Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis.

The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). We studied their order of action within the RdDM pathway by testing their ability to target methylation in different mutants. We also evaluated ectopic siRNA biogenesis, RNA polymerase V (Pol V) recruitment, targeted DNA methylation, and gene-expression changes at thousands of ZF-RdDM targets. We found that co-targeting both arms of the RdDM pathway, siRNA biogenesis and Pol V recruitment, dramatically enhanced targeted methylation. This work defines how RdDM components establish DNA methylation and enables new strategies for epigenetic gene regulation via targeted DNA methylation.

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis.

RNA-directed DNA methylation in Arabidopsis thaliana is driven by the plant-specific RNA Polymerase IV (Pol IV). It has been assumed that a Pol IV transcript can give rise to multiple 24-nt small interfering RNAs (siRNAs) that target DNA methylation. Here, we demonstrate that Pol IV-dependent RNAs (P4RNAs) from wild-type Arabidopsis are surprisingly short in length (30 to 40 nt) and mirror 24-nt siRNAs in distribution, abundance, strand bias, and 5'-adenine preference. P4RNAs exhibit transcription start sites similar to Pol II products and are featured with 5'-monophosphates and 3'-misincorporated nucleotides. The 3'-misincorporation preferentially occurs at methylated cytosines on the template DNA strand, suggesting a co-transcriptional feedback to siRNA biogenesis by DNA methylation to reinforce silencing locally. These results highlight an unusual mechanism of Pol IV transcription and suggest a "one precursor, one siRNA" model for the biogenesis of 24-nt siRNAs in Arabidopsis.

A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase.

DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.

huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level.

T-cell receptors (TCRs) and B-cell receptors (BCRs) are critical in recognizing antigens and activating the adaptive immune response. Stochastic V(D)J recombination generates massive TCR/BCR repertoire diversity. Single-cell immune profiling with transcriptome analysis allows the high-throughput study of individual TCR/BCR clonotypes and functions under both normal and pathological settings. However, a comprehensive database linking these data is not yet readily available. Here, we present the human Antigen Receptor database (huARdb), a large-scale human single-cell immune profiling database that contains 444 794 high confidence T or B cells (hcT/B cells) with full-length TCR/BCR sequence and transcriptomes from 215 datasets. All datasets were processed in a uniform workflow, including sequence alignment, cell subtype prediction, unsupervised cell clustering, and clonotype definition. We also developed a multi-functional and user-friendly web interface that provides interactive visualization modules for biologists to analyze the transcriptome and TCR/BCR features at the single-cell level. HuARdb is freely available at https://huarc.net/database with functions for data querying, browsing, downloading, and depositing. In conclusion, huARdb is a comprehensive and multi-perspective atlas for human antigen receptors.

DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis.

DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. Here, we present genome-wide chromatin accessibility profiles of 18 Arabidopsis mutants that are deficient in CG, CHG, or CHH DNA methylation. We find that DNA methylation in all three sequence contexts impacts chromatin accessibility in heterochromatin. Many chromatin regions maintain inaccessibility when DNA methylation is lost in only one or two sequence contexts, and signatures of accessibility are particularly affected when DNA methylation is reduced in all contexts, suggesting an interplay between different types of DNA methylation. In addition, we found that increased chromatin accessibility was not always accompanied by increased transcription, suggesting that DNA methylation can directly impact chromatin structure by other mechanisms. We also observed that an increase in chromatin accessibility was accompanied by enhanced long-range chromatin interactions. Together, these results provide a valuable resource for chromatin architecture and DNA methylation analyses and uncover a pivotal role for methylation in the maintenance of heterochromatin inaccessibility.

Alterations in the sequence and bioactivity of food-derived oligopeptides during simulated gastrointestinal digestion and absorption: a review.

Food-derived oligopeptides (FOPs) exhibit various bioactivities. However, little was known about their sequence changes in the gastrointestinal tract and the effect of changes on bioactivities. FOPs' sequence features, changes and effects on bioactivities have been summarised. The sequence length of FOPs decreases with increased exposure of hydrophobic and basic amino acids at the terminal during simulated gastrointestinal digestion. A decrease in bioactivities after simulated intestinal absorption has correlated with a decrease of Leu, Ile, Arg, Tyr, Gln and Pro. The sequence of FOPs that pass readily through the intestinal epithelium corresponds to transport modes, and FOPs whose sequences remain unchanged after transport are the most bioactive. These include mainly dipeptides to tetrapeptides, consisting of numerous hydrophobic and basic amino acids, found mostly at the end of the peptide chain, especially at the C-terminal. This review aims to provide a foundation for applications of FOPs in nutritional supplements and functional foods.

Additive interactions between obesity and insulin resistance on hypertension in a Chinese rural population.

BACKGROUND: Adiposity and insulin resistance (IR) are closely associated with hypertension; however, the role of interactions between obesity phenotypes and IR in hypertension is unclear. This study aimed to evaluate the interactions of body mass index (BMI), waist circumference (WC), and body fat percentage (BF%) with IR on hypertension risk. METHODS: We analyzed data from 4888 participants (mean age 57 years, 41.2% men) in the China Northwest Natural Population Cohort, Ningxia Project. BMI, WC, and BF% were determined using bioelectrical impedance analysis devices. IR was estimated using a homeostasis model assessment index (HOMA-IR). Multivariable-adjusted logistic regression was used to evaluate the association between HOMA-IR and hypertension risk. We calculated the relative excess risk and attributable proportion with their 95% confidence intervals (CIs) to assess whether adiposity phenotypes modified the effect of HOMA-IR on hypertension risk. RESULTS: The crude prevalence of hypertension was 52.2%. The multivariable-adjusted odds ratio of HOMA-IR was 1.80 (95% CI: 1.23-2.65) for the risk of hypertension in the highest versus the lowest quartiles, but this association became marginal in models further adjusting for BMI, WC, and BF% (P for trend = 0.056). Relative excess risk and attributable proportion for interaction between high HOMA-IR and high BF% were 0.32 (0.04-0.59) and 0.33 (0.06-0.60), respectively. Additionally, high truncal and leg BF% and high HOMA-IR accounted for the hypertension risk in women, but not in men. We did not observe any significant interactions between BMI or WC and HOMA-IR on hypertension. CONCLUSION: BF% modified the association between IR and increased risk of hypertension in women with high truncal and leg BF%, but not in men.

Quantitative flood disaster loss-resilience with the multilevel hybrid evaluation model.

The severity of global flood disasters is growing, causing loss of human life and property. Building a high-resilience social system, an important means of sustainable flood control, can address these flood-related issues. Numerous studies have carried out disaster resilience evaluations and explored the correlation between flood disaster loss and intensity, but neglected to analyze the role of resilience construction in disaster loss reduction. This study proposed a research route for linking flood loss and disaster loss to quantify the relationship between the two. Take Guangdong Province, China as a study case, the mixed-effects (ME) model and multilevel hybrid evaluation model (MHEM) were established to assess disaster loss and resilience of cities, respectively. Subsequently, disaster resilience curves were built to quantitatively evaluate disaster resilience and corresponding disaster loss. The results show that (1) the ME model can concurrently build the disaster intensity-loss curves of multiple cities with high fitting accuracy. The MHEM combines multiple methods to determine the evaluation result with the highest consistency, showing high reliability. (2) The central and southern regions of Guangdong Province have low disaster loss and high resilience, while the northern regions have high disaster loss and low resilience. (3) With the improvement of disaster resistance, the reduction in disaster loss gradually decreases. Disaster loss in low-resilience cities exhibits greater randomness than that in high-resilience cities, and increasing their resilience can more significantly reduce their level of loss. This study provides a quantitative basis and available methods for comprehensive responses to natural disasters and adaptation to global climate change.

A comprehensive meta-analysis of the impacts of intensified drought and elevated CO2 on forage growth.

Forage crops are used worldwide as key feed sources for dairy systems. However, their productivity and quality are limited due to intensified drought events, elevated carbon dioxide (CO2), and their interaction with climate change, with consequences for the security of animal husbandry and the agricultural economy. Although studies have quantified the impacts of such stresses on forage growth, these impacts have been less systematically investigated in a global context due to differences among various forage groups, regional microclimates, and environmental factors. Herein we employed nine forage growth-related variables involving three perspectives, i.e., photosynthetic parameters, production, and quality, from research articles published between 1990 and 2021 via a meta-analysis. A linear mixed-effect model was then used to explore the quantitative relationship between these factors in a restricted dataset. Decreasing trends in all four photosynthetic parameters were detected across different eco-geographical regions with increasing drought stress. The maximum decrease in DMY occurred in the Mediterranean, with 52.8% under drought conditions. Globally, eCO2 significantly increased photosynthetic rate (Pn) and instantaneous water use efficiency (WUEi) by 40.8% and 62.1%, respectively, which also had positive effects on forage dry matter yield (DMY) (+25.1%), especially for forage in Northern Europe. However, this stress would significantly decrease forage quality by decreasing crude protein (CP) (-19.7%) and nitrogen content (N content) (-13.5%). These negative impacts would be aggravated under the co-occurrence of drought and eCO2, including a significant increase in WUEi (+111.1%) and a decrease in DMY (-12.3%). Gramineae showed a more sensitive response to drought stress in photosynthetic parameters and DMY than Leguminosae, but the latter exhibited a better response in photosynthetic parameters and production under eCO2. Our analysis provides a consensus concerning how the growth parameters of forage have changed under environmental stresses.

Pyrene-Based Covalent Organic Frameworks for Photocatalytic Hydrogen Peroxide Production.

Four highly porous covalent organic frameworks (COFs) containing pyrene units were prepared and explored for photocatalytic H2 O2 production. The experimental studies are complemented by density functional theory calculations, proving that the pyrene unit is more active for H2 O2 production than the bipyridine and (diarylamino)benzene units reported previously. H2 O2 decomposition experiments verified that the distribution of pyrene units over a large surface area of COFs plays an important role in catalytic performance. The Py-Py-COF though contains more pyrene units than other COFs which induces a high H2 O2 decomposition due to a dense concentration of pyrene in close proximity over a limited surface area. Therefore, a two-phase reaction system (water-benzyl alcohol) was employed to inhibit H2 O2 decomposition. This is the first report on applying pyrene-based COFs in a two-phase system for photocatalytic H2 O2 generation.

RAD: a web application to identify region associated differentially expressed genes.

SUMMARY: With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually less focused, largely due to the lack of reliable tools to link these regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes (DEGs). With DEGs and genomic regions of interest (gROI) as input, RAD maps the up- and down-regulated genes associated with any gROI and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance. AVAILABILITY AND IMPLEMENTATION: RAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available at https://labw.org/rad as online web service. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Validity and reliability of a semi-quantitative food frequency questionnaire in groups at high risk for cardiovascular diseases.

BACKGROUND: Diet is a modifiable risk factor for cardiovascular diseases (CVD), but there is still a lack of tools to assess dietary intakes of this high-risk population in Ningxia, China. OBJECTIVE: We aim to evaluate the validity and reliability of the semi-quantitative food frequency questionnaire (SFFQ) in the groups in Ningxia using a 24-hour dietary recall method. METHOD: Two hundred five participants were included in the analysis. The two FFQs were 6 months apart, and during this time two 24-hour dietary recalls (24HDRs) were completed. Statistical methods were compared using inter-class correlation coefficient, unadjusted, energy-adjusted, de-attenuated correlation coefficient, quartile classification, weighted K values, and 95% limits of agreement (LOA). RESULTS: The inter-class correlation coefficients between FFQ1 and FFQ2 ranged from 0.25 to 0.73. The number of subjects classified as identical or adjacent was 72.2 to 85.9%. The crude correlation coefficient between FFQs and 24HDRs was 0.30 ~ 0.81, the energy-adjusted correlation coefficient was 0.16 ~ 0.83, and the de-attenuated correlation coefficient was 0.19 ~ 0.98. Weighted k statistics and Bland-Altman plots showed acceptable agreement between FFQs and 24HDRs. CONCLUSION: The FFQ developed for the population at high risk of cardiovascular and cerebrovascular diseases in areas of Ningxia can be used to measure the dietary intake of nutrients and food groups reliably and validly.

Fat-to-muscle ratio as a predictor for dyslipidaemia in transitional-age youth.

BACKGROUND: Although dyslipidaemia may have a crucial impact on cardiovascular health in adults, there is a lack of specific data in transitional-age youth. Therefore, this study attempted to evaluate the association of dyslipidaemia with fat-to-muscle ratio (FMR), and establish FMR thresholds for diagnosing dyslipidaemia in transitional-age youth. METHODS: One thousand six hundred sixty individuals aged 16 to 24 years from the baseline of a subcohort in the Northwest China Natural Population Cohort: Ningxia Project were analysed. Anthropometric characteristics were gauged by a bioelectrical impedance analyser, and dyslipidaemia components were measured using a Beckman AU480 chemistry analyser. Additionally, this study used logistic regression to estimate the risk of dyslipidaemia based on FMR quintiles, and calculate the gender-specific ideal cut-off values of dyslipidaemia and its components by the receiver operating characteristic (ROC) curve. RESULTS: Of the 1660 participants, aged 19.06 ± 1.14 years, 558 males and 1102 females. The prevalence of dyslipidaemia was 13.4% and was significantly associated with FMR quintiles among all participants (P < 0.05). The ideal values of FMR in diagnosing dyslipidaemia were 0.2224 for males and 0.4809 for females, while males had a higher AUC than females (0.7118 vs. 0.6656). Meanwhile, high FMR values were significantly associated with adverse outcomes of dyslipidaemia, hypercholesterolemia and hypertriglyceridaemia (P < 0.05). CONCLUSIONS: The FMR was positively correlated with the prevalence of dyslipidaemia. The FMR can be used as an effective body composition index for diagnosing dyslipidaemia, especially in males, and preventive strategies should be initiated in transitional-age youth to decrease obesity-related dyslipidaemia.

Identification of SRSF3 target mRNAs using inducible TRIBE.

Serine and arginine-rich splicing factor 3 (SRSF3), the smallest member of the Ser/Arg-rich (SR) RNA-binding protein family, regulates multiple aspects of post-transcriptional gene expression program. Although SRSF3 is essential for early embryo development, reprogramming, and pluripotency maintenance, the RNA targets and specificity of RNA recognition of SRSF3 are not well understood in human pluripotent stem cells. In this study, we used inducible TRIBE (targets of RNA binding sites by editing) to identify RNA targets and binding motifs of SRSF3 in human embryonic stem cells (hESCs). We identified 3888 confident binding sites of SRSF3, corresponding to 1222 gene targets. Our results showed that nearly half of the binding sites were distributed in exons, reflecting the alternative splicing function of SRSF3. Motif analysis demonstrated that two of the SRSF3 recognition sequences were the same as the motifs identified in mouse embryonic stem cells, suggesting the recognition sequences of SRSF3 may be conserved in mammals. Overall, our analyses revealed the RNA targets of SRSF3 and uncovered its RNA recognition specificity, providing a valuable resource for understanding the function of SRSF3 in human embryonic stem cells.

Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain.

DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is fwa, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing up-regulation of FWA and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA up-regulation, and a heritable late-flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF-TET1cd fusions, the SunTag-TET1cd system is able to target demethylation and activate gene expression when directed to the FWA or CACTA1 loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis.

Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion. This enabled us to identify high-confidence differentially methylated regions (hcDMRs) by comparing each test library to over 50 high-quality wild-type controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their effect on DNA methylation. In addition to confirming existing relationships, we revealed unanticipated connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at nonoverlapping regions of CMT2 targeted heterochromatin. Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes and can also be adopted for other genomics datasets.

A Visible-Light-Harvesting Covalent Organic Framework Bearing Single Nickel Sites as a Highly Efficient Sulfur-Carbon Cross-Coupling Dual Catalyst.

Covalent Organic Frameworks (COFs) have recently emerged as light-harvesting devices, as well as elegant heterogeneous catalysts. The combination of these two properties into a dual catalyst has not yet been explored. We report a new photosensitive triazine-based COF, decorated with single Ni sites to form a dual catalyst. This crystalline and highly porous catalyst shows excellent catalytic performance in the visible-light-driven catalytic sulfur-carbon cross-coupling reaction. Incorporation of single transition metal sites in a photosensitive COF scaffold with two-component synergistic catalyst in organic transformation is demonstrated for the first time.

Estimating 24-h urinary sodium excretion from casual spot urine specimen among hypertensive patients in Northwest China: the Salt Substitute and Stroke Study.

OBJECTIVE: To develop an equation that can estimate the 24-h urinary Na excretion by using casual spot urine specimen for older hypertensive participants in rural Ningxia and further to compare with the INTERSALT method, Kawasaki method and Tanaka method. DESIGN: Older hypertensive participants in rural Ningxia provided their casual spot urine samples and 24-h urine samples between January 2015 and February 2017. Sex-specific equation was developed using linear forward stepwise regression analysis. Model fit was assessed using adjusted R2. Approximately half of all participants were randomly selected to validate the equation. Mean differences, intraclass correlation coefficients and Bland-Altman plots were used to evaluate the performance of all methods. SETTING: Pingluo County and Qingtongxia County in Ningxia Hui Autonomous Region, China. PARTICIPANTS: Older hypertensive participants in rural Ningxia. RESULTS: Totally, 807 of 1120 invited participants provided qualified 24-h urine samples and spot urine samples. There was no statistical difference comparing the laboratory-based method against the new method and the INTERSALT method, while Kawasaki method had the largest bias with a mean difference of 40·81 g/d (95 % CI 39·27, 42·35 g/d). Bland-Altman plots showed similar pattern of the results. CONCLUSION: The INTERSALT method and the new equation have the potential to estimate the 24-h urinary Na excretion in this study population. However, the extrapolation of the results to other population needs to be careful. Future research is required to establish a more reliable method to estimate 24-h urinary Na excretion.

Vascular endothelial growth factor C participates in regulation of maspin in extravillous trophoblast cell migration and invasion.

Mammary serine protease inhibitor (maspin ; also known as serpin family B member 5 (SERPINB5)) plays a vital role in regulating the biological functions of extravillous trophoblast (EVT) cells, but the mechanism remains unclear. Vascular endothelial growth factor (VEGF ) C is a signature angiogenic molecule expressed and secreted by first-trimester trophoblasts, and bioinformatics analyses has revealed upregulation of VEGFC in pre-eclampsia. The aim of this study was to explore whether maspin regulates EVT cells by regulating the expression of VEGFC . Reverse transcription-polymerase chain reaction and western blotting were used to investigate the effects of hypoxia on the expression of VEGFC in EVT cells. Cells were treated with recombinant (r) maspin and decitabine (to selectively inhibit DNA methyltransferases and then upregulate maspin gene expression), and the effects on VEGFC expression evaluated. In addition, the effects of rVEGFC on the biological functions of EVT cells invitro were evaluated using cell migration and invasion assays. Hypoxia increased the expression of VEGFC in EVT cells. rMaspin upregulated the expression of VEGFC in normoxic EVT cells, and downregulated the expression of VEGFC in hypoxic EVT cells at 24h. Decitabine increased VEGFC expression in normoxic EVT cells, but had no significant effect on VEGFC expression in hypoxic EVT cells. rVEGFC promoted the migration and invasion of normoxic EVT cells and inhibited the invasion of hypoxic EVT cells. These results suggest that VEGFC is involved in the regulation of maspin in EVT cell migration and invasion. However, other molecular mechanisms may be involved and require further investigation.

Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes.

The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions. In Arabidopsis, AtMORC1, AtMORC2, and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements. Here, we studied Arabidopsis AtMORC4 and AtMORC7. We found that, in contrast to AtMORC1,2,6, they act to suppress a wide set of non-methylated protein-coding genes that are enriched for those involved in pathogen response. Furthermore, atmorc4 atmorc7 double mutants show a pathogen response phenotype. We found that AtMORC4 and AtMORC7 form homomeric complexes in vivo and are concentrated in discrete nuclear bodies adjacent to chromocenters. Analysis of an atmorc1,2,4,5,6,7 hextuple mutant demonstrates that transcriptional de-repression is largely uncoupled from changes in DNA methylation in plants devoid of MORC function. However, we also uncover a requirement for MORC in both DNA methylation and silencing at a small but distinct subset of RNA-directed DNA methylation target loci. These regions are characterized by poised transcriptional potential and a low density of sites for symmetric cytosine methylation. These results provide insight into the biological function of MORC proteins in higher eukaryotes.