROME, X-LINKED (ATRX) chromatin remodeler (Wang et al. 2018). The deposition of centromeric H3 (cenH3) is regulated by the conserved NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) chaperone in Arabidopsis (Le Goff et al. 2020). Conversely, its removal, at least in pollen vegetative cells, is mediated by the CELL DIVISION CYCLE 48A (CDC48A) chaperone, involved in the SUMO-targeted cenH3 degradation (Mérai et al. 2014).

H2A-H2B, H2A.Z-H2B, and H2A.W-H2B Assembly and Deposition

In plants, the transport and deposition of H2A-H2B are mediated by the histone chaperones NUCLEOSOME ASSEMBLY PROTEIN (NAP1;1 to NAP1;4) and NAP1-Related Protein 1 (NRP1) and NRP2 (Zhou et al. 2015; Luo et al. 2020a). H2A.Z-H2B is deposited by the SWR1 chromatin remodeler. Additionally, Arabidopsis thaliana Chaperones for H2A.Z-H2B 1A (AtChz1A) and AtChz1B assist SWR1 for H2A.Z deposition (Wu et al. 2023b), while chaperones NRP1/2 reduce the excessive H2A.Z deposition mediated by SWR1 at heterochromatin (Wang et al. 2020).

The INO80 remodeler also participates in H2A.Z-H4 homeostasis in plants although its specific function remains unclear (see section "Function of Snf2 chromatin remodelers"). On the other hand, DDM1 mediates H2A.W deposition, replaces H2A.Z, and facilitates DNA unwrapping for access to DNA methyltransferases (Jamge et al. 2023; Osakabe et al. 2023). Recent data also suggests that DDM1 promotes H3.3-H3.1 exchange during this process (Lee et al. 2023).

Canonical H2A-H2B and H3-H4, and H1 Assembly and Deposition

Some chaperones, like nucleoplasmins and Facilitates Chromatin Transcription (FACT), can interact with both H2A-H2B and H3-H4 pairs, participating in general nucleosome assembly and transcription-mediated nucleosome assembly/disassembly, respectively (Grasser 2020; Kumar and Vasudevan 2020). Interestingly, a recent study revealed an unexpected role for a predicted histone deacetylase as a nucleoplasmin with chaperone activity (Bobde et al. 2022). Furthermore, it has been recently demonstrated that the FACT complex is involved in H2A.X deposition in mammals (Piquet et al. 2018), although whether this role is conserved in plants remains unclear.

Importantly, to our knowledge, designated H1 chaperones have not been reported in plants, although similar functions have been characterized in other organisms (Shintomi et al. 2005; Gadad et al. 2011; Wang et al. 2012; Kajitani et al. 2017).

Importantly, the landscape of nucleosomes and linker histones is dynamic in the nucleus. External and internal stimuli, such as environmental stresses and developmental programs, trigger genome-wide changes in chromatin accessibility as a result of dynamic changes in processes like transcription, replication, and mitosis (Feng et al. 2022; Kim et al. 2022; Wu et al. 2022). These events are partly mediated by stimuli-triggered reprogramming of the epigenome and the mobilization of specific chromatin regulators, collectively shaping the nucleosome landscape (Perrella et al. 2020). Technological advances in methods for profiling chromatin accessibility have played a pivotal role in the recent surge of studies investigating chromatin dynamics in various plants, growth conditions, and cell types (Fig. 2).

Figure 2.

Current methods to profile chromatin accessibility and conformation in plants. A) FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing): Chromatin crosslinked with formaldehyde is fragmented through sonication, and the accessible (or nucleosome-free) DNA is isolated using a phenol-chloroform–based phase separation, and then used for library preparation. FAIRE-seq stands out as a simple and cost-effective, non-enzymatic method that enables the genome-wide characterization of open chromatin regions (Baum et al. 2020). B) MNase-seq: A brief enzymatic incubation of chromatin with Micrococcal Nuclease (MNase) digests internucleosomal DNA, allowing the isolation of nucleosome-bound DNA. Subsequently, the DNA corresponding to mononucleosomes (147 bp) is isolated, purified, and then used for library preparation. This method enables precise identification of nucleosome positions. By using different enzyme concentrations or incubation times, one can distinguish stable nucleosomes from those with high turnover, known as fragile nucleosomes (Zhang and Jiang 2018). Variants of this method, such as MNase-defined cistrome-Occupancy Analysis sequencing (MOA-seq) and MNase hypersensitivity sequencing (MH-seq), employ milder MNase treatments to recover subnucleosomal DNA fragments that represent TF footprints (Tao et al. 2020; Zhao et al. 2020; Savadel et al. 2021). C) ATAC-seq: The hyperactive Tn5 transposase simultaneously cleaves and attaches sequencing adapters to accessible DNA, expediting library construction after DNA isolation and size selection. Tagmentation has led to shorter, more streamlined protocols with reduced input requirements (enabling single-cell studies), making ATAC-seq the gold standard for characterizing highly accessible chromatin regions today (Bajic et al. 2018). Recent advances in single-cell technologies have led to the development of single-cell ATAC-seq protocols in plants (scATAC-seq) (Dorrity et al. 2021; Marand et al. 2021). Additionally, recent protocols like Single-cell combinatorial fluidic indexing ATAC-seq (scifi-ATAC-seq) aim to enhance throughput (Zhang et al. 2023b). Moreover, the Cleavage Under Targets and Tagmentation (CUT&Tag) method, which coupled the Tn5-based tagmentation with antibody-specific chromatin targeting, can be used to study chromatin accessibility over specific chromatin regions (Henikoff et al. 2020). D) Hi-C: Crosslinked chromatin is digested, biotinylated, and then re-ligated in a manner that exclusively forms ligation products from fixed DNA-DNA interactions. These DNA hybrids are subsequently sheared and purified by pulling down biotin before library construction (Pérez-de Los Santos et al. 2022). A variant of this method, known as Open Chromatin Enrichment and Network Hi-C (OCEAN-C), integrates Hi-C and FAIRE-seq protocols to identify interactions between open chromatin regions in species with large genomes, such as wheat (Yuan et al. 2022). Combined INTACT and Hi-C protocols have recently been employed to isolate cells from the endosperm and leaves, profiling their 3D organization (Yadav et al. 2021). Created with BioRender.com.

