Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed

Epigenetic modification brings new opportunities for gene capture by transposable elements in allopolyploid Brassica napus

Polyploids are widespread in plants and are important drivers for evolution and biodiversity. Allopolyploidy activates transposable elements (TEs) and causes genomic shock. Plant genomes can regulate gene expression by changing the epigenetic modification of TEs, but the mechanism for TEs to capture genes remains to be explored. Helitron TEs used the 'peel-and-paste' mechanism to achieve gene capture. We identified 3156 capture events and 326 donor genes of Helitron TEs in Brassica napus (AnAnCnCn). The donor genes captured by TEs were related to the number, length, and location of their exons. The gene-capturing TEs carrying donor gene fragments were evenly distributed on the genome, and more than half of them were involved in the construction of pseudogenes, becoming the reserve force for polyploid evolution. Gene fragment copies enhanced information storage, providing opportunities for gene mutation and the formation of new genes. Simultaneously, the siRNAs targeting TEs may act on the donor genes due to siRNA crosstalk, and the gene methylation levels increased and the expression levels decreased. The genome sought a balance between sacrificing donor gene expression and silencing TEs, allowing TEs to hide in the genome. In addition, epigenetic modifications may temporarily relax the control of gene capture during allopolyploidization. Our study identified and characterized gene capture events in B. napus, analyzed the effects of DNA methylation and siRNA on gene capture events, and explored the regulation mechanism of gene expression by TE epigenetic modification during allopolyploidization, which will contribute to understanding the formation and evolution mechanism of allopolyploidy.

Receptor kinase LecRK-I.9 regulates cell wall remodelling during lateral root formation in Arabidopsis

Assembling and remodelling the cell wall is essential for plant development. Cell wall dynamics are controlled by cell wall proteins, polysaccharide biosynthesis, and a variety of sensor and receptor systems. LecRK-I.9, an Arabidopsis thaliana plasma membrane-localized lectin receptor kinase, was previously shown to be involved in cell wall-plasma membrane contacts and to play roles in plant-pathogen interactions, but until now its role in development was not known. LecRK-I.9 is transcribed at a high level in root tissues including the pericycle. Comparative transcript profiling of a loss-of-function mutant versus the wild type identified LecRK-I.9 as a regulator of cell wall metabolism. Consistently, lecrk-I.9 mutants displayed an increased pectin methylesterification level correlated with decreased pectin methylesterase and increased polygalacturonase activities. Also, LecRK-I.9 negatively impacted lateral root development through the direct or indirect regulation of genes encoding (i) cell wall remodelling proteins during early events of lateral root initiation, and (ii) cell wall signalling peptides (CLE2 and CLE4) repressing lateral root emergence and growth. Furthermore, low nitrate reduced LecRK-I.9 expression in roots, particularly in the lateral root emergence zone: even in these conditions, the control of CLE2 and CLE4 expression is maintained. Altogether, the results show that LecRK-I.9 is a key player in negatively regulating both pre-branch site formation and lateral root emergence.

Genome-wide association studies and transcriptomics reveal mechanisms explaining the diversity of wheat root responses to nutrient availability

Nutrient availability profoundly influences plant root system architecture, which critically determines crop productivity. While Arabidopsis has provided important insights into the genetic responses to nutrient deficiency, translating this knowledge to crops, particularly wheat, remains a subject of inquiry. Here, examining a diverse wheat population under varying nitrogen (N), phosphorus (P), potassium (K), and iron (Fe) levels, we uncover a spectrum of root responses, spanning from growth inhibition to stimulation, highlighting genotype-specific strategies. Furthermore, we reveal a nuanced interplay between macronutrient deficiency (N, P, and K) and Fe availability, emphasizing the central role of Fe in modulating root architecture. Through genome-wide association mapping, we identify 11 quantitative trait loci underlying root traits under varying nutrient availabilities, including homologous genes previously validated in Arabidopsis, supporting our findings. In addition, utilizing transcriptomics, reactive oxygen species (ROS) imaging, and antioxidant treatment, we uncover that wheat root growth inhibition by nutrient deficiency is attributed to ROS accumulation, akin to the role of ROS in governing Arabidopsis root responses to nutrient deficiency. Therefore, our study reveals the conservation of molecular and physiological mechanisms between Arabidopsis and wheat to adjust root growth to nutrient availability, paving the way for targeted crop improvement strategies aimed at increasing nutrient use efficiency.

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.

