ZMP recruits and excludes Pol IV-mediated DNA methylation in a site-specific manner

Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants

Methylation at the fifth position of the cytosine base (5mC) is a critical DNA modification with important functions in gene silencing, genome imprinting, and suppression of transposable elements in eukaryotes. Biochemically, DNA methylation is dynamically regulated by three critical processes: the de novo establishment of DNA methylation, the maintenance of DNA methylation by preexisting methylation patterns, and the removal of DNA methylation. In plants, DNA methylation is very complex with unique features. In past decades, a series of biochemical and structural studies, especially empowered by the recent breakthroughs of high-resolution cryogenic electron microscopy, have helped uncover the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation in plants. This review summarizes recent research advances in these three aspects of DNA methylation and lays out a molecular view of plant DNA methylation from biochemical and structural perspectives.

Transcription factors instruct DNA methylation patterns in plant reproductive tissues

DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to male or female reproductive tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. These findings not only reveal RIMs as the first sex-specific RdDM proteins but also establish a critical role for genetic information in targeting DNA methylation. This novel mode of targeting expands our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

Epigenetic gene regulation in plants and its potential applications in crop improvement

DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.

Unlocking the small RNAs: local and systemic modulators for advancing agronomic enhancement

Small regulatory RNAs (sRNAs) are essential regulators of gene expression across a wide range of organisms to precisely modulate gene activity based on sequence-specific recognition. In model plants like Arabidopsis thaliana, extensive research has primarily concentrated on 21 to 24-nucleotide (nt) sRNAs, particularly microRNAs (miRNAs). Recent advancements in cell and tissue isolation techniques, coupled with advanced sequencing technologies, are revealing a diverse array of preciously uncharacterized sRNA species. These include previously novel structural RNA fragments as well as numerous cell- and tissue-specific sRNAs that are active during distinct developmental stages, thereby enhancing our understanding of the precise and dynamic regulatory roles of sRNAs in plant development regulation. Additionally, a notable feature of sRNAs is their capacity for amplification and movement between cells and tissues, which facilitates long-distance communication-an adaptation critical to plants due to their sessile nature. In this review, we will discuss the classification and mechanisms of action of sRNAs, using legumes as a primary example due to their essential engagement for the unique organ establishment of root nodules and long-distance signaling, and further illustrating the potential applications of sRNAs in modern agricultural breeding and environmentally sustainable plant protection strategies.

CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing

Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here, we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null and clsy quadruple mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.

Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation

DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.

The plant siRNA landscape

Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.

CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing

Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.

How transposable elements are recognized and epigenetically silenced in plants?

Plant genomes are littered with transposable elements (TEs). Because TEs are potentially highly mutagenic, host organisms have evolved a set of defense mechanisms to recognize and epigenetically silence them. Although the maintenance of TE silencing is well studied, our understanding of the initiation of TE silencing is limited, but it clearly involves small RNAs and DNA methylation. Once TEs are silent, the silent state can be maintained to subsequent generations. However, under some circumstances, such inheritance is unstable, leading to the escape of TEs to the silencing machinery, resulting in the transcriptional activation of TEs. Epigenetic control of TEs has been found to be closely linked to many other epigenetic phenomena, such as genomic imprinting, and is known to contribute to regulation of genes, especially those near TEs. Here we review and discuss the current models of TE silencing, its unstable inheritance after hybridization, and the effects of epigenetic regulation of TEs on genomic imprinting.

Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development

DNA methylation is a conserved modification that must be precisely regulated during development to facilitate its roles in silencing transposable elements and regulating gene expression. In plants, DNA methylation changes during reproduction are widely documented and, in many cases, the underlying mechanisms are well understood. In somatic tissues, the diversity of methylation patterns are only recently emerging but they are often associated with the RNA-directed DNA methylation (RdDM) pathway. Here, we discuss advances in our understanding of how the locus-specific targeting and tissue-specific expression of RdDM proteins regulate methylation patterns, how the targeting of methylation at loci with imperfect homology expands the purview of RdDM, and how natural variation within RdDM factors impacts DNA methylation patterns.

DNA-dependent RNA polymerases in plants

DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.