Beyond the linear nucleosome organization, genomes are organized in higher-order structures, including loops, topological associated domains, compartments, and chromosome territories (Doğan and Liu 2018) (Fig. 1). All these assemblies depend on the function of diverse factors, including remodelers and structural proteins (Magaña-Acosta and Valadez-Graham 2020). A recent study in Arabidopsis reported the impact of four ATP-dependent remodeler families on 3D chromatin structure (Yang et al. 2022). Results indicated that all studied families induced switches between compartments and weakened compartmental strength. Additionally, both internal and external stimuli can trigger changes in 3D structure. For instance, recent research revealed the global impact of heat stress weakening chromatin compartmentalization (Sun et al. 2020). Importantly, the formation of membraneless biomolecular condensates through phase separation by chromatin and chromatin-associated proteins has emerged in recent years as an important mechanism of regulation of chromatin organization (Narlikar 2020; Wang et al. 2023e).

In the forthcoming sections of this review, we will focus on current knowledge and recent findings regarding the role of epigenetic marks, including DNA methylation, histone modifications, and histone variants, as well as histone chaperones and ATP-dependent remodelers in chromatin accessibility and nucleosome dynamics in plants.

DNA methylation and chromatin accessibility

DNA methylation is a conserved epigenetic mark found across eukaryotes that participates in various nuclear processes such as gene expression, DNA repair, and recombination (Zhang et al. 2018b). In plants, methylation is established by DNA methyltransferases (DNMTs), namely METHYLTRANSFERASE 1 (MET1), Chromomethylases (CMTs), and DOMAINS REARRANGED METHYLASE (DRM), and occurs in the CG, CHG, and CHH sequence contexts (where H stands for A, T, or C). Demethylation pathways counteract the function of these enzymes to maintain DNA methylation homeostasis across the genome throughout a plant’s life (Zhang et al. 2018b). The relationship between DNA methylation and chromatin compaction in plants is known for long time. For instance, mutations in the main CG methyltransferase, MET1, causes global loss of DNA methylation and chromatin decondensation at chromocenters (Soppe et al. 2002). A recent study examined changes in chromatin accessibility by ATAC-seq in multiple DNA methylation mutants affecting various methylation pathways (Zhong et al. 2021). The results indicate that simultaneous loss of DNA methylation over the CG, CHG, and CHH contexts is required to promote accessibility. Conversely, loss of CG methylation over gene bodies triggered either no change or reduced accessibility. Moreover, the increase in accessibility was linked to an increase in long-range interactions, as measured by Hi-C. Importantly, these gains in chromatin accessibility were not always correlated with derepression of gene expression, indicating an influence of DNA methylation on chromatin compaction and 3D architecture that operates independently of transcription dynamics (Zhong et al. 2021). Similar conclusions were drawn from a Hi-C study in rice that examined the impact of OsMET1 mutation on 3D architecture (Wang et al. 2022a).

The influence of DNA methylation on chromatin accessibility can be explained through different mechanisms (Li et al. 2022). DNA methylation can influence the geometry and mechanical properties of DNA and, consequently, nucleosome dynamics, although its specific role is still controversial and requires further investigation (Li et al. 2022). It can also prevent the binding of multiple TFs to DNA (O’Malley et al. 2016) (Fig. 3A). This can indirectly influence the deposition and positioning of nucleosomes competing with a TF for a DNA region. Additionally, nucleosome-associated DNA is a preferred substrate for DNMTs compared with linker DNA, reinforcing the crosstalk between DNA methylation and nucleosome positioning (Chodavarapu et al. 2010). Importantly, this requires the function of the DECREASED DNA METHYLATION 1 (DDM1) remodeler to allow access to the DNMTs (Lyons and Zilberman 2017). Lastly, DNA methylation can be recognized by reader proteins that can lead to silencing and chromatin compaction (Fig. 3A). For example, the mammalian Methyl CpG binding protein 2 (MeCP2) can read methylated DNA and recruit histone deacetylases (HDACs), causing chromatin compaction and silencing (Nan et al. 1998). Notably, recent studies in plants reported the function of the DNA methylation readers Methyl-CpG-binding domains 5 (MBD5) and MBD6 in a plant repressor complex that presents various subunits, including the J-domain protein SILENZIO and the α-crystalline domain containing protein 15 (ACD15) and ACD21 (Ichino et al. 2021, 2022; Boone et al. 2023). Importantly, this repressor complex operates through an unknown mechanism that does not seem to involve HDACs, like mammalian MeCP2. Additionally, DNA methylation recruits the plant Microrchidia (MORC) proteins, at least in part through their interaction with the RNA-directed DNA methylation (RdDM) DNA methylation reader module SUVH2/9-DRD1-DMS3-RDM1 (Lorković et al. 2012; Liu et al. 2014; Gallego-Bartolomé et al. 2019), to promote gene silencing and chromatin compaction (Moissiard et al. 2012; Xue et al. 2021b).

Figure 3.