Multiple layers of regulators emerge in the network controlling lateral root organogenesis

Lateral root (LR) formation is a postembryonic organogenesis process that is crucial for plant root system development and adaptation to heterogenous soil environments. Since the early 1990s, a wealth of experimental data on arabidopsis (Arabidopsis thaliana) has helped reveal the LR formation regulatory network, in which dynamic auxin distribution and transcriptional cascades direct root cells through their organogenesis pathway. Some parts of this network appear conserved across diverse plant species or distinct developmental contexts. Recently, our knowledge of this process dramatically expanded thanks to technical advances, from single cell profiling to whole-root system phenotyping. Interestingly, new players are now emerging in this network, such as fatty acids and reactive oxygen species (ROS), transforming our knowledge of this hidden half of plant biology.

Epigenetic control during root development and symbiosis

The roots of plants play multiple functions that are essential for growth and development, including anchoring to the soil as well as water and nutrient acquisition. These underground organs exhibit the plasticity to modify their root system architecture in response to environmental cues, allowing adaptation to change in water and nutrient availability. In addition, roots enter in mutualistic interactions with soil microorganisms, for example, the root nodule symbiosis (RNS) established between a limited group of plants and nitrogen-fixing soil bacteria and the arbuscular mycorrhiza symbiosis involving most land plants and fungi of the Glomeromycetes phylum. In the past 20 years, genetic approaches allowed the identification and functional characterization of genes required for the specific programs of root development, root nodule, and arbuscular mycorrhiza symbioses. These genetic studies provided evidence that the program of the RNS recruited components of the arbuscular mycorrhiza symbiosis and the root developmental programs. The execution of these programs is strongly influenced by epigenetic changes-DNA methylation and histone post-translational modifications-that alter chromatin conformation modifying the expression of key genes. In this review, we summarize recent advances that highlight how DNA methylation and histone post-translational modifications, as well as chromatin remodeling factors and long noncoding RNAs, shape the root system architecture and allow the successful establishment of both root nodule and arbuscular mycorrhiza symbioses. We anticipate that the analysis of dynamic epigenetic changes and chromatin 3D structure in specific single cells or tissue types of root organs will illuminate our understanding of how root developmental and symbiotic programs are orchestrated, opening exciting questions and new perspectives to modulate agronomical and ecological traits linked to nutrient acquisition.

Overexpression of Auxin/Indole-3-Acetic Acid Gene TrIAA27 Enhances Biomass, Drought, and Salt Tolerance in Arabidopsis thaliana

White clover (Trifolium repens L.) is an important forage and aesthetic plant species, but it is susceptible to drought and heat stress. The phytohormone auxin regulates several aspects of plant development and alleviates the effects of drought stress in plants, including white clover, by involving auxin/indole acetic acid (Aux/IAA) family genes. However, Aux/IAA genes and the underlying mechanism of auxin-mediated drought response remain elusive in white clover. To extend our understanding of the multiple functions of Aux/IAAs, the current study described the characterization of a member of the Aux/IAA family TrIAA27 of white clover. TrIAA27 protein had conserved the Aux/IAA family domain and shared high sequence similarity with the IAA27 gene of a closely related species and Arabidopsis. Expression of TrIAA27 was upregulated in response to heavy metal, drought, salt, NO, Ca2+, H2O2, Spm, ABA, and IAA treatments, while downregulated under cold stress in the roots and leaves of white clover. TrIAA27 protein was localized in the nucleus. Constitutive overexpression of TrIAA27 in Arabidopsis thaliana led to enhanced hypocotyl length, root length, plant height, leaf length and width, and fresh and dry weights under optimal and stress conditions. There was Improved photosynthesis activity, chlorophyll content, survival rate, relative water content, endogenous catalase (CAT), and peroxidase (POD) concentration with a significantly lower electrolyte leakage percentage, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) concentration in overexpression lines compared to wild-type Arabidopsis under drought and salt stress conditions. Exposure to stress conditions resulted in relatively weaker roots and above-ground plant growth inhibition, enhanced endogenous levels of major antioxidant enzymes, which correlated well with lower lipid peroxidation, lower levels of reactive oxygen species, and reduced cell death in overexpression lines. The data of the current study demonstrated that TrIAA27 is involved in positively regulating plant growth and development and could be considered a potential target gene for further use, including the breeding of white clover for higher biomass with improved root architecture and tolerance to abiotic stress.

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small RNAs (sRNAs) mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in the sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its likely paternal imprinted nature. These important features are modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines, we observe defects in endosperm development and a loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms are also dependent on OsCLSY3. We observed that many imprinted genes and seed development-associated genes are under the control of OsCLSY3. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.

Enigmatic role of auxin response factors in plant growth and stress tolerance

Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.

Population epigenetics: DNA methylation in the plant omics era

DNA methylation plays an important role in many biological processes. The mechanisms underlying the establishment and maintenance of DNA methylation are well understood thanks to decades of research using DNA methylation mutants, primarily in Arabidopsis (Arabidopsis thaliana) accession Col-0. Recent genome-wide association studies (GWASs) using the methylomes of natural accessions have uncovered a complex and distinct genetic basis of variation in DNA methylation at the population level. Sequencing following bisulfite treatment has served as an excellent method for quantifying DNA methylation. Unlike studies focusing on specific accessions with reference genomes, population-scale methylome research often requires an additional round of sequencing beyond obtaining genome assemblies or genetic variations from whole-genome sequencing data, which can be cost prohibitive. Here, we provide an overview of recently developed bisulfite-free methods for quantifying methylation and cost-effective approaches for the simultaneous detection of genetic and epigenetic information. We also discuss the plasticity of DNA methylation in a specific Arabidopsis accession, the contribution of DNA methylation to plant adaptation, and the genetic determinants of variation in DNA methylation in natural populations. The recently developed technology and knowledge will greatly benefit future studies in population epigenomes.

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.

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.

Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa)

BACKGROUND

Auxin/indoleacetic acid (AUX/IAA) genes encoding short-lived proteins participate in AUX signaling transduction and play crucial roles in plant growth and development. Although the AUX/IAA gene family has been identified in many plants, a systematic analysis of AUX/IAA genes in Brassica rapa ssp. rapa has not yet been reported.

RESULTS

We performed a comprehensive genome-wide analysis and found 89 AUX/IAA genes in turnip based on the conserved AUX/IAA domain (pfam02309). Phylogenetic analysis of AUX/IAA genes from turnip, Arabidopsis, and cabbage revealed that these genes cluster into six subgroups (A1, A2, A3, A4, B1, and B2). The motif distribution was also conservative among the internal members of the clade. Enhanced yellow fluorescent protein (EYFP) signals of BrrIAA-EYFPs showed that BrrIAA members functioned as nucleoproteins. Moreover, transcriptional analysis revealed that the expression patterns of AUX/IAA genes in turnip were tissue-dependent. Because orthologs have similar biological functions and interaction networks in plant growth and development, BrrIAA66 in turnip possibly played a role in embryo axis formation, vascular development, lateral root formation, and floral organ development by interacting with BrrARF19 and BrrTIR1.

CONCLUSION

These results provide a theoretical basis for further investigation of BrrAUX/IAA genes and lay the foundation for functional analysis of BrrIAA66 in turnip.

Comparative Microscopic, Transcriptome and IAA Content Analyses Reveal the Stem Growth Variations in Two Cultivars Ilex verticillata

Ilex verticillata is not only an excellent ornamental tree species for courtyards, but it is also a popular bonsai tree. 'Oosterwijk' and 'Red sprite' are two varieties of Ilex verticillata. The former has a long stem with few branches, while the latter has a short stem. In order to explain the stem growth differences between the two cultivars 'Oosterwijk' and 'Red sprite', determination of the microstructure, transcriptome sequence and IAA content was carried out. The results showed that the xylem thickness, vessel area and vessel number of 'Oosterwijk' were larger than in 'Red sprite'. In addition, our analysis revealed that the differentially expressed genes which were enriched in phenylpropanoid biosynthesis; phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis in the black and tan modules of the two varieties. We found that AST, HCT and bHLH 94 may be key genes in the formation of shoot difference. Moreover, we found that the IAA content and auxin-related DEGs GH3.6, GH3, ATRP5, IAA27, SAUR36-like, GH3.6-like and AIP 10A5-like may play important roles in the formation of shoot differences. In summary, these results indicated that stem growth variations of 'Oosterwijk' and 'Red sprite' were associated with DEGs related to phenylpropanoid biosynthesis, phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis, as well as auxin content and DEGs related to the auxin signaling pathway.

Phosphorus Regulates the Level of Signaling Molecules in Rice to Reduce Cadmium Toxicity

Phosphorus treatment can reduce Cd accumulation and Cd toxicity in rice, but alterations in the internal regulatory network of rice during this process have rarely been reported. We have removed the effect of cadmium phosphate precipitation from the hydroponic system, treated a pair of different Cd-response rice varieties with different levels of phosphorus and cadmium and examined the changes in physiological indicators and regulatory networks. The results demonstrated that phosphorus treatment significantly reduced Cd accumulation in both types of rice, although the antioxidant systems within the two types of rice produced opposite responses. Overall, 3 mM phosphorus treatment to Cd-N decreased the expression of OsIAA17 and OsACO1 by 32% and 37%, respectively, while increasing the expression of OsNR2 by 83%; these three genes regulate the synthesis of auxin, ethylene, and nitric oxide in rice. IAA and NO levels in rice shoots increased by 24% and 96%, respectively, and these changes contribute to Cd detoxification. The cadmium transporter genes OsHMA2, OsIRT1, and OsABCC1 were significantly down-regulated in Cd-N roots after triple phosphorus treatment. These data suggest that phosphorus treatment can reduce Cd accumulation and enhance Cd resistance in rice by affecting the expression of signaling molecules.

Nutrient-hormone relations: Driving root plasticity in plants

Optimal plant development requires root uptake of 14 essential mineral elements from the soil. Since the bioavailability of these nutrients underlies large variation in space and time, plants must dynamically adjust their root architecture to optimize nutrient access and acquisition. The information on external nutrient availability and whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates to trigger a systemic or locally restricted developmental response. Timing and extent of such local root responses depend on the overall nutritional status of the plant that is transmitted from shoots to roots in the form of phytohormones or other systemic long-distance signals. The integration of these systemic and local signals then determines cell division or elongation rates in primary and lateral roots, the initiation, emergence, or elongation of lateral roots, as well as the formation of root hairs. Here, we review the cascades of nutrient-related sensing and signaling events that involve hormones and highlight nutrient-hormone relations that coordinate root developmental plasticity in plants.

Analysis of unigenes involved in lateral root development in Bupleurum chinense and B. scorzonerifolium

We identified IAA13 negatively associated with lateral root number by comparing the differential expressed genes between Bupleurum chinense and B. scorzonerifolium. Dried roots of the genus Bupleurum L. are used as a herbal medicine for diseases in Asia. Bupleurum chinense has a greater number of lateral roots than B. scorzonerifolium, but the genetic mechanisms for such differences are largely unknown. We (a) compared the transcriptome profiles of the two species and (b) identified a subset of candidate genes involved in auxin signal transduction and explored their functions in lateral root development. By isoform sequencing (Iso-Seq) analyses of the whole plant, more unigenes were found in B. scorzonerifolium (118,868) than in B. chinense (93,485). Given the overarching role of indole-3-acetic acid (IAA) as one of the major regulators of lateral root development, we identified 539 unigenes associated with auxin signal transduction. Fourteen and 44 unigenes in the pathway were differentially expressed in B. chinense and B. scorzonerifolium, respectively, and 3 unigenes (LAX2, LAX4, and IAA13) were expressed in both species. The number of lateral root primordia increased after exogenous auxin application at 8 h and 12 h in B. scorzonerifolium and B. chinense, respectively. Since overexpression of IAA13 in Arabidopsis reduced the number of lateral roots, we hypothesized that IAA13 is involved in the reduction of the number of lateral roots in B. scorzonerifolium.

Gibberellin signaling mediates lateral root inhibition in response to K+-deprivation

The potassium ion (K+) is vital for plant growth and development, and K+-deprivation leads to reduced crop yields. Here we describe phenotypic, transcriptomic, and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis (Arabidopsis thaliana) Columbia. We showed effects on root architecture are mediated through a reduction in cell division in the lateral root (LR) meristems, the rate of LR initiation is reduced but LR density is unaffected, and primary root growth is reduced only slightly. This was primarily regulated through gibberellic acid (GA) signaling, which leads to the accumulation of growth-inhibitory DELLA proteins. The short LR phenotype was rescued by exogenous application of GA but not of auxin or by the inhibition of ethylene signaling. RNA-seq analysis showed upregulation by K+-deprivation of the transcription factors JUNGBRUNNEN1 (JUB1) and the C-repeat-binding factor (CBF)/dehydration-responsive element-binding factor 1 regulon, which are known to regulate GA signaling and levels that regulate DELLAs. Transgenic overexpression of JUB1 and CBF1 enhanced responses to K+ stress. Attenuation of the reduced LR growth response occurred in mutants of the CBF1 target gene SFR6, implicating a role for JUB1, CBF1, and SFR6 in the regulation of LR growth in response to K+-deprivation via DELLAs. We propose this represents a mechanism to limit horizontal root growth in conditions where K+ is available deeper in the soil.

Coordinated homeostasis of essential mineral nutrients: a focus on iron

In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.

Chromatin regulation in plant hormone and plant stress responses

The gene expression is tightly regulated temporally and spatially to ensure the plant and animal proper development, function, growth, and survival under different environmental conditions. Chromatin regulation plays a central role in the gene expression by providing transcription factors and the transcription machinery with dynamic access to an otherwise tightly packaged genome. In this review, we will summarize recent progress in understanding the roles of chromatin regulation in the gene expression, and their contribution to the plant hormone and stress responses. We highlight the most recent publications within this topic and underline the roles of chromatin regulation in gene expression.

Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis

Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we develop a genome browser, SRBrowse, optimised for visualising and analysing sequencing data at single-read resolution.