RESUMO
The high-yielding Green Revolution varieties of cereal crops are characterized by a semidwarf architecture and lodging resistance. Plant height is tightly regulated by the availability of phosphate (Pi), yet the underlying mechanism remains obscure. Here, we report that rice (Oryza sativa) R2R3-type Myeloblastosis (MYB) transcription factor MYB110 is a Pi-dependent negative regulator of plant height. MYB110 is a direct target of PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) and regulates OsPHR2-mediated inhibition of rice height. Inactivation of MYB110 increased culm diameter and bending resistance, leading to enhanced lodging resistance despite increased plant height. Strikingly, the grain yield of myb110 mutants was elevated under both high- and low-Pi regimes. Two divergent haplotypes based on single nucleotide polymorphisms in the putative promoter of MYB110 corresponded with its transcript levels and plant height in response to Pi availability. Thus, fine-tuning MYB110 expression may be a potent strategy for further increasing the yield of Green Revolution cereal crop varieties.
Assuntos
Grão Comestível , Oryza , Grão Comestível/genética , Oryza/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Produtos Agrícolas , Fosfatos/metabolismoRESUMO
The genome of an individual from an admixed population consists of segments originated from different ancestral populations. Most existing ancestry inference approaches focus on calling these segments for the extant individual. In this paper, we present a general ancestry inference approach for inferring recent ancestors from an extant genome. Given the genome of an individual from a recently admixed population, our method can estimate the proportions of the genomes of the recent ancestors of this individual that originated from some ancestral populations. The key step of our method is the inference of ancestors (called founders) right after the formation of an admixed population. The inferred founders can then be used to infer the ancestry of recent ancestors of an extant individual. Our method is implemented in a computer program called PedMix2. To the best of our knowledge, there is no existing method that can practically infer ancestors beyond grandparents from an extant individual's genome. Results on both simulated and real data show that PedMix2 performs well in ancestry inference.
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Genética Populacional , Avós , Humanos , Software , Genoma Humano/genéticaRESUMO
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, and then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature, and there are excellent tools available for inferring phylogenetic trees from a large number of biomolecular sequences. A tree-child network is a phylogenetic network satisfying the condition that every nonleaf node has at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference. Our new program, named ALTS, is fast enough to infer a tree-child network with a large number of reticulations for a set of up to 50 phylogenetic trees with 50 taxa that have only trivial common clusters in about a quarter of an hour on average.
Assuntos
Algoritmos , Genoma , Humanos , FilogeniaRESUMO
Centromeres in most multicellular eukaryotes are composed of long arrays of repetitive DNA sequences. Interestingly, several transposable elements, including the well-known long terminal repeat centromeric retrotransposon of maize (CRM), were found to be enriched in functional centromeres marked by the centromeric histone H3 (CENH3). Here, we report a centromeric long interspersed nuclear element (LINE), Celine, in Populus species. Celine has colonized preferentially in the CENH3-associated chromatin of every poplar chromosome, with 84% of the Celine elements localized in the CENH3-binding domains. In contrast, only 51% of the CRM elements were bound to CENH3 domains in Populus trichocarpa. These results suggest different centromere targeting mechanisms employed by Celine and CRM elements. Nevertheless, the high target specificity seems to be detrimental to further amplification of the Celine elements, leading to a shorter life span and patchy distribution among plant species compared with the CRM elements. Using a phylogenetically guided approach, we were able to identify Celine-like LINE elements in tea plant (Camellia sinensis) and green ash tree (Fraxinus pennsylvanica). The centromeric localization of these Celine-like LINEs was confirmed in both species. We demonstrate that the centromere targeting property of Celine-like LINEs is of primitive origin and has been conserved among distantly related plant species.
Assuntos
Centrômero , Cromossomos de Plantas , Populus , Retroelementos , Populus/genética , Centrômero/genética , Centrômero/metabolismo , Cromossomos de Plantas/genética , Retroelementos/genética , Elementos Nucleotídeos Longos e Dispersos/genética , Filogenia , Histonas/metabolismo , Histonas/genéticaRESUMO
Seed germination represents a major developmental switch in plants that is vital to agriculture, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis thaliana requires a chromatin mechanism that progressively silences 9-CIS-EPOXYCAROTENOID DIOXYGENASE 6 (NCED6), which encodes a rate-limiting enzyme in abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocked germination and synergistically derepressed NCEDs and hundreds of genes. At NCED6, in part by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also an H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis revealed that RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination, when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate for and synergize with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via the RNA-binding protein RZ-1 and PRC2 acting in synergy, a process that is vital for seed germination.
Assuntos
Proteínas de Arabidopsis , Arabidopsis , Ácido Abscísico/metabolismo , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cromatina/genética , Regulação da Expressão Gênica de Plantas/genética , Germinação/genética , Histonas/genética , Histonas/metabolismo , SementesRESUMO
3D carbon-based porous sponges are recognized for significant potential in oil absorption and electromagnetic interference (EMI). However, their widespread application is hindered by a common compromise between high performance and affordability of mass production. Herein, a novel approach is introduced that involves laser-assisted micro-zone heating melt-blown spinning (LMHMS) to address this challenge by creating pitch-based submicron carbon fibers (PSCFs) sponge with 3D interconnected structures. These structures bestow the resulting sponge exceptional characteristics including low density (≈20 mg cm-3), high porosity (≈99%), remarkable compressibility (80% maximum strain), and superior conductivity (≈628 S m-1). The resultant PSCF sponges realize an oil/organic solvent sorption capacity over 56 g/g and possess remarkable regenerated ability. In addition to their effectiveness in cleaning up oil/organic solvent spills, they also demonstrated strong electromagnetic shielding capabilities, with a total shielding effectiveness (SE) exceeding 60 dB across the X-band GHz range. In virtue of extreme lightweight of ≈20 mg cm-3, the specific SE of the PSCF sponge reaches as high as ≈1466 dB cm3 g-1, surpassing the performance of numerous carbon-based porous structures. Thus, the unique blend of properties renders these sponges promising for transforming strategies in addressing oil/organic solvent contaminations and providing effective protection against EMI.
RESUMO
Identification of transcription factor binding sites (TFBSs) is essential to understanding of gene regulation. Designing computational models for accurate prediction of TFBSs is crucial because it is not feasible to experimentally assay all transcription factors (TFs) in all sequenced eukaryotic genomes. Although many methods have been proposed for the identification of TFBSs in humans, methods designed for plants are comparatively underdeveloped. Here, we present PlantBind, a method for integrated prediction and interpretation of TFBSs based on DNA sequences and DNA shape profiles. Built on an attention-based multi-label deep learning framework, PlantBind not only simultaneously predicts the potential binding sites of 315 TFs, but also identifies the motifs bound by transcription factors. During the training process, this model revealed a strong similarity among TF family members with respect to target binding sequences. Trans-species prediction performance using four Zea mays TFs demonstrated the suitability of this model for transfer learning. Overall, this study provides an effective solution for identifying plant TFBSs, which will promote greater understanding of transcriptional regulatory mechanisms in plants.
Assuntos
Regulação da Expressão Gênica , Fatores de Transcrição , Humanos , Sítios de Ligação , Ligação Proteica , Fatores de Transcrição/metabolismo , Redes Neurais de ComputaçãoRESUMO
N 6-methyladenosine (m6A), the most prevalent mRNA modification in eukaryotes, is an emerging player of gene regulation at transcriptional and translational levels. Here, we explored the role of m6A modification in response to low temperature in Arabidopsis (Arabidopsis thaliana). Knocking down mRNA adenosine methylase A (MTA), a key component of the modification complex, by RNA interference (RNAi) led to drastically reduced growth at low temperature, indicating a critical role of m6A modification in the chilling response. Cold treatment reduced the overall m6A modification level of mRNAs especially at the 3' untranslated region. Joint analysis of the m6A methylome, transcriptome and translatome of the wild type (WT) and the MTA RNAi line revealed that m6A-containing mRNAs generally had higher abundance and translation efficiency than non-m6A-containing mRNAs under normal and low temperatures. In addition, reduction of m6A modification by MTA RNAi only moderately altered the gene expression response to low temperature but led to dysregulation of translation efficiencies of one third of the genes of the genome in response to cold. We tested the function of the m6A-modified cold-responsive gene ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE 1 (DGAT1) whose translation efficiency but not transcript level was reduced in the chilling-susceptible MTA RNAi plant. The dgat1 loss-of-function mutant exhibited reduced growth under cold stress. These results reveal a critical role of m6A modification in regulating growth under low temperature and suggest an involvement of translational control in chilling responses in Arabidopsis.
Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Regulação da Expressão Gênica , Transcriptoma/genética , Temperatura Baixa , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Diacilglicerol O-Aciltransferase/metabolismoRESUMO
BACKGROUND: The role of miR-145-5p in non-small cell lung cancer (NSCLC) has been studied, however, the regulation of hBMSCs-derived exosomes (Exo) transmitted miR-145-5p in NSCLC was still unknown. This study aimed to investigate the role of hBMSCs-derived exosomes (Exo) in the progression of NSCLC. METHODS: The Exo was extracted from hBMSCs and added to A549 and H1299 cell culture, followed by the detection of cell proliferation, migration, and invasion. The correlation between the expression of miR-145-5p and SOX9, as well as their binding relationship was determined by correlation analysis, luciferase gene reporter assay and RNA pull-down assays. The in vivo animal model was established to further verify the impact of hBMSCs-Exo. RESULTS: It showed that miR-145-5p was downregulated and SOX9 was upregulated in NSCLC tissues. HBMSCs-derived Exo, and hBMSCs-Exo with overexpression of miR-145-5p could inhibit cell proliferation, migration, and invasion of both A549 and H1299 cells, and prevent against tumor progression in vivo. MiR-145-5p and SOX9 were found to be able to bind to each other, and a negative correlation were observed between the expression of them in NSCLC tissues. Furthermore, inhibition of SOX9 could reversed the suppressed role of miR-145-5p in vitro and in vivo. CONCLUSION: Therefore, HBMSCs-Exo effectively transmitted miR-145-5p, leading to the suppression of malignant development in NSCLC through the regulation of SOX9.
Assuntos
Carcinoma Pulmonar de Células não Pequenas , Movimento Celular , Proliferação de Células , Exossomos , Neoplasias Pulmonares , Células-Tronco Mesenquimais , MicroRNAs , Fatores de Transcrição SOX9 , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Fatores de Transcrição SOX9/metabolismo , Fatores de Transcrição SOX9/genética , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/metabolismo , Animais , Exossomos/metabolismo , Exossomos/genética , Camundongos , Proliferação de Células/genética , Células-Tronco Mesenquimais/metabolismo , Movimento Celular/genética , Progressão da Doença , Regulação Neoplásica da Expressão Gênica , Linhagem Celular Tumoral , Masculino , Feminino , Células A549 , Ensaios Antitumorais Modelo de XenoenxertoRESUMO
The transformation of the global power structure caused by the carbon neutrality goal will promote copper consumption. It is crucial to explore the decarbonization pathways of the copper industry to help fulfill greenhouse gas (GHG) emission reduction targets. This study utilized material flow analysis and life cycle assessment methods to investigate 12 different subscenarios based on international trade, circular economy, technology evolution, and environmental market factors. Policy combination scenario is employed to reveal the mechanism of decarbonization. The results show that refined copper consumption in China is expected to increase by 62.3% in 2060 compared to 2020. The GHG emissions of China's copper industry will reach 9.1 million tonnes (Mt) CO2e in 2060, technology evolution and environmental market are crucial for realizing carbon neutrality goal of this industry, accounting for 26.4 and 47.2% of emissions reductions, respectively, between 2020 and 2060. International trade and circular economy play important roles in the high-quality carbon peaking stage; however, imported copper and domestic secondary copper will constitute the basic supply of copper resources in China in the long run, and the comparative advantages of them will gradually weaken. Policy combination scenario can achieve the incentive synergy effect, with GHG reduced to 0.5 Mt CO2e in 2060. The enhanced application of policies such as material substitution and carbon emission trading will further promote industry to achieve net-zero GHG emission. We suggest regulating the industry's structure based on the international systemic circulation pattern and accelerating the construction of a green circular chain in the short term to achieve sustainable copper supply and high-quality carbon peaking. Promoting a high-quality technology development strategy and enhancing the environmental markets are recommended in the long term to achieve carbon neutrality.
Assuntos
Efeito Estufa , Gases de Efeito Estufa , Cobre , Carbono , Comércio , Internacionalidade , China , Dióxido de Carbono/análiseRESUMO
Alzheimer's disease (AD) and osteoarthritis (OA) are both senile degenerative diseases. Clinical studies have found that OA patients have a significantly increased risk of AD in their later life. This study hypothesized that chronic aseptic inflammation might lead to AD in KOA patients. However, current research has not yet clarified the potential mechanism between AD and KOA. Therefore, this study intends to use KOA transcriptional profiling and single-cell sequencing analysis technology to explore the molecular mechanism of KOA affecting AD development, and screen potential molecular biomarkers and drugs for the prediction, diagnosis, and prognosis of AD in KOA patients. It was found that the higher the expression of TXNIP, MMP3, and MMP13, the higher the risk coefficient of AD was. In addition, the AUC of TXNIP, MMP3, and MMP13 were all greater than 0.70, which had good diagnostic significance for AD. Finally, through the virtual screening of core proteins in FDA drugs and molecular dynamics simulation, it was found that compound Cobicistat could be targeted to TXNIP, Itc could be targeted to MMP3, and Isavuconazonium could be targeted to MMP13. To sum up, TXNIP, MMP3, and MMP13 are prospective molecular markers in KOA with AD, which could be used to predict, diagnose, and prognosis.
RESUMO
Nonsense-mediated mRNA decay (NMD) is an important RNA quality control pathway. It aids in degrading harmful erroneous mRNA, thereby preserving a stable and healthy internal environment. In this study, we employed CRISPR/Cas9 and amiRNA technology to generate knock out or knock down mutants of realted genes in the rice NMD pathway. Through transcriptome sequencing and observing phenotype changes, the study explored the impact of NMD pathway defects on rice gene expression and alternative splicing. The results suggest that even partial defects will induce phenotypic changes such as plant height and pollen vitality to different degrees, showing necessity of NMD factors. Gene expression analysis reveals that most differentially expressed genes are upregulated in the mutants, with ko-upf1-like and kd-upf1 defects having a more significant impact than kd-upf2 and kd-upf3. Specifically, NMD pathway defects result in increased expression levels of rice defense response-related genes and decreased expression levels of secondary metabolism-related genes, with a wider range of affected genes observed in 60-day-old senescence mutants. Transcript analysis indicates that different NMD related genes defects alter hundreds of alternative splicing events, mostly enriched in genes involving alternative splicing regulatory pathways. Approximately half of these events are shared among different mutants, and a substantial number of affected transcripts show NMD target features. NMD could affect both the transcript abundance and their splicing subtypes to regulate the defense response and early-senescence associated pathways, which plays a vital role in rice growth and reproduction.
Assuntos
Regulação da Expressão Gênica de Plantas , Degradação do RNAm Mediada por Códon sem Sentido , Oryza , Fenótipo , Transcriptoma , Oryza/genética , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Degradação do RNAm Mediada por Códon sem Sentido/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Processamento AlternativoRESUMO
BACKGROUND: Structural variation (SV), which ranges from 50 bp to [Formula: see text] 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Three types of signals, including discordant read-pairs, reads depth and split reads, are commonly used for SV detection from high-throughput sequence data. Many tools have been developed for detecting SVs by using one or multiple of these signals. RESULTS: In this paper, we develop a new method called EigenDel for detecting the germline submicroscopic genomic deletions. EigenDel first takes advantage of discordant read-pairs and clipped reads to get initial deletion candidates, and then it clusters similar candidates by using unsupervised learning methods. After that, EigenDel uses a carefully designed approach for calling true deletions from each cluster. We conduct various experiments to evaluate the performance of EigenDel on low coverage sequence data. CONCLUSIONS: Our results show that EigenDel outperforms other major methods in terms of improving capability of balancing accuracy and sensitivity as well as reducing bias. EigenDel can be downloaded from https://github.com/lxwgcool/EigenDel .
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Aprendizado de Máquina não Supervisionado , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genômica/métodos , Genoma Humano , Análise de Sequência de DNA , Variação Estrutural do Genoma , SoftwareRESUMO
Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under cold stress. Here, the B. purpurascens under low temperature were subjected to transcriptomics analysis to explore the candidate genes and pathways that involved in the cold tolerance of B. purpurascens. Compared with the control treatment, we found 9,600 up-regulated differentially expressed genes (DEGs) and 7,055 down-regulated DEGs. A significant number of DEGs were involved in the Ca2+ signaling pathway, mitogen-activated protein kinase (MAPK) cascade, plant hormone signaling pathway, and lipid metabolism. A total of 400 transcription factors were found to respond to cold stress, most of which belonged to the MYB and AP2/ERF families. Five novel genes were found to be potential candidate genes involved in the cold tolerance of B. purpurascens. The study provide insights into further investigation of the molecular mechanism of how B. purpurascens survives under cold stress.
Assuntos
Resposta ao Choque Frio , Regulação da Expressão Gênica de Plantas , Humanos , Resposta ao Choque Frio/genética , Perfilação da Expressão Gênica , Sistema de Sinalização das MAP Quinases , Transdução de Sinais , Temperatura Baixa , TranscriptomaRESUMO
DFT calculations and kinetic analysis have been employed to comprehensively explore the possibility to prepare epoxides by one-step method using the in-situ generated peroxy radicals or hydroperoxides as epoxidizing agents. Computational studies demonstrated that the selectivities for the reaction systems of O2 /R2/R1, O2 /CuH/R1, O2 /CuH/styrene, O2 /AcH/R1 were 68.2%, 69.6%, 100% and 93.3%, respectively. The in-situ generated peroxide radicals, such as HOOË, CuOOË and AcOOË, could react with R1 or styrene by attacking the CC double bond to form a CO bond and subsequently undergoing a cleavage of OO bond to yield epoxides. Peroxide radicals could abstract a hydrogen atom from methyl group on R1, forming unwanted by-products. It should be noted that the hydrogen atoms of HOOË is easy to be abstracted by CC double bond and simultaneously the oxygen atom is connected to the CH moiety to form an alkyl peroxy radical (Rad11), greatly limiting the selectivity. The comprehensive mechanistic studies provide a deep understanding on preparing epoxides by one-step method.
RESUMO
CRISPR-based directed evolution is an effective breeding biotechnology to improve agronomic traits in plants. However, its gene diversification is still limited using individual single guide RNA. We described here a multiplexed orthogonal base editor (MoBE), and a randomly multiplexed sgRNAs assembly strategy to maximize gene diversification. MoBE could induce efficiently orthogonal ABE (<36.6%), CBE (<36.0%), and A&CBE (<37.6%) on different targets, while the sgRNA assembling strategy randomized base editing events on various targets. With respective 130 and 84 targets from each strand of the 34th exon of rice acetyl-coenzyme A carboxylase (OsACC), we observed the target-scaffold combination types up to 27 294 in randomly dual and randomly triple sgRNA libraries. We further performed directed evolution of OsACC using MoBE and randomly dual sgRNA libraries in rice, and obtained single or linked mutations of stronger herbicide resistance. These strategies are useful for in situ directed evolution of functional genes and may accelerate trait improvement in rice.
Assuntos
Edição de Genes , Oryza , Sistemas CRISPR-Cas/genética , RNA Guia de Sistemas CRISPR-Cas , Oryza/genética , Melhoramento VegetalRESUMO
The regulatory roles of RNA splicing in plant immunity are emerging but still largely obscure. We reported previously that Phytophthora pathogen effector Avr3c targets a soybean protein SKRP (serine/lysine/arginine-rich protein) to impair soybean basal immunity by regulating host pre-mRNA alternative splicing, while the biochemical nature of SKRP remains unknown. Here, by using Arabidopsis as a model, we studied the mechanism of SKRP in regulating pre-mRNA splicing and plant immunity. AtSKRP confers impaired plant immunity against Phytophthora capsici and associates with spliceosome component PRP8 and splicing factor SR45, which positively and negatively regulate plant immunity, respectively. Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) showed AtSKRP is a novel RNA-binding protein that targets exon 3' end of unspliced RNA. Such position-specific binding of SKRP is associated with its activity in suppressing intron retention, including at positive immune regulatory genes UBP25 and RAR1. In addition, we found AtSKRP self-interact and forms oligomer, and these properties are associated with its function in plant immunity. Overall, our findings reveal that the immune repressor SKRP is a spliceosome-associated protein that targets exon 3' end to regulate pre-mRNA splicing in Arabidopsis.
Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , RNA/metabolismo , Precursores de RNA/genética , Precursores de RNA/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Splicing de RNA/genética , Éxons/genética , Imunidade Vegetal/genética , Processamento Alternativo/genética , RNA de Plantas/genética , RNA de Plantas/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismoRESUMO
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. Although the mechanism of RdDM has been well studied in Arabidopsis (Arabidopsis thaliana), most mutations in RdDM genes cause no remarkable developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 (OsRDR2) in rice (Oryza sativa). Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH (H = A, C, or T) methylation. Moreover, male and female reproductive development was disturbed, which led to sterility in osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation may regulate the expression of multiple key genes involved in stamen development, meiosis, and pollen viability. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of CHH methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity, which includes OsRDR2 activity. Our results, which revealed a global increase in CHH methylation through enhancement of RdDM activity in reproductive organs, suggest a crucial role for OsRDR2 in the sexual reproduction of rice.
Assuntos
Metilação de DNA/genética , Oryza/crescimento & desenvolvimento , Oryza/genética , RNA de Plantas/metabolismo , Reprodução/genética , Produtos Agrícolas/genética , Produtos Agrícolas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Variação Genética , Genótipo , Mutação , RNA de Plantas/genéticaRESUMO
RNA-dependent RNA polymerase 6 (RDR6) is a core component of the small RNA biogenesis pathway, but its function in meiosis is unclear. Here, we report a new allele of OsRDR6 (Osrdr6-meiosis [Osrdr6-mei]), which causes meiosis-specific phenotypes in rice (Oryza sativa). In Osrdr6-mei, meiotic double-strand break (DSB) formation is partially blocked. We created a biallelic mutant with more severe phenotypes, Osrdr6-bi, by crossing Osrdr6-mei with a knockout mutant, Osrdr6-edit In Osrdr6-bi meiocytes, 24 univalents were observed, and no histone H2AX phosphorylation foci were detected. Compared with the wild type, the number of 21-nucleotide small RNAs in Osrdr6-mei was dramatically lower, while the number of 24-nucleotide small RNAs was significantly higher. Thousands of differentially methylated regions (DMRs) were discovered in Osrdr6-mei, implying that OsRDR6 plays an important role in DNA methylation. There were 457 genes downregulated in Osrdr6-mei, including three genes, CENTRAL REGION COMPONENT1, P31 comet , and O. sativa SOLO DANCERS, related to DSB formation. Interestingly, the downregulated genes were associated with a high level of 24-nucleotide small RNAs but less strongly associated with DMRs. Therefore, we speculate that the alteration in expression of small RNAs in Osrdr6 mutants leads to the defects in DSB formation during meiosis, which might not be directly dependent on RNA-directed DNA methylation.
Assuntos
Quebras de DNA de Cadeia Dupla , Reparo do DNA , Meiose , Oryza/genética , Proteínas de Plantas/genética , RNA Polimerase Dependente de RNA/genética , Metilação de DNA , Reparo do DNA/fisiologia , Regulação da Expressão Gênica de Plantas , Mutação , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , RNA de Plantas/biossíntese , RNA Polimerase Dependente de RNA/metabolismoRESUMO
Background: The Serum creatinine/cystatin C ratio (Cr/CysC ratio) is an emerging alternative index for muscle mass loss, a risk factor for cardiovascular diseases (CVDs). However, the association between the Cr/CysC ratio and CVD morbidity and mortality remains unknown. Methods: A total of 11,150 participants of the National Health and Nutrition Examination Survey (NHANES) were included in this study. Univariable and multivariable logistic regression models were employed to assess the association between the Cr/CysC ratio and self-reported CVD morbidity. Cox proportional hazard models were used to estimate the hazard ratio (HR) and 95% confidence interval (CI) of the Cr/CysC ratio for CVD mortality. Results: At baseline, 1181 (7.90%) participants had self-reported CVDs. Lower Cr/CysC ratios were found in participants with CVDs (1.18 ± 0.30 vs. 1.05 ± 0.23, p < 0.001). In the multivariable logistic regression model, the Cr/CysC ratio was inversely linked to CVD morbidity (odds ratio: 0.65, 95% CI: 0.52-0.81, p < 0.001, per standard deviation [SD] increase). 997 (8.94%) CVD deaths were documented during a median follow-up of 16.9 years. A higher Cr/CysC ratio was associated with a decreasing risk of CVD mortality (adjusted HR: 0.54, 95% CI: 0.46-0.65, p < 0.001, per SD increase). Conclusions: In NHANES participants, the Cr/CysC ratio had an inverse correlation with CVD morbidity and mortality.