Epigenetic regulation of chromatin accessibility. A) DNA methylation exerts a negative influence on chromatin accessibility by impeding TF binding to their targets and promoting the recruitment of reader complexes that lead to gene silencing and chromatin compaction. B) Histone PTMs exert both direct and indirect effects on nucleosome stability and chromatin compaction. Histone acetylation, catalyzed by HATs and removed by HDACs, reduces histone tail-DNA affinities, promoting an open conformation. Additionally, acetylated histones recruit complexes such as the SWI/SNF remodeler complex to further loosen chromatin. For example, the BAS SWI/SNF complex incorporates multiple Bromodomain readers in the BRM and BRD subunits. In the absence of acetylation, histone tails interact more closely with DNA, restricting access. Histone ubiquitination, catalyzed by HUBs and removed by DUBs, adds bulky moieties that decrease interactions between chromatin fibers. While H2Bub is associated with active transcription, H2Aub is recognized by the PRC2 polycomb complex, leading to gene silencing and chromatin compaction. Histone methylation, catalyzed by HMTs and removed by DMTs, can be associated with gene expression and an open chromatin conformation, as exemplified in the cartoon by the H3K4me3-mediated binding of the ARID5-containing CRAF ISWI complex. Conversely, methylation at other residues can lead to gene silencing and chromatin compaction, exemplified in the cartoon by the H3K27me3-mediated recruitment of the Polycomb PRC1 complex. C) Histone variants exert distinct effects on nucleosome stability, DNA accessibility, and chromatin condensation. Among them, H2A.Z has the strongest negative impact on nucleosome stability. H2A.W decreases the accessibility to entry and exit nucleosomal DNA. H1 facilitates the condensation of the same chromatin fiber, while H2A.W promotes compaction by bridging distinct chromatin fibers. Additionally, the histone variant H2B.8 promotes chromatin condensation via phase separation. D) Different families of ATP-dependent chromatin remodelers perform a wide range of functions on the nucleosomal landscape, broadly categorized into nucleosome sliding, eviction, exchange, maturation, and spacing. Created with BioRender.com.

Histone post-translational modifications

Histone tails and cores undergo various PTMs, including acetylation, phosphorylation, methylation, SUMOylation, and ubiquitination. These PTMs serve as chemical labels that establish diverse chromatin environments, thereby regulating various nuclear processes such as gene expression, replication, and repair (Millán-Zambrano et al. 2022).

The dynamics of histone PTMs are orchestrated by an extensive array of writer and eraser proteins, which modulate the levels and distribution of PTMs across the genome and throughout the cell cycle (Musselman et al. 2012). Histone PTMs can influence chromatin accessibility ranging from the local nucleosome dynamics to the folding of higher-order chromatin structures. On the one hand, they can produce direct effects by altering histone charge or introducing bulky moieties, thereby modifying DNA-histone and histone-histone interactions. On the other hand, indirect effects are often mediated by specific reader proteins that modulate chromatin through diverse mechanisms (Zentner and Henikoff 2013). In plants, several families of histone readers exist, including Bromo Adjacent Homology (BAH), Plant Homeodomain (PHD), chromodomain, and bromodomain, that recognize specific PTMs to trigger downstream signaling events (Scheid et al. 2021).

In this section, we will briefly describe how 3 important PTMs—acetylation, methylation, and ubiquitination—affect chromatin accessibility and compaction in both open and closed chromatin conformations, including some new findings in plants. Due to the large amount of data available, we will only discuss the role of these PTMs at representative histone residues. More detailed information about these and other PTMs can be found elsewhere (Bannister and Kouzarides 2011; Chan and Maze 2020; Millán-Zambrano et al. 2022)

Histone PTMs and open chromatin conformation

One extensively studied histone PTM known for promoting an open chromatin conformation is histone lysine acetylation, which neutralizes the positive charge of histone tails, decreasing their affinity for negatively charged DNA (Fig. 3B). Consequently, interactions between acetylated histones and nucleosomal DNA, linker DNA, or adjacent histones are weakened, leading to an open and permissive chromatin state (Chen et al. 2022). Furthermore, acetylation can exert indirect effects on chromatin through the recruitment of chromatin remodeler complexes, such as the SWItch/Sucrose Non-fermenting (SWI/SNF) complexes in animals and plants (Bieluszewski et al. 2023) (Fig. 3B). There are multiple complexes involved in the acetylation and deacetylation of histones (Kumar et al. 2021). Recent studies in plants have elucidated the composition and specific functions of the Histone acetyltransferase (HAT) Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and identified a plant-specific HAT complex called Plant-ADA2A-GCN5-acetyltransferase (PAGA) (Wu et al. 2021; Wu et al. 2023a). Notably, while both complexes promote acetylation at different sets of target genes, they play antagonistic effects on gene expression and development (Wu et al. 2023a). Furthermore, recent studies in plants have reported novel insights into the function of the Nucleosome acetyltransferase of H4 (NuA4) HAT complex in acetylating histones H4 and H2A.Z, impacting crucial processes like chloroplast development, photosynthesis, plastid transcription, and environmental response (Crevillén et al. 2019; Barrero-Gil et al. 2022; Bieluszewski et al. 2022; Zhou et al. 2022).

Another PTM that promotes an open chromatin conformation is the monoubiquitination of H2B (H2Bub), as the addition of a bulky moiety disrupts chromatin fiber folding and high-order chromatin structure formation (Fierz et al. 2011). H2Bub is strongly associated with RNA polymerase II (RNAPII) transcription and is established by the RING-type E3 ubiquitin ligases HISTONE MONO-UBIQUITINATION1 (HUB1) and HUB2, which have recently been implicated in various processes in plants, including mRNA processing, stress response, and double-strand break (DSB) repair (Zhou et al. 2017; Woloszynska et al. 2019; Li et al. 2023a). Notably, a recent study identified a mechanism for regulating H2Bub homeostasis through DE-ETIOLATED 1 (DET1)-mediated degradation of the H2B deubiquitination (DUB) machinery, establishing a direct connection between an environmental cue, light, and chromatin dynamics (Nassrallah et al. 2018) (Fig. 3B).

Methylation is another well-known PTM that can positively influence chromatin accessibility (Fig. 3B). This modification occurs at different arginine (R) and lysine (K) positions and can be found in three different levels, mono-, di-, and tri-methylation, contributing to define functionally distinct chromatin landscapes (Bannister and Kouzarides 2011). For instance, tri-methylation of H3K4 (H3K4me3) is predominantly found over transcription start site (TSS) regions, whereas H3K4me1 and H3K36me3 are evenly distributed over gene bodies of actively transcribed genes. The impact of methylation on nucleosomes is site specific and unlikely to directly affect nucleosome structure (Millán-Zambrano et al. 2022). It rather exerts its function through the recruitment of various reader proteins. There are multiple complexes involved in the methylation and demethylation of histones (Kumar et al. 2021). A recent study in plants revealed the composition of three plant Complex of Proteins Associated with Set1 (COMPASS) Histone methyltransferase (HMT) subclasses and highlighted that the ARABIDOPSIS TRITHORAX 4 (ATX4) and ATX5-containing COMPASS subclass interacts, through the JmJC domain-containing JMJ24 protein, with the Inositol requiring 80 (INO80) remodeler complex to coordinate the homeostasis of H3K4me3 and H2A.Z variant (Shang et al. 2021). Another report showed that the ATX1/2-containing COMPASS subclass is recruited to specific loci by JMJ28 to regulate plant immunity (Xie et al. 2023). Counteracting the function of COMPASS, the plant DREAM complex prevents H3K4me3 deposition through the interaction between Barrier of transcription elongation 1 (BTE1) and WD Repeat Domain 5A (WDR5A) to repress gene expression (Wang et al. 2022b). Also, the TELOMERE REPEAT BINDING (TRB) proteins contribute to H3K4me3 demethylation at some loci through the recruitment of the JMJ14 demethylase (Wang et al. 2023c). Interestingly, recent findings suggest that in mammals, H3K4me3 plays a main role in releasing RNAPII pausing rather than in transcriptional initiation, as initially thought (Wang et al. 2023a). Notably, the H3K4me3 reader-writer machinery requires histone acetylation to function correctly, explaining the strong association between these two modifications over transcribed loci (Jain et al. 2023). In line with this strong association, a recent study in mammals reported that both methyl and acetyl groups can exist in the same lysine residue, known as the KAcMe mark (Lu-Culligan et al. 2023).

Histone PTMs and close chromatin conformation

Ubiquitination and methylation also participate in shaping heterochromatin (Fig. 3B). Monoubiquitination of histone H2A (H2Aub) and tri-methylation of H3K27 (H3K27me3) are hallmarks of facultative heterochromatin, which define silent regions of the genome that are transcriptionally activated under specific developmental conditions or tissues. Here, these marks contribute to gene silencing, reduced chromatin accessibility, and higher-order chromatin structure formation (Barbour et al. 2020; Guo et al. 2021; Guo and Wang 2022). A comprehensive review about these marks in plants is available here (Baile et al. 2022). The machineries involved for depositing H3K27me3 and H2Aub, Polycomb repressive complex 2 (PRC2) and PRC1, respectively, are conserved across eukaryotes, although plants lack several canonical PRC1 components and incorporate plant-specific ones (Li et al. 2018; Huang et al. 2019; Zhu et al. 2020). Recent findings indicate that these marks collectively influence chromatin structure, maintaining intra-compartment interactions while differentially affecting long-range chromatin interactions (Yin et al. 2023). Also, they can independently regulate chromatin accessibility at distinct loci (Yin et al. 2021): H2Aub alone is associated with less accessible but still transcriptionally responsive chromatin at regulatory hotspots. The incorporation of H3K27me3 into H2Aub-marked genes further reduces accessibility and expression, whereas H3K27me3-only marked genes are less accessible and responsive in comparison. Additionally, H1 colocalizes with H3K27me3 to promote chromatin compaction. Interestingly, it prevents the accumulation of the H3K27me3 mark over telomeric regions by restricting access to the PRC2-recruiting factor TRB (Teano et al. 2023). In animals, PRC1 complexes form nuclear condensates called Polycomb bodies, where Polycomb-mediated heterochromatin formation and gene silencing takes place (Plys et al. 2019; Tatavosian et al. 2019). Interestingly, in plants, components associated with PRC2, rather than PRC1, have been found in subnuclear bodies reminiscent of Polycomb bodies (Baile et al. 2022).

In conjunction with DNA methylation, H3K27me1 and H3K9 methylation are representative marks of constitutive heterochromatin, where they play essential roles in silencing of transposable elements (TE) (Hu and Du 2022). H3K27me1 deposition is catalyzed by the ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6 DNMTs and has a strong impact on genome stability, causing accumulation of excess DNA corresponding to heterochromatic regions (Jacob et al. 2009). Notably, these effects are promoted by GCN5-mediated histone acetylation, whose establishment is normally prevented by the H3K27me1 modification (Dong et al. 2021). H3K27me1 also affects chromatin compaction because plants with lower levels of this mark exhibit decondensed chromocenters (Jacob et al. 2009). These defects can be partially attributed to the ectopic function of the H3.1 reader TONSOKU (TSK), which is typically repelled by H3K27me1 and causes genomic instability in H3K27me1-depleted plants (Davarinejad et al. 2022). The establishment and maintenance of H3K9 methylation are interconnected with DNA methylation in a positive-feedback loop (Du et al. 2015). Whereas H3K9 methylation in animals and fungi promotes chromatin compaction through phase separation mediated by the Heterochromatin protein 1 (HP1) reader, the homolog of HP1 in plants, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), does not participate in this pathway. Notably, recent studies have reported a protein that performs similar functions to HP1 in plants, namely AGENET DOMAIN-CONTAINING P1 (ADCP1, aka AGDP1) (Zhang et al. 2018a; Zhao et al. 2019). Interestingly, although TE repression is mainly controlled by H3K9me2 and DNA methylation in multiple plant species, this function was taken by H3K27me3 in early plant lineages, suggesting an ancient role for PRC2 and H3K27me3 in TE silencing (Montgomery et al. 2020; Hisanaga et al. 2023).

Histone variants

Histone variants are paralogs distinguished from canonical histones by the incorporation of specific sequence motifs or substitutions (Probst 2022). Importantly, some of these variants can impact chromatin accessibility by altering nucleosome dynamics, for example, modulating the strength of the DNA-histone interaction. In addition, they can also play a regulatory role by promoting or preventing interactions with diverse chromatin-binding proteins. Furthermore, these variants are selectively deposited into specific chromatin states and positions, and some are specific to certain cell types or cell cycle phases (Probst 2022; Jiang and Berger 2023). The significance of histone variants in chromatin regulation becomes evident when considering their conservation across the eukaryotic evolution. Although the great diversity of variants present in extant eukaryotes results from lineage-specific evolution, it has been recently suggested that the genome of the Last Eukaryotic Common Ancestor already presented five variants broadly conserved in eukaryotes: H3.3, CENTROMERIC HISTONE H3 (CenH3), H2A.Z, H2A.X, and MacroH2A (the latter being conserved mainly across metazoans) (Grau-Bové et al. 2022).

Histone H2A variants

The core histone H2A displays three main variants, H2A.Z, H2A.W, and H2A.X, which are mainly distinguished by sequences in the C-terminal tail (responsible for mediating the interaction with the linker DNA), L1 loop (involved in histone folding, dimerization, and DNA interaction), and the docking domain (responsible for the interaction with H3-H4) (Kawashima et al. 2015). These distinctions endow them with particular biochemical properties that modulate nucleosome stability and chromatin accessibility (Osakabe et al. 2018). According to in vitro assays and modeling studies, H2A.Z is the H2A variant that induces greater instability, favoring H2A.Z-H2B dissociation from the nucleosome, and increases the accessibility to the linker DNA by spontaneously promoting nucleosome entry and exit linker DNA unwrapping (Osakabe et al. 2018; Lewis et al. 2021; Li et al. 2023b) (Fig. 3B). In plants, H2A.Z is located immediately downstream of the TSS of transcriptionally active genes in euchromatin, while it is enriched over gene bodies in facultative heterochromatin (Probst 2022). Importantly, its impact on transcription, whether positive or negative, is correlated with H2A.Z acetylation by the NuA4 complex or ubiquitination by the PCR1 complex (Crevillén et al. 2019; Gómez-Zambrano et al. 2019; Bieluszewski et al. 2022). Moreover, H2A.Z is absent over constitutive heterochromatin, consistent with the negative correlation between this mark and DNA methylation (Zilberman et al. 2008). The H2A.W variant is enriched over constitutive heterochromatin and is involved in transposon silencing (Osakabe et al. 2021). This variant contains a longer C-terminal tail with a KSPK motif, which restricts DNA accessibility in vitro by protecting the linker DNA (Fig. 3B) (Lei et al. 2021). More importantly, it mediates chromatin condensation by establishing long-range chromatin fiber-to-fiber interactions (Yelagandula et al. 2014). Interestingly, H2A.W prevents excessive accumulation of H1, regulating balanced heterochromatic DNA accessibility (Bourguet et al. 2021). Moreover, its deposition is pivotal for maintaining the epigenetic inheritance of repressive chromatin (Lee et al. 2023; Osakabe et al. 2023; Wang et al. 2023b). The H2A.X variant is involved in DNA repair and accumulates over gene bodies of active genes (Jiang and Berger 2023). Near DSBs, a conserved H2A.X SQ motif is specifically phosphorylated and recognized by the BCP3 and BCP4 readers, recently identified in plants, which activate the downstream DNA damage response (Fan et al. 2022; Lorković et al. 2023). According to in vitro experiments, phosphorylated H2A.X promotes the accessibility of nucleosome entry and exit DNA and decreases H1 binding (Li et al. 2010; Sharma et al. 2019). However, to our knowledge, no comprehensive in vivo study has analyzed the potential effect of this histone variant on chromatin accessibility in the context of DNA repair.

Histone H2B variants

Despite the high diversity of H2B variants, their characterization is limited compared with the extensively studied H2A functional diversity. A recent study reported the expression and genomic distribution of the eleven H2B variants found in Arabidopsis (Jiang et al. 2020). Among them, the most divergent angiosperm-specific H2B.8 variant, also known as H2B.S, plays a role in sperm cell compaction (Buttress et al. 2022). This variant exhibits an extended N-terminal tail with an intrinsically disordered region that mediates the aggregation of dispersed AT-rich transcriptionally inactive regions via phase separation, allowing chromatin condensation without compromising transcription (Fig. 3C).

Histone H3 variants

Plants possess three major H3 variants: H3.1, H3.3, and CenH3. The most divergent among them is the centromere-specific CenH3, which directs kinetochore formation and is therefore crucial for proper genetic segregation during cell division (Wu et al. 2023c). On the other hand, H3.1 differs from H3.3 by just 4 amino acids. Nevertheless, these substitutions have a significant impact on their specific deposition, post-translational modifications, and recognition by reader proteins (Wu et al. 2023c). Although H3.1 and H3.3 have been associated with heterochromatin and euchromatin, respectively, a recent study showed that this distinction is oversimplified. Accessibility is likely determined by the joint deposition of H2A and H3 variants, as well as their specific PTMs (Jamge et al. 2023). H3.1 acts as the canonical histone incorporated during replication and is enriched in silent regions of the genome (Stroud et al. 2012). Recent studies suggested that within a short window of time following replication, H3.1 promotes the specific recruitment of the histone reader TSK to nascent chromatin before chromatin maturation, regulating DNA repair and promoting the epigenetic inheritance and maintenance of heterochromatin, including H2A.W and repressive PTMs (Davarinejad et al. 2022; Wang et al. 2023b). In addition to preserving heterochromatin, a recent study suggested the requirement of H3.1 deposition in the establishment of chromocenters (Benoit et al. 2019). H3.3 deposition is replication independent and preferentially replaces H3.1 in gene bodies, as well as in some promoters of actively expressed genes (Shu et al. 2014). Although H3.3 is enriched at 3′ ends, which correlates with restricted chromatin accessibility and cryptic transcription, it can also be found over 5′ regions of genes. This 5′ distribution is essential in seeds to promote the accessibility of regulatory sequences governing post-embryonic development (Zhao et al. 2022). In vegetative tissues, this 5′ distribution is found over some loci like FLOWERING LOCUS C (FLC), facilitating its looping and transcriptional activation (Zhao et al. 2021). Furthermore, two recent studies reported the function of the atypical H3 histone variants H3.15 and H3.10, which act in callus formation and sperm cells, respectively (Borg et al. 2020; Yan et al. 2020). Notably, these variants are immune to trimethylation of H3K27, facilitating the expression of specific genes.

Histone H1 and H4 variants

The linker histone H1 has an essential role in regulating chromatin accessibility and compaction through its ability to bind to the core nucleosomal DNA and bridge the entering and exiting linker DNA, thereby stabilizing the nucleosome and promoting higher-order chromatin structures (Bednar et al. 2017). Arabidopsis contains three H1 variants, and their potentially redundant and specific effects on DNA accessibility require further investigation (Jiang and Berger 2023). The main variants, H1.1 and H1.2, are ubiquitously expressed except for some stages of germline development (She et al. 2013; Hsieh et al. 2016; Han et al. 2022). On the other hand, H1.3 is induced by drought and low-light stress and is constitutively expressed in guard cells (Rutowicz et al. 2015). Recent studies have revealed that H1 depletion triggered changes in nucleosome distribution and mobility and impacted 3D genome architecture and chromocenter formation (Rutowicz et al. 2019; Teano et al. 2023). The H1-promoted chromatin compaction negatively affects the function of the CMT2 DNA methyltransferase, which requires the activity of the DDM1 remodeler to access their targets (Zemach et al. 2013; Lyons and Zilberman 2017). Additionally, H1 prevents the activity of the euchromatin-associated RdDM pathway over heterochromatic regions (Papareddy et al. 2020; Choi et al. 2021; Harris et al. 2023). Furthermore, H1 influences the accumulation of various histone marks, such as H3K27me3, H3K4me3, and H3K9ac (Rutowicz et al. 2019; Teano et al. 2023). Notably, whereas H1 promotes the accumulation of H3K27me3 at most PRC2 targets, it prevents the enrichment of this modification over telomeric regions by antagonizing TRB-mediated PRC2 activity (Teano et al. 2023).

H4 variants are infrequent compared with other histones (Probst 2022). Importantly, the functional characterization of a novel Oryza genus-specific H4 variant, known as H4.V, indicates that it prevents the deposition of transcriptional activation marks, like H4K5ac (Vivek et al. 2023). Furthermore, H4.V redistribution under salt stress facilitated the correct incorporation of stress-dependent H4K5ac and alterations in gene expression. Notably, biochemical studies suggested that H4.V confers specific properties to nucleosomes and reduces the accessibility to the nucleosomal exit/entry DNA.

Function of Snf2 chromatin remodelers

To manipulate nucleosomes, eukaryotes have evolved a diverse series of ATP-dependent DNA translocases from the Snf2 family that can disrupt the interaction between DNA and histones promoting the sliding, ejection, or deposition of nucleosomes. Consequently, they can impact multiple DNA-mediated processes, such as transcription, replication, and repair (Clapier et al. 2017). These remodelers can act as monomers or form multiprotein complexes that, in turn, can be divided into subclasses according to the incorporation of signature subunits. Moreover, the incorporation of subunit paralogs largely increases the combinatorial possibilities of their assemblies (Clapier et al. 2017; Mashtalir et al. 2018). These complexes are recruited to their targets through diverse mechanisms like the interaction with TFs, DNA and histones through their reader subunits, and noncoding RNAs (Zhu et al. 2013; Clapier et al. 2017; Shang and He 2022).

Multiple recent studies have elucidated the functions of various Snf2 remodelers in plants. Some are involved in gene silencing and operate over heterochromatic regions. For example, the Lsh1 homolog DDM1 was recently shown to promote the replacements of H2A.Z and H3.3 for H2A.W and H3.1 variants, respectively, to promote the epigenetic inheritance of DNA methylation (Osakabe et al. 2021; Jamge et al. 2023; Lee et al. 2023). Also, the Snf2 protein MAINTENANCE OF METHYLATION 1 (MOM1) has been shown to participate in silencing processes (Amedeo et al. 2000). Interestingly, this protein does not require its translocase domain for such activity (Čaikovski et al. 2008). Recently, the MOM1 complex has been shown to be involved in the recruitment of the GHKL ATPase MORC6 to promote silencing at RdDM loci (Li et al. 2023c). Other RdDM-related Snf2 proteins have been shown to participate in silencing, such as CLASSY (CLSY), DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1), FRINGE (FRG), and CHROMATIN REMODELING 19 (CHR19) (Smith et al. 2007; Law et al. 2010; Groth et al. 2014; Han et al. 2014). However, their direct activity on nucleosomes remains to be explored. Moreover, previous studies reported the impact of the SWI/SNF remodelers on DNA methylation, heterochromatin remodeling, and TE silencing (Zhu et al. 2013; Liu et al. 2016).

On the other hand, four conserved families have been extensively studied for their roles in euchromatic regulation: SWI/SNF, Imitation switch (ISWI), INO80, and Chromodomain helicase DNA-binding (CHD). A wealth of information is available in animal and fungal models, and important recent advances have been made in plants (Clapier et al. 2017; Shang and He 2022). In the following sections, we will describe in more detail the activity of these complexes on nucleosomes and recent findings in plants (Fig. 3D).

SWI/SNF

Several studies in diverse organisms suggest that the SWI/SNF family plays an important role in the control of the position and occupancy of nucleosomes through sliding and ejection activities, promoting an open conformation on promoter and regulatory regions (Bieluszewski et al. 2023). A comprehensive evolutionary analysis of the conservation of SWI/SNF subunits predicted the presence of two mayor complex subclasses across eukaryotes (Hernández-García et al. 2022). Notably, recent research reported the composition of three SWI/SNF subclasses in plants, namely BRAHMA-associated SWI/SNF (BAS), SPLAYED-associated SWI/SNF (SAS), and MINUSCULE-associated SWI/SNF (MAS), that are defined by the BRAHMA (BRM), SPLAYED (SYD), and MINUSCULE (MINU) ATPases, respectively, and the incorporation of multiple conserved and plant-specific signature subunits (Supplementary Table S1) (Guo et al. 2022; Fu et al. 2023). Studies using Micrococcal Nuclease sequencing (MNase-seq) suggest different activities of the BAS and MAS complexes on nucleosomes: While the BAS complex stabilizes nucleosomes bound by the complex and destabilizes adjacent nucleosomes (Torres and Deal 2019), the MAS complex controls the positioning of the upstream genic nucleosomes to prevent their repositioning towards promoter regions (Diego-Martin et al. 2022). Importantly, a precise map of the nucleosomal landscape in SAS complex mutants through MNase-seq is missing. Nevertheless, ATAC-seq studies showed a shared positive effect on chromatin accessibility for the three subclasses over thousands of genes with subtle differences: The SAS complex preferentially acts on distal promoter and intergenic regions, whereas the BAS and MAS complexes function preferentially over proximal promoter regions (Guo et al. 2022). Consistent with this, the three subclasses are found over the TSS regions of thousands of genes, where the SAS complex is slightly enriched over promoter regions, MAS is enriched downstream of TSS, and BAS has an intermediate distribution (Guo et al. 2022). There are multiple instances of TFs interacting with these complexes, especially with BAS and SAS components (Shang and He 2022). Notably, two recent studies reported new interactions between the brassinosteroid-related TF BRASSINAZOLE-RESISTANT 1 (BZR1) and BRM, and the transcription elongation factor Suppressor of Ty6-like (SPT6L) with BRM and SYD. Both studies showed that these interactions are important to maintain an open chromatin conformation at target genes (Shu et al. 2022; Zhu et al. 2023).

INO80-C and SWR1

The conserved INO80-C and SWI2/SNF2-Related 1 (SWR1) complexes, which represent the INO80 family, are characterized by a large insertion between the two halves of the ATPase domain and a tight association with the AAA + RuvB Like AAA ATPase1 (RuvBL1) and RuvBL2 helicase-like ATPases (Clapier et al. 2017). While it is accepted that SWR1’s main function across eukaryotes is the incorporation of the H2A.Z variant, the INO80-C has been involved in H2A.Z removal in yeast but has been shown to play other activities in mammals, such as the deposition of H2A.Z at promoters of developmental genes, as well as nucleosome-sliding activity (Clapier et al. 2017; Willhoft et al. 2017; Yu et al. 2021). In plants, the involvement of the complex in H2A.Z homeostasis appears to be complex. Two recent studies have reported that INO80-C was involved in the deposition of H2A.Z at FLC and MAF4/5 genes and genome wide (Zhang et al. 2015; Yang et al. 2020). However, other studies proposed the opposite role because the ino80 mutant exhibits a higher density of H2A.Z at specific genes (Zander et al. 2019; Xue et al. 2021a). Additionally, a genome-wide study reported altered nucleosomal occupancy in the ino80 mutant, suggesting activities beyond H2A.Z regulation, as has been shown in animals (Yang et al. 2022). Recent studies have revealed the composition of the INO80-C and SWR1 complexes in Arabidopsis (Supplementary Table S1) (Luo et al. 2020b; Shang et al. 2021). Interestingly, both complexes show plant-specific interactions with other remodeler complexes that might reflect unique chromatin dynamics in plants. The SWR1 complex incorporates the CHR11 or CHR17 ATPases from the ISWI family, most likely to couple H2A.Z deposition and histone nucleosome spacing. Furthermore, the INO80-C complex interacts with the COMPASS histone methyltransferase complex to coordinate H2A.Z homeostasis and H3K4me3 marking (Shang et al. 2021). The genomic targets of SWR1 and INO80 complexes have been unraveled in the last years. Consistent with their genome-wide impact on H2A.Z levels, characterization of the targets of SWR1 subunits MBD9, SWC4, and PIE1 indicate that this complex is bound to thousands of genes (Gómez-Zambrano et al. 2018; Potok et al. 2019; Luo et al. 2020b). Similarly, target characterization of the EEN subunit of the INO80-C showed enrichment over the gene bodies of H2A.Z-marked environmentally responsive genes (Zander et al. 2019). The targeting of SWR1 and INO80-C is mediated through their interactions with diverse TFs (Shang and He 2022). Recent examples of the interaction between INO80-C with PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF7 TFs expand this catalog and explain the participation of the complex in processes like thermomorphogenesis and light reception (Willige et al. 2021; Xue et al. 2021a).

ISWI

Studies in different organisms, including plants, indicate that the ISWI complex participates in multiple nuclear processes acting as a nucleosome spacer, setting the distance between two adjacent nucleosomes (Shang and He 2022). Consistent with the ability of animal ISWI to form multiple subclasses, plant ISWI complexes can form three subclasses, CHR11/17-RLT1/2-ARID5-FHA2 (CRAF), CHR11/17-DDP1/2/3-MSI3 (CDM), and CHR11/17-DDR/W (CDD), that are defined by the CHR11-CHR17 ATPases and a cohort of conserved and plant-specific subunits (Supplementary Table S1) (Shang and He 2022). Importantly, the impact on the nucleosomal landscape of the CRAF and CDD subclasses has been recently studied. CRAF mutants show altered nucleosomal distribution over gene bodies and also exhibit changes in nucleosomal occupancy (Corcoran et al. 2022). Similarly, the ddr4 mutant of the CDD subclass shows changes in nucleosomal occupancy at numerous loci, although it does not display changes in spacing, which could be due to the known redundancy with DDT-RELATED PROTEIN 5 (DDR5) (Zhang et al. 2023a). These results suggest a subfunctionalization of the ISWI subclasses, although this would require further research. Furthermore, consistent with their broad impact on genic nucleosome positioning, the genomic location of CHR11 and the CRAF-specific subunit ARID5 indicates enrichment over the gene bodies of thousands of genes (Tan et al. 2020; Luo et al. 2020b). Notably, the H3K4me3- and AT-rich-reader activities of ARID5 are important for the recruitment of the CRAF complex (Tan et al. 2020). Moreover, the CRAF subclass incorporates the H2A.Z-reader FHA2 protein although its influence on the complex recruitment remains unexplored (Gu et al. 2020).

CHD

The CHD remodelers belong to a highly divergent family that has been extensively characterized in various organisms. Research in animals and yeast shows they can exert a broad range of activities like nucleosome assembly, positioning and spacing, and deposition of the H3.3 variant (Clapier et al. 2017). This is explained by functional differences between subclasses or even within specific subclasses. Although Arabidopsis presents four classes of CHD ATPases, namely PICKLE (PKL), PICKLE RELATED 1 (PKR1), PKR2, and CHR5, only the remodeling function of PKL and CHR5 have been characterized (Supplementary Table S1) (Hu et al. 2014). In vitro studies showed that the CHD3-like PKL is able to mobilize nucleosomes (Ho et al. 2013). In line with these results, a recent genomic study showed that PKL mutant exhibited altered nucleosomal occupancy (Yang et al. 2022). Moreover, PKL promotes prenucleosome maturation, an activity also reported for PKL's orthologs in other organisms, therefore affecting chromatin assembly (Carter et al. 2018). Consistent with a broad impact on gene expression, PKL has been found over the TSS and transcription termination site of thousands of genes (Liang et al. 2022). This could be mediated through its ability to interact with multiple TFs (Shang and He 2022). For example, a recent study reported that the PRC1 components VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 interact with PKL and are required for its recruitment to repress the expression of certain genes (Liang et al. 2022). Besides, PKL presents two chromodomains and a PHD domain that probably influence its genomic location (Hu et al. 2014). Regarding the impact on chromatin of the CHD1-related CHR5 remodeler, a recent genome-wide study showed that its mutation caused higher nucleosomal occupancy, especially over promoter regions, indicating that it may possibly modulate chromatin accessibility by nucleosome ejection (Zou et al. 2017). Notably, its genomic targets and modes of recruitment to chromatin remain unexplored.

Concluding remarks

The precise regulation of nucleosomes and chromatin structure is fundamental for the proper execution of numerous nuclear processes. In this review, we offered an overview of the current state of knowledge regarding the impact of epigenetic marks and nucleosome remodelers on these pivotal aspects. Notably, several knowledge gaps remain to be addressed concerning the regulation of chromatin accessibility, the biology and mechanisms of action of chromatin regulators, and their interplay with epigenetic marks and other nuclear factors across various cellular environments (see Outstanding Questions). An important challenge in the study of chromatin features, such as accessibility, in the field of plant biology is the frequent use of bulk tissue, which can lead to incorrect interpretations of the data due to average signals from thousands of cells. The adoption of techniques to sort distinct cell types, such as Fluorescence-Activated Cell Sorting (FACS), as well as the emerging use of single-cell methodologies, will undoubtedly enhance our understanding of the functions and dynamics of chromatin players and accessibility in plants. Another unresolved issue in chromatin studies is the difficulty of separating correlation from causation. With the development of the epigenome engineering field, novel tools can be designed to study the direct impact of epigenetic marks and chromatin regulators on chromatin accessibility, gene expression or any other process of interest (Gallego-Bartolomé 2020; Dubois and Roudier 2021; Wang et al. 2023d). Furthermore, the application of methodologies such as cryogenic electron microscopy (cryoEM) and single-molecule approaches (Chanou and Hamperl 2021; Takizawa and Kurumizaka 2022) will greatly assist in the detailed study of the specific mechanisms of action of plant chromatin regulators.

Author contribution

JC-F, BD-M, JP-A, and JG-B wrote the manuscript. JC-F and BD-M drew the figures. JG-B coordinated the review.

Supplementary data

The following materials are available in the online version of this article.

Supplementary Table S1. Function and composition of the SWI/SNF, ISWI, INO80, and CHD remodelers in Arabidopsis.

Funding

This work was supported by grants RYC2018-024108-I, PID2019-108577GA-I00, and PID2022-140355NB-100 from MCIN/AEI/10.13039/501100011033 to JG-B and predoctoral contracts to JC-F (PRE2020-094943 from the Spanish Ministry of Science and Innovation), BD-M (FPU19/05694 from the Spanish Ministry of Universities), and JP-A (CIACIF/2021/432 from the Generalitat Valenciana).

Dive Curated Terms

The following phenotypic, genotypic, and functional terms are of significance to the work described in this paper:

• INO80 Gramene: AT3G57300

• INO80 Araport: AT3G57300

• Chr5 Gramene: AT2G13370

• Chr5 Araport: AT2G13370

• MET1 Gramene: AT5G49160

• MET1 Araport: AT5G49160

• MBD5 Gramene: AT3G46580

• MBD5 Araport: AT3G46580

• MBD6 Gramene: AT5G59380

• MBD6 Araport: AT5G59380

• MBD9 Gramene: AT3G01460

• MBD9 Araport: AT3G01460

• NRP1 Gramene: AT1G74560

• NRP1 Araport: AT1G74560

• NRP2 Gramene: AT1G18800

• NRP2 Araport: AT1G18800

• PIF4 Gramene: AT2G43010

• PIF4 Araport: AT2G43010

• PIF7 Gramene: AT5G61270

• PIF7 Araport: AT5G61270

• CHR11 Gramene: AT3G06400

• CHR11 Araport: AT3G06400

• PIE1 Gramene: AT3G12810

• PIE1 Araport: AT3G12810

• CAF1 Gramene: AT2G20020

• CAF1 Araport: AT2G20020

• CHR17 Gramene: AT5G18620

• CHR17 Araport: AT5G18620

• FLC Gramene: AT5G10140

• FLC Araport: AT5G10140

• DDM1 Gramene: AT5G66750

• DDM1 Araport: AT5G66750

• ARID5 Gramene: AT3G43240

• ARID5 Araport: AT3G43240

• VAL2 Gramene: AT4G32010

• VAL2 Araport: AT4G32010

• LHP1 Gramene: AT5G17690

• LHP1 Araport: AT5G17690