RESUMEN
Aging is the main risk factor of cognitive neurodegenerative diseases such as Alzheimer's disease, with epigenome alterations as a contributing factor. Here, we compared transcriptomic/epigenomