Biology subjects

Zheng, K.

Publications and source records attributed to Zheng, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Multi-Scale Protein Language Model for Unified Molecular Modeling

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pretraining on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in proteinmolecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins.1

bioinformatics↗

bioRxiv2024

Mitochondrial respiration is essential for photosynthesis-dependent ATP supply of the plant cytosol

Plants rely on solar energy to synthesize ATP and NADPH for photosynthetic carbon fixation. Since a substantial proportion of cellular ATP is consumed in the cytosol, photosynthesis-derived ATP needs to be supplied there. While the triose phosphate shuttle and mitochondrial respiration can both deliver ATP to the cytosol, the significance of the different mechanisms in vivo has been difficult to assess. Although mitochondrial respiration is essential in plants, whether this is due to heterotrophic bottlenecks during plant development or rather a need for respiration in photosynthetically active cells, has not been resolved. In this study, we examined in vivo changes of cytosolic ATP concentration in response to light, employing a biosensing strategy in the moss Physcomitrium patens. Our measurements revealed increased cytosolic ATP concentration caused by photosynthetic activity. Moss tissue depleted of respiratory complex I showed decreased cytosolic ATP accumulation, highlighting a critical role of mitochondrial respiration in light-dependent ATP supply of the cytosol. Consistently, targeting mitochondrial ATP production directly, through the construction of mutants deficient in mitochondrial ATPase (complex V), led to drastic growth reduction, despite only minor alterations in photosynthetic electron transport activity. Since P. patens is photoautotrophic throughout its development, we conclude that heterotrophic bottlenecks cannot account for the indispensable role of mitochondrial respiration in plants. Instead, our results offer compelling evidence that mitochondrial respiration is essential for ATP provision to the cytosol in actively photosynthesizing cells. Mitochondrial respiration provides metabolic integration, ensuring a reliable supply of cytosolic ATP essential for supporting plant growth and development.

plant biology↗

bioRxiv2023

Modeling Sex Differences in the Effects of Diuretics in Renal Epithelial Transport during Angiotensin II-induced Hypertension

Chronic angiotensin II (AngII) infusion is an experimental model that induces hypertension in rodents. The natriuresis, diuresis, and blood pressure responses differ between males and females, perhaps unexpectedly, given the rodent kidney, which plays a key role in blood pressure regulation, exhibit marked sex differences. Those sex differences include morphology, hemodynamics, and, under healthy (undrugged) conditions, solute and electrolyte transporter abundance. Notably, compared to the male rat nephron, the female rat nephron exhibits lower Na+/H+ exchanger 3 (NHE3) activity along the proximal tubule, but higher Na+ transporter activities along the distal segments. AngII infusion-induced hypertension induces a pressure natriuretic response that reduces NHE3 activity and shifts Na+ transport capacity downstream, to different extents in the two sexes. The goals of this study are (i) to understand how the sexually dimorphic responses differentially impact segmental electrolyte transport following a 14- day AngII infusion, and (ii) to identify and explain any sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics. To achieve those goals, we developed sex-specific computational models of renal epithelial transport of electrolytes and water. Model simulations suggest that the NHE3 downregulation in the proximal tubule is a major contributor to natriuresis and diuresis in hypertension, with a stronger effect in males. Due to the downstream shift of Na+ transport load in hypertension, all three diuretic classes are predicted to induce stronger natriuretic and diuretic effects under hypertension compared to normotension, especially in females. New and NoteworthySex differences in the prevalence of hypertension are found in humans and animal models. The kidney, which plays an important role in blood pressure regulation, exhibits sex differences in morphology, hemodynamics, and membrane transporter distributions. This computational modeling study provides insights into how the sexually dimorphic responses to a 14-day angiotensin II infusion differentially impact segmental electrolyte transport. Simulations results also explain sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics.

physiology↗

bioRxiv2023

Protein migration and topography mapping reveals endogenous protein processing and homomers in Nicotiana benthamiana.

Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant protein in plants, yet only few processing events have been described in agroinfiltrated Nicotiana benthamiana, which has emerged as a favorite transient protein expression platform in plant science and molecular pharming. Here, we used in-gel digests and mass spectrometry to monitor the migration and topography of 5,040 plant proteins of agroinfiltrated N. benthamiana within a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel. These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. For instance, this analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor-like kinases. Transient expression of double-tagged candidate proteins confirmed various processing events in vivo. This extensive proteomic dataset can be investigated further and demonstrates that most plant proteins are proteolytically processed and implicates an extensive proteolytic machinery shaping the proteome of agroinfiltrated N. benthamiana.

plant biology↗

bioRxiv2023

Three Conserved Immune Dysfunction and Exclusion Subtypes in Bladder and Pan-cancers: Prognostic and Immunotherapeutic Significance

Molecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, its clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. We identified 69 TIDE biomarker genes and classified BC samples into three subtypes. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples. This subtyping method was proved to be more efficient than known methods in identifying non-responders to immunotherapy. We also found that combining our TIDE subtypes with known biomarkers can improve the sensitivity and specificity in predicting ICB response. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, the TIDE subtypes are conserved across pan-tumors. In conclusion, our novel TIDE-based strategy is a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized immunotherapy.

bioinformatics↗

bioRxiv2023

Increased epithelial mTORC1 activity in chronic rhinosinusitis with nasal polyps

BackgroundThe airway epithelium plays a central role in the pathogenesis of chronic respiratory diseases such as asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), but the mechanisms by which airway epithelial cells (EpCs) maintain inflammation are poorly understood. ObjectiveWe hypothesized that transcriptomic assessment of sorted airway EpCs across the spectrum of differentiation would allow us to define mechanisms by which EpCs perpetuate airway inflammation. MethodsEthmoid sinus EpCs from adult patients with CRS were sorted into 3 subsets, bulk RNA sequenced, and analyzed for differentially expressed genes and pathways. Single cell RNA-seq (scRNA-seq) datasets from eosinophilic and non-eosinophilic CRSwNP and bulk RNA-seq of EpCs from mild/moderate and severe asthma were assessed. Immunofluorescent staining and ex vivo functional analysis of sinus EpCs were used to validate our findings. ResultsAnalysis within and across purified EpC subsets revealed an enrichment in glycolytic programming in CRSwNP vs CRSsNP. Correlation analysis identified mammalian target of rapamycin complex 1 (mTORC1) as a potential regulator of the glycolytic program and identified EpC expression of cytokines and wound healing genes as potential sequelae. mTORC1 activity was upregulated in CRSwNP, and ex vivo inhibition demonstrated that mTOR is critical for EpC generation of CXCL8, IL-33, and CXCL2. Across patient samples, the degree of glycolytic activity was associated with T2 inflammation in CRSwNP, and with both T2 and non-T2 inflammation in severe asthma. ConclusionsTogether, these findings highlight a metabolic axis required to support epithelial generation of cytokines critical to both chronic T2 and non-T2 inflammation in CRSwNP and asthma. KEY MESSAGESO_LIEpithelial mTORC1 activity is upregulated in CRSwNP. C_LIO_LImTOR regulates EpC cytokine generation. C_LIO_LIEpithelial metabolic reprograming correlates with T2 inflammation in CRSwNP, and with both T2 and non-T2 inflammation in asthma. C_LI CAPSULE SUMMARYmTORC1 mediates EpC cytokine generation in CRSwNP.

immunology↗

bioRxiv2023

Phosphorylation barcodes direct biased chemokine signaling at CXCR3

G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered {beta}-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.

biochemistry↗

bioRxiv2022

Increasing the sensitivity, recovery, and integrality of spatially resolved proteomics by LCM-MTA

Conventional proteomic approaches neglect tissue heterogeneity and spatial localization information. Laser capture microdissection (LCM) can isolate specific cell populations or histological areas from heterogeneous tissue specimens while preserving spatial localization information. Formalin-fixed paraffin-embedded (FFPE) is currently a standardized method for long-term stable preservation of clinical tissue specimens. However, spatially resolved proteomics (SRP) studies of FFPE tissues by combined LCM and mass spectrometry (MS)-based proteomics face challenges, such as formalin-induced protein crosslinking limits protein extraction and digestion, protein loss during sample preparation, and the detectability of MS for trace tissues. Therefore, it is necessary to specifically develop SRP sample preparation methods and MS methods suitable for trace FFPE tissues. Here, we provide an SRP method suitable for trace FFPE tissues produced by LCM, termed LCM-Magnetic Trace Analysis (LCM-MTA), which can significantly increase the sensitivity, recovery, and integrality of SRP. The starting material has been reduced to about 15 cells, which resolution is comparable to existing spatially resolved transcriptome (SRT). We also apply our LCM-MTA into SRP studies on clinical colorectal cancer (CRC) tissues and accurately distinguish the functional differences of different cell types. In conclusion, LCM-MTA is a convenient, universal, and scalable method for SRP of trace FFPE tissues, which can be widely used in clinical and non-clinical research fields.

systems biology↗

bioRxiv2022

E6AP is important for HPV E6 role in regulating epithelial homeostasis and its loss impairs keratinocyte commitment to differentiation

Human papillomaviruses (HPV) typically cause chronic infections by modulating homeostasis of infected basal cell to ensure persistence. Using FUCCI and cell-cell competition assays, we established the role of two common viral targets of low-risk and high-risk E6 proteins, E6AP and NHERF1, on four key components of epithelial homeostasis. These includes cell density, proliferation, commitment to differentiation and basal layer delamination. Our RNA sequencing results validated E6s effects on homeostasis and revealed similar transcriptional gene regulation of E6-expressing cells and E6AP-/- cells. For example, yes-associated protein (YAP) target genes were up-regulated by either E6 expression or E6AP depletion. This is also supported by YAP expression pattern in both monolayer cell culture and HPV-infected clinical tissues. As the conserved binding partner of Alpha group HPV E6 proteins, the precise role of E6AP in modulating keratinocyte phenotype and associated signalling pathways have not been defined. We demonstrate that deletion of E6AP in keratinocytes delayed the onset of differentiation and the abundance of E6AP is reduced in HPV-infected tissue. This suggests that Alpha E6 regulates epithelium homeostasis by inhibiting E6APs activity, leading to alteration of multiple downstream pathways including YAP activation. Potential treatments can thus be developed to resolve the reservoir of HPV infection.

pathology↗

bioRxiv2022

Redefining and subtyping of major depression based on brain functional connectivity signatures with high generalization: an ensemble hybrid framework

Current clinical diagnosis of major depression is solely based on subjective symptoms and signs rather than the underlying biological mechanisms, which has hindered the improvement in treatment effectiveness and outcomes. Redefining and subtyping major depressive disorder (MDD) based on neural circuits has been an emerging consensus. Here, we proposed a novel ensemble hybrid deep-learning framework based on graph neural network for redefining and subtyping of MDD with the brains "fingerprinting", i.e. nuanced functional connectivity profiles. A graph neural network (GNN) based supervised model was first employed to discriminate MDD patients from healthy controls. The graph embedding features obtained from the supervised classifier was then employed for subtyping of MDD with an unsupervised clustering by fast search and find of density peaks (CFDP) approach. The generalization accuracy and reproducibility of the proposed framework were further validated with one of the largest resting-state fMRI data set for MDD which included 2428 participants recruited from 25 independent sites. Our classifier showed a high generalization of 75% for leave-one-site-out cross validation. In addition, we obtained three biologically homogenous MDD subtypes characterized by impairments in subcortical-limbic, DMN-FPN, VN-SMN circuits, respectively. Notably, we demonstrated that subtyping of MDD according to graph embedding features showed high robustness and reproducibility across different sites. The proposed framework is not only essential for redefining and subtyping of MDD, but also paves the way towards precision medicine of mental disorders.

neuroscience↗

bioRxiv2022

Pliable synaptic fidelity and excitatory inter-synaptic crosstalk in the intact brain

Memory formation in neural circuits may involve changes in synaptic efficacy and in cell intrinsic excitability, yet how this process unfolds in the living brain has remained elusive. Here, we employed multiplexed imaging of genetically encoded indicators of glutamate and Ca2+ in mouse barrel cortex to detect increased fidelity coupled with reduced excitation of thalamocortical connections that undergo whisker-stimulation induced LTP. High-resolution imaging revealed that whisker stimuli trigger excitatory synaptic activity that generates extrasynaptic glutamate transients reaching the bulk of neighbouring synapses in the target cortical area. Our findings pave the way to understanding basic plasticity features of the synaptic connectome while revealing a significant component of volume-transmitted glutamatergic signalling among cells in the intact brain. One Sentence SummarySensory-stimulation LTP increases fidelity while reducing excitation at individual thalamocortical connections which generate spatially intersecting glutamate discharges

neuroscience↗

bioRxiv2022

Genomic and phylogenetic analysis of the first myovirus isolated from Oceanospirillaceae, representing a novel viral cluster prevalent in polar oceans

The marine bacterial family Oceanospirillaceae, which is abundant in the deep-seas and polar oceans, is closely associated with algal blooms and petroleum hydrocarbons degradation. However, only a few Oceanospirillaceae-infecting phages have so far been reported. Here we report on a novel Oceanospirillum phage, vB_OsaM_PD0307, which is the first myovirus to be found that infects Oceanospirillaceae. vB_OsaM_PD0307 with a 44,421 bp linear dsDNA genome. Phylogenetic analysis and average nucleotide sequence identities suggest that vB_OsaM_PD0307 is different from other phage isolates and represents a novel genus-level myoviral cluster with two high-quality uncultured viral genomes, designed as Oceanospimyovirus. Additionally, the biogeographical distribution of the vB_OsaM_PD0307 cluster suggests that they are widespread in the oceans and abundant in polar areas. In summary, our findings expand the current understanding of the phylogenetic diversity, genomic characteristic and function of Oceanospimyovirus phages, and highlight the role of the vB_OsaM_PD0307 phage as a major ecological agent that can infect certain key bacterial groups associated with polar algal blooms. ImportanceOceanospirillumphage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae and represents a novel viral genus, Oceanospimyovirus. This study provides insights into the genomic, phylogenetic, and ecological characteristics of myoviruses infecting Oceanospirillaceae and improves our understanding of the interactions between Oceanospirillaceae and their phages in the oceans.

genomics↗

bioRxiv2022

Location bias contributes to functionally selective responses of biased CXCR3 agonists

Some G protein-coupled receptor (GPCR) ligands act as "biased agonists" which preferentially activate specific signaling transducers over others. Although GPCRs are primarily found at the plasma membrane, GPCRs can traffic to and signal from many subcellular compartments. Here, we determine that differential subcellular signaling contributes to the biased signaling generated by three endogenous ligands of the chemokine GPCR CXCR3. The signaling profile of CXCR3 changed as it trafficked from the plasma membrane to endosomes in a ligand-specific manner. Endosomal signaling was critical for biased activation of G proteins, {beta}-arrestins, and ERK1/2. In CD8+ T cells, the chemokines promoted unique transcriptional responses predicted to regulate inflammatory pathways. In a mouse model of contact hypersensitivity, {beta}-arrestin-biased CXCR3-mediated inflammation was dependent on receptor internalization. Our work demonstrates that differential subcellular signaling is critical to the overall biased response observed at CXCR3, which has important implications for drugs targeting chemokine receptors and other GPCRs.

biochemistry↗

bioRxiv2021

In vivo CGG repeat RNA binding protein capture identifies RAN translation modifiers and suppressors of repeat toxicity.

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder caused by a transcribed CGG repeat expansion in the 5 UTR of FMR1. Expanded CGG repeat RNAs both sequester RNA-binding proteins (RBPs) into nuclear foci and undergo repeat-associated non-AUG (RAN) translation into toxic homopolymeric peptides. RBPs that interact with CGG repeats may play a pivotal role in foci formation and/or RAN translation. Here we employed a CGG repeat RNA-tagging system to capture and identify CGG repeat binding RBPs in vivo under different cellular conditions. We found that several SR (serine/arginine-rich domain) proteins interact with CGG repeat RNAs basally and under cellular stress. These same proteins strongly modify toxicity in a Drosophila model of FXTAS, improving eye degeneration and survival. Furthermore, genetic or pharmacological targeting of the serine/arginine protein kinases (SRPKs) suppresses RAN translation in cellular reporters and toxicity in fly models of FXTAS and C9orf72 ALS/FTD. Finally, pharmacological targeting of SRPK1 supressed CGG repeat toxicity and enhanced survival in rodent neurons. Taken together, these findings demonstrate roles for CGG repeat RNA binding proteins in both RAN translation and repeat toxicity and suggest SRPK inhibition may serve as a possible therapeutic strategy in repeat expansion disorders.

neuroscience↗

bioRxiv2020

Alisertib exerts KRAS allele specific anticancer effects in colorectal cancer

Colorectal cancer (CRC) is a common cancer causing substantial mortality and morbidity worldwide. Oncogene RAS mutations occur notably in [~]45% of CRCs, associated with a poor prognosis. KRAS is subject to multiple tiers of regulation, including kinase. Aurora kinases has been implicated in many types of tumor onsets and progression, making them as a promising therapeutic targets. Alisertib (ALS), selectively inhibits Aurora kinase A (AURKA) and exerts potent anticancer activities in vitro and in vivo studies, but the latent anticancer effect of ALS on CRC remains unclear in the context of different KRAS mutations. This study aimed to assess the effects of ALS on RAS signaling pathway in a panel of CRC lines expressing different KRAS alleles, including Caco-2 (KRAS WT), Colo-678 (KRAS G12D), SK-CO-1 (KRAS G12V), HCT116 (KRAS G13D), CCCL-18 (KRAS A146T), and HT29 (BRAF V600E). The results showed that ALS modulated the active form of KRAS in a RAS allele specific manner across the panel of CRC lines; ALS differentially regulated RAS signal via PI3K/Akt and MAPK pathways; and ALS induced apoptosis and autophagy in a RAS allele specific manner. Of note, in combination of ALS and MEK inhibitor, selumetinib, enhanced ALS regulatory effects in CRC lines in a RAS allele specific manner on apoptosis, autophagy, and cell growth. Taken together, this study suggests that ALS differentially regulates RAS signaling pathway and manipulates cell apoptosis and autophagy in RAS allele specific manner. The combinatorial approach of ALS and MEK inhibitor may represent a new therapeutic strategy for precision therapy of CRC in a RAS allele manner.

cancer biology↗

bioRxiv2020

DLDTI: A learning-based framework for identification of drug-target interaction using neural networks and network representation

To elucidate novel molecular mechanisms of known drugs, efficient and feasible computational methods for predicting potential drug-target interactions (DTI) would be of great importance. A novel calculation model called DLDTI was generated for predicting DTI based on network representation learning and convolutional neural networks. The proposed approach simultaneously fuses the topology of complex networks and diverse information from heterogeneous data sources and copes with the noisy, incomplete, and high-dimensional nature of large-scale biological data by learning low-dimensional and rich depth features of drugs and proteins. Low-dimensional feature vectors were used to train DLDTI to obtain optimal mapping space and infer new DTIs by ranking DTI candidates based on their proximity to optimal mapping space. DLDTI achieves promising performance under 5-fold cross-validation with AUC values of 0.9172, which was higher than that of the method based on different classifiers or different feature combination technique. Moreover, biomedical experiments were also completed to validate DLDTIs performance. Consistent with the predicted result, tetramethylpyrazine, a member of pyrazines, reduced atherosclerosis progression and inhibited signal transduction in platelets, via PI3K/Akt, cAMP and calcium signaling pathways. The source code and datasets explored in this work are available at https://github.com/CUMTzackGit/DLDTI

bioinformatics↗

bioRxiv2020

SPRDA: a matrix completion approach based on the structural perturbation to infer disease-associated Piwi-Interacting RNAs

Emerging evidence suggests that PIWI-interacting RNAs (piRNAs) are one of the most influential small non-coding RNAs (ncRNAs) that regulate RNA silencing. piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. The main motivation of this work is tantamount to fill the gap in research on large-scale prediction of disease-related piRNAs. In this study, a novel computational model based on the structural perturbation method is proposed, called SPRDA. In detail, the duplex network is constructed based on the piRNA similarity network and disease similarity network extracted from piRNA sequence information, Gaussian interaction profile kernel similarity information and gene-disease association information. The structural perturbation method is then used to predict the potential associations on the duplex network, which is more predictive than other network structures in terms of structural consistency. In the five-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

Global reinforcement of DNA methylation through enhancement of RNA-directed DNA methylation ensures sexual reproduction in rice

DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. In Arabidopsis, however, mutations in RdDM genes cause no visible developmental defects, which raising the question of the biological significance of RdDM in plant development. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes an RNA-dependent RNA polymerase. Mutation in FEM1 substantially decreased genome-wide CHH methylation levels and abolished the accumulation of 24-nt small interfering RNAs. Moreover, male and female reproductive development was disturbed, which led to the sterility of fem1 mutants. In wild-type (WT) plants but not in fem1 mutants, genome-wide CHH DNA methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of methylation in reproductive organs of the WT was attributed to enhancement of RdDM activity including FEM1 activity. More than half of all encoding genes in the rice genome overlapped with hypermethylated regions in the sexual organs of the WT, and many of them appear to be directly regulated by an increase in DNA methylation.Our results demonstrate that a global increase of DNA methylation through enhancement of RdDM activity in reproductive organs ensures sexual reproduction of rice.View Full Text

plant biology↗