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1.
Trends Genet ; 40(4): 352-363, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38320883

RESUMO

Plant biotechnology plays a crucial role in developing modern agriculture and plant science research. However, the delivery of exogenous genetic material into plants has been a long-standing obstacle. Nanoparticle-based delivery systems are being established to address this limitation and are proving to be a feasible, versatile, and efficient approach to facilitate the internalization of functional RNA and DNA by plants. The nanoparticle-based delivery systems can also be designed for subcellular delivery and controlled release of the biomolecular cargo. In this review, we provide a concise overview of the recent advances in nanocarriers for the delivery of biomolecules into plants, with a specific focus on applications to enhance RNA interference, foreign gene transfer, and genome editing in plants.


Assuntos
Nanopartículas , Ácidos Nucleicos , Sistemas CRISPR-Cas , Genoma de Planta , Plantas/genética , Biotecnologia , Edição de Genes , Plantas Geneticamente Modificadas/genética
2.
Commun Biol ; 6(1): 1234, 2023 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-38057635

RESUMO

Fungal pathogens that impact perennial plants or natural ecosystems require management strategies beyond fungicides and breeding for resistance. Rust fungi, some of the most economically and environmentally important plant pathogens, have shown amenability to double-stranded RNA (dsRNA) mediated control. To date, dsRNA treatments have been applied prior to infection or together with the inoculum. Here we show that a dsRNA spray can effectively prevent and cure infection by Austropuccinia psidii (cause of myrtle rust) at different stages of the disease cycle. Significant reductions in disease coverage were observed in plants treated with dsRNA targeting essential fungal genes 48 h pre-infection through to 14 days post-infection. For curative treatments, improvements in plant health and photosynthetic capacity were seen 2-6 weeks post-infection. Two-photon microscopy suggests inhibitory activity of dsRNA on intercellular hyphae or haustoria. Our results show that dsRNA acts both preventively and curatively against myrtle rust disease, with treated plants recovering from severe infection. These findings have immediate potential in the management of the more than 10-year epidemic of myrtle rust in Australia.


Assuntos
Fungicidas Industriais , RNA de Cadeia Dupla , RNA de Cadeia Dupla/genética , Ecossistema , Melhoramento Vegetal , Austrália
3.
Int J Mol Sci ; 24(15)2023 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-37569766

RESUMO

Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.


Assuntos
Agentes de Controle Biológico , Praguicidas , Ecossistema , Interferência de RNA , RNA Interferente Pequeno/genética , Produtos Agrícolas/genética , Doenças das Plantas/genética , Doenças das Plantas/prevenção & controle , Doenças das Plantas/microbiologia
4.
Plants (Basel) ; 12(5)2023 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-36903960

RESUMO

Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.

5.
Mol Plant Pathol ; 24(3): 191-207, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36528383

RESUMO

Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems.


Assuntos
Basidiomycota , RNA de Cadeia Dupla , RNA de Cadeia Dupla/genética , Ecossistema , Basidiomycota/genética , Fungos/genética , Interferência de RNA , Genômica
6.
Plants (Basel) ; 11(19)2022 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-36235411

RESUMO

Most flowering plant species contain at least two copies of the DEFECTIVE EMBRYO AND MERISTEMS (DEM) gene with the encoded DEM proteins lacking homology to proteins of known biochemical function. In tomato (Sl; Solanum lycopersicum), stable mutations in the SlDEM1 locus result in shoot and root meristem defects with the dem1 mutant failing to progress past the cotyledon stage of seedling development. Generation of a Somatic Mutagenesis of DEM1 (SMD) transformant line in tomato allowed for the characterization of SlDEM1 gene function past the seedling stage of vegetative development with SMD plants displaying a range of leaf development abnormalities. Further, the sectored or stable in planta expression of specific regions of the SlDEM1 coding sequence also resulted in the generation of tomato transformants that displayed a range of vegetative development defects, which when considered together with the dem1 mutant seedling and SMD transformant line phenotypic data, allowed for the assignment of SlDEM1 gene function to early embryo development, adaxial epidermis cell development, lateral leaf blade expansion, and mesophyll cell proliferation and differentiation.

7.
Plant Physiol ; 190(4): 2187-2202, 2022 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-36135825

RESUMO

RNA interference is triggered in plants by the exogenous application of double-stranded RNA or small interfering RNA (siRNA) to silence the expression of target genes. This approach can potentially provide insights into metabolic pathways and gene function and afford plant protection against viruses and other plant pathogens. However, the effective delivery of biomolecules such as siRNA into plant cells is difficult because of the unique barrier imposed by the plant cell wall. Here, we demonstrate that 40-nm layered double hydroxide (LDH) nanoparticles are rapidly taken up by intact Nicotiana benthamiana leaf cells and by chloroplasts, following their application via infiltration. We also describe the distribution of infiltrated LDH nanoparticles in leaves and demonstrate their translocation through the apoplast and vasculature system. Furthermore, we show that 40-nm LDH nanoparticles can greatly enhance the internalization of nucleic acids by N. benthamiana leaf cells to facilitate siRNA-mediated downregulation of targeted transgene mRNA by >70% within 1 day of exogenous application. Together, our results show that 40-nm LDH nanoparticle is an effective platform for delivery of siRNA into intact plant leaf cells.


Assuntos
Nanopartículas , RNA de Cadeia Dupla , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Argila , Interferência de RNA , Folhas de Planta/genética , Folhas de Planta/metabolismo
8.
Pathogens ; 11(7)2022 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-35889991

RESUMO

Tospoviruses infect numerous crop species worldwide, causing significant losses throughout the supply chain. As a defence mechanism, plants use RNA interference (RNAi) to generate virus-derived small-interfering RNAs (vsiRNAs), which target viral transcripts for degradation. Small RNA sequencing and in silico analysis of capsicum and N. benthamiana infected by tomato spotted wilt virus (TSWV) or capsicum chlorosis virus (CaCV) demonstrated the presence of abundant vsiRNAs, with host-specific differences evident for each pathosystem. Despite the biogenesis of vsiRNAs in capsicum and N. benthamiana, TSWV and CaCV viral loads were readily detectable. In response to tospovirus infection, the solanaceous host species also generated highly abundant virus-activated small interfering RNAs (vasiRNAs) against many endogenous transcripts, except for an N. benthamiana accession lacking a functional RDR1 gene. Strong enrichment for ribosomal protein-encoding genes and for many genes involved in protein processing in the endoplasmic reticulum suggested co-localisation of viral and endogenous transcripts as a basis for initiating vasiRNA biogenesis. RNA-seq and RT-qPCR-based analyses of target transcript expression revealed an inconsistent role for vasiRNAs in modulating gene expression in N. benthamiana, which may be characteristic of this tospovirus-host pathosystem.

9.
Plant Physiol ; 187(2): 886-899, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-34608968

RESUMO

Topical application of double-stranded RNA (dsRNA) can induce RNA interference (RNAi) and modify traits in plants without genetic modification. However, delivering dsRNA into plant cells remains challenging. Using developing tomato (Solanum lycopersicum) pollen as a model plant cell system, we demonstrate that layered double hydroxide (LDH) nanoparticles up to 50 nm in diameter are readily internalized, particularly by early bicellular pollen, in both energy-dependent and energy-independent manners and without physical or chemical aids. More importantly, these LDH nanoparticles efficiently deliver dsRNA into tomato pollen within 2-4 h of incubation, resulting in an 89% decrease in transgene reporter mRNA levels in early bicellular pollen 3-d post-treatment, compared with a 37% decrease induced by the same dose of naked dsRNA. The target gene silencing is dependent on the LDH particle size, the dsRNA dose, the LDH-dsRNA complexing ratio, and the treatment time. Our findings indicate that LDH nanoparticles are an effective nonviral vector for the effective delivery of dsRNA and other biomolecules into plant cells.


Assuntos
Argila/química , Inativação Gênica , Nanopartículas/química , Pólen/genética , Interferência de RNA , RNA de Cadeia Dupla/farmacologia , Solanum lycopersicum/genética , Solanum lycopersicum/efeitos dos fármacos , Pólen/crescimento & desenvolvimento , RNA de Cadeia Dupla/química , Transgenes
10.
Nat Commun ; 12(1): 2787, 2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-33986281

RESUMO

Transgenes that are stably expressed in plant genomes over many generations could be assumed to behave epigenetically the same as endogenous genes. Here, we report that whereas the histone H3K9me2 demethylase IBM1, but not the histone H3K4me3 demethylase JMJ14, counteracts DNA methylation of Arabidopsis endogenous genes, JMJ14, but not IBM1, counteracts DNA methylation of expressed transgenes. Additionally, JMJ14-mediated specific attenuation of transgene DNA methylation enhances the production of aberrant RNAs that readily induce systemic post-transcriptional transgene silencing (PTGS). Thus, the JMJ14 chromatin modifying complex maintains expressed transgenes in a probationary state of susceptibility to PTGS, suggesting that the host plant genome does not immediately accept expressed transgenes as being epigenetically the same as endogenous genes.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Metilação de DNA/genética , Regulação da Expressão Gênica de Plantas/genética , Histona Desmetilases com o Domínio Jumonji/genética , Epigênese Genética/genética , Genoma de Planta/genética , Interferência de RNA/fisiologia , Transgenes/genética
11.
PLoS Genet ; 17(5): e1009561, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33999950

RESUMO

The DEFECTIVE EMBRYO AND MERISTEMS 1 (DEM1) gene encodes a protein of unknown biochemical function required for meristem formation and seedling development in tomato, but it was unclear whether DEM1's primary role was in cell division or alternatively, in defining the identity of meristematic cells. Genome sequence analysis indicates that flowering plants possess at least two DEM genes. Arabidopsis has two DEM genes, DEM1 and DEM2, which we show are expressed in developing embryos and meristems in a punctate pattern that is typical of genes involved in cell division. Homozygous dem1 dem2 double mutants were not recovered, and plants carrying a single functional DEM1 allele and no functional copies of DEM2, i.e. DEM1/dem1 dem2/dem2 plants, exhibit normal development through to the time of flowering but during male reproductive development, chromosomes fail to align on the metaphase plate at meiosis II and result in abnormal numbers of daughter cells following meiosis. Additionally, these plants show defects in both pollen and embryo sac development, and produce defective male and female gametes. In contrast, dem1/dem1 DEM2/dem2 plants showed normal levels of fertility, indicating that DEM2 plays a more important role than DEM1 in gamete viability. The increased importance of DEM2 in gamete viability correlated with higher mRNA levels of DEM2 compared to DEM1 in most tissues examined and particularly in the vegetative shoot apex, developing siliques, pollen and sperm. We also demonstrate that gamete viability depends not only on the number of functional DEM alleles inherited following meiosis, but also on the number of functional DEM alleles in the parent plant that undergoes meiosis. Furthermore, DEM1 interacts with RAS-RELATED NUCLEAR PROTEIN 1 (RAN1) in yeast two-hybrid and pull-down binding assays, and we show that fluorescent proteins fused to DEM1 and RAN1 co-localize transiently during male meiosis and pollen development. In eukaryotes, RAN is a highly conserved GTPase that plays key roles in cell cycle progression, spindle assembly during cell division, reformation of the nuclear envelope following cell division, and nucleocytoplasmic transport. Our results demonstrate that DEM proteins play an essential role in cell division in plants, most likely through an interaction with RAN1.


Assuntos
Arabidopsis/citologia , Arabidopsis/genética , Genes Essenciais , Genes de Plantas/genética , Células Germinativas/metabolismo , Alelos , Proteínas de Arabidopsis/metabolismo , Divisão Celular , Sobrevivência Celular/genética , Evolução Molecular , Dosagem de Genes , Regulação da Expressão Gênica de Plantas , Teste de Complementação Genética , Células Germinativas/citologia , Meiose , Família Multigênica , Especificidade de Órgãos , Pólen/crescimento & desenvolvimento , RNA Mensageiro/genética , Proteínas de Ligação a RNA/metabolismo , Sementes , Transgenes , Proteína ran de Ligação ao GTP/metabolismo
12.
Plant Methods ; 16: 16, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32082406

RESUMO

BACKGROUND: Forward genetic screens are a powerful approach for identifying the genes contributing to a trait of interest. However, mutants arising in genes already known can obscure the identification of new genes contributing to the trait. Here, we describe a strategy called Candidate gene-Sequencing (Can-Seq) for rapidly identifying and filtering out mutants carrying new alleles of known and candidate genes. RESULTS: We carried out a forward genetic screen and identified 40 independent Arabidopsis mutants with defects in systemic spreading of RNA interference (RNAi), or more specifically in root-to-shoot transmission of post-transcriptional gene silencing (rtp). To classify the mutants as either representing a new allele of a known or candidate gene versus carrying a mutation in an undiscovered gene, bulk genomic DNA from up to 23 independent mutants was used as template to amplify a collection of 47 known or candidate genes. These amplified sequences were combined into Can-Seq libraries and deep sequenced. Subsequently, mutations in the known and candidate genes were identified using a custom Snakemake script (https://github.com/Carroll-Lab/can_seq), and PCR zygosity tests were then designed and used to identify the individual mutants carrying each mutation. Using this approach, we showed that 28 of the 40 rtp mutants carried homozygous nonsense, missense or splice site mutations in one or more of the 47 known or candidate genes. We conducted complementation tests to demonstrate that several of the candidate mutations were responsible for the rtp defect. Importantly, by exclusion, the Can-Seq pipeline also identified rtp mutants that did not carry a causative mutation in any of the 47 known and candidate genes, and these mutants represent an undiscovered gene(s) required for systemic RNAi. CONCLUSIONS: Can-Seq offers an accurate, cost-effective method for classifying new mutants into known versus unknown genes. It has several advantages over existing genetic and DNA sequencing approaches that are currently being used in forward genetic screens for gene discovery. Using Can-Seq in conjunction with map-based gene cloning is a cost-effective approach towards identifying the full complement of genes contributing to a trait of interest.

13.
Nucleic Acids Res ; 47(17): 9104-9114, 2019 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-31372641

RESUMO

Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3' regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Metilação de DNA , Inativação Gênica , RNA Polimerase Dependente de RNA/genética , Proteínas de Arabidopsis/metabolismo , DNA-Citosina Metilases/genética , DNA-Citosina Metilases/metabolismo , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Metiltransferases/genética , Metiltransferases/metabolismo , Modelos Genéticos , Plantas Geneticamente Modificadas/genética , RNA de Cadeia Dupla/metabolismo , RNA Interferente Pequeno/metabolismo , RNA Polimerase Dependente de RNA/metabolismo
14.
Neuroendocrinology ; 109(4): 299-309, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30884492

RESUMO

BACKGROUND: Using high-frequency blood sampling, we demonstrate glucocorticoid fast feedback (FF) mediated by endogenous cortisol in 6 normal humans. METHODS: We stimulated adrenocorticotropic hormone (ACTH) secretion by ovine corticotropin-releasing hormone (oCRH) with the experimental paradigm in which a high-frequency blood sampling was designed for plasma ACTH and cortisol determinations. RESULTS: We saw previously unrecognized variability in the timing of key events such as onsets of ACTH and cortisol secretion, onset and offset of FF, and in FF duration. This variability mandated analyses referenced to case-wise event times rather than referenced simply to time since oCRH administration. The mean time of FF onset was 4.0 min (range 0-9; median 3) after cortisol secretion began, and the mean FF duration was 7.5 min (range 3-18; median 6.0). The FF effect was rate-sensitive and does not reflect level-sensitive cortisol feedback. In agreement with previous estimates using hydrocortisone infusions, the rate of rise of cortisol that triggered FF was approximately 44 nmol/L/min or 1.6 µg/dL/min. FF onset followed the trigger cortisol slope with an average lag of 1 min (range 0-3; median 0). Unexpectedly, this trigger cortisol slope quickly declined within the FF period. CONCLUSIONS: This experimental design may enable new physiological studies of human FF that is mediated by endogenous cortisol, including mechanisms, reproducibility, and generalizability to other activating stimuli.


Assuntos
Hormônio Adrenocorticotrópico/sangue , Retroalimentação/efeitos dos fármacos , Hidrocortisona/farmacologia , Adolescente , Adulto , Animais , Hormônio Liberador da Corticotropina , Feminino , Voluntários Saudáveis , Humanos , Hidrocortisona/sangue , Infusões Intravenosas , Masculino , Pessoa de Meia-Idade , Ovinos , Adulto Jovem
15.
Plant Cell Physiol ; 59(11): 2169-2187, 2018 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-30169685

RESUMO

Small regulatory RNAs guide gene silencing at the DNA or RNA level through repression of complementary sequences. The two main forms of small RNAs are microRNA (miRNA) and small interfering RNA (siRNAs), which are generated from the processing of different forms of double-stranded RNA (dsRNA) precursors. These two forms of small regulatory RNAs function in distinct but overlapping gene silencing pathways in plants. Gene silencing pathways in eukaryotes evolved from an ancient prokaryotic mechanism involved in genome defense against invasive genetic elements, but has since diversified to also play a crucial role in regulation of endogenous gene expression. Here, we review the biogenesis of the different forms of small RNAs in plants, including miRNAs, phased, secondary siRNAs (phasiRNAs) and heterochromatic siRNAs (hetsiRNAs), with a focus on their functions in genome defense, transcriptional and post-transcriptional gene silencing, RNA-directed DNA methylation, trans-chromosomal methylation and paramutation. We also discuss the important role that gene duplication has played in the functional diversification of gene silencing pathways in plants, and we highlight recently discovered components of gene silencing pathways in plants.


Assuntos
Evolução Molecular , Magnoliopsida/genética , Pequeno RNA não Traduzido/metabolismo , Duplicação Gênica/genética , Inativação Gênica , Variação Genética/genética , Magnoliopsida/metabolismo , Pequeno RNA não Traduzido/genética
16.
Cell ; 174(5): 1095-1105.e11, 2018 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-30057112

RESUMO

Transcriptional downregulation caused by intronic triplet repeat expansions underlies diseases such as Friedreich's ataxia. This downregulation of gene expression is coupled with epigenetic changes, but the underlying mechanisms are unknown. Here, we show that an intronic GAA/TTC triplet expansion within the IIL1 gene of Arabidopsis thaliana results in accumulation of 24-nt short interfering RNAs (siRNAs) and repressive histone marks at the IIL1 locus, which in turn causes its transcriptional downregulation and an associated phenotype. Knocking down DICER LIKE-3 (DCL3), which produces 24-nt siRNAs, suppressed transcriptional downregulation of IIL1 and the triplet expansion-associated phenotype. Furthermore, knocking down additional components of the RNA-dependent DNA methylation (RdDM) pathway also suppressed both transcriptional downregulation of IIL1 and the repeat expansion-associated phenotype. Thus, our results show that triplet repeat expansions can lead to local siRNA biogenesis, which in turn downregulates transcription through an RdDM-dependent epigenetic modification.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Epigênese Genética , Íntrons , RNA de Plantas/genética , RNA Interferente Pequeno/genética , Ribonuclease III/genética , Transcrição Gênica , Metilação de DNA , DNA Polimerase beta/genética , Regulação para Baixo , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Oligonucleotídeos Antissenso/genética , Fenótipo , Interferência de RNA , Transgenes , Expansão das Repetições de Trinucleotídeos
17.
J Alzheimers Dis ; 63(1): 395-405, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29614656

RESUMO

BACKGROUND: There is a growing concern that general anesthesia could increase the risk of dementia. However, the relationship between anesthesia and subsequent dementia is still undetermined. OBJECTIVE: To determine whether the risk of dementia increases after exposure to general anesthesia. METHODS: A population-based prospective cohort study analyzing the Korean National Health Insurance Service-National Sample Cohort database was conducted of all persons aged over 50 years (n = 219,423) from 1 January 2003 and 31 December 2013. RESULTS: 44,956 in the general anesthesia group and 174,469 in the control group were followed for 12 years. The risk of dementia associated with previous exposure to general anesthesia was increased after adjusting for all covariates such as gender, age, health care visit frequency, and co-morbidities (Hazard ratio = 1.285, 95% confidence interval = 1.262-1.384, time-varying Cox hazard model). In addition, the number of anesthetic agents administered, the number of exposures to general anesthesia, the cumulative exposure time, and the organ category involved in surgery were associated with risk of dementia. CONCLUSION: In light of the increasing societal burden of dementia, careful surveillance for dementia and prevention guidelines for patients after general anesthesia are needed.


Assuntos
Anestesia Geral/efeitos adversos , Demência/induzido quimicamente , Demência/epidemiologia , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Estudos de Coortes , Planejamento em Saúde Comunitária , Monitoramento Epidemiológico , Feminino , Humanos , Seguro Saúde/estatística & dados numéricos , Masculino , Pessoa de Meia-Idade , Modelos de Riscos Proporcionais , República da Coreia/epidemiologia , Fatores de Risco
18.
Psychiatry Investig ; 15(4): 344-354, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29614852

RESUMO

OBJECTIVE: Suicide is a significant public health concern worldwide. Social media data have a potential role in identifying high suicide risk individuals and also in predicting suicide rate at the population level. In this study, we report an advanced daily suicide prediction model using social media data combined with economic/meteorological variables along with observed suicide data lagged by 1 week. METHODS: The social media data were drawn from weblog posts. We examined a total of 10,035 social media keywords for suicide prediction. We made predictions of national suicide numbers 7 days in advance daily for 2 years, based on a daily moving 5-year prediction modeling period. RESULTS: Our model predicted the likely range of daily national suicide numbers with 82.9% accuracy. Among the social media variables, words denoting economic issues and mood status showed high predictive strength. Observed number of suicides one week previously, recent celebrity suicide, and day of week followed by stock index, consumer price index, and sunlight duration 7 days before the target date were notable predictors along with the social media variables. CONCLUSION: These results strengthen the case for social media data to supplement classical social/economic/climatic data in forecasting national suicide events.

19.
Bioinformatics ; 34(15): 2670-2672, 2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-29554210

RESUMO

Summary: Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. Availability and implementation: The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license. Source code, multiplatform binaries and a Docker image can be accessed via https://sfletc.github.io/scram/. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Análise de Sequência de RNA/métodos , Software
20.
J Psychiatr Res ; 100: 47-55, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29486402

RESUMO

We investigated the effects of a large range of clinical factors on the long-term risk of suicide in the general population of South Korea. We analyzed the National Health Insurance Service-National Sample Cohort (NHIS-NSC) database in South Korea. A total of 300,232 individuals were followed for up to 12 years. We obtained information on demographic variables (age and sex), lifestyle variables (cigarette smoking, alcohol drinking and exercise), psychiatric and physical disorders, laboratory examination results and physical examination findings. We conducted a competing risk survival analysis to estimate the risk of completed suicide. 725 individuals (241/100,000) died by suicide in the follow-up period. After Bonferroni correction, we found a significant suicide risk associated with 6 variables: Parkinson's disease, depressive disorder, obsessive-compulsive disorder (inverted association), elevated serum aspartate aminotransferase levels, male gender and age. Before Bonferroni correction, variables such as cigarette smoking, heavy alcohol drinking, psychotic disorder, other psychiatric disorder, benzodiazepine use and higher fasting glucose showed some significant association. In addition, body mass index and height were inversely related to completed suicide before Bonferroni correction. However, only the 6 variables listed above were robust predictors of suicide in the fully adjusted analyses with multiple test correction. Common medical conditions had no clear influence on suicide. Diverse clinical factors influenced the long-term risk of completed suicide in this general population sample. Comprehensive assessment of these risk factors will facilitate more focused suicide surveillance measures.


Assuntos
Aspartato Aminotransferases/sangue , Transtornos Mentais/epidemiologia , Doença de Parkinson/epidemiologia , Suicídio/estatística & dados numéricos , Adolescente , Adulto , Fatores Etários , Idoso , Estudos de Coortes , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , República da Coreia/epidemiologia , Fatores de Risco , Fatores Sexuais , Adulto Jovem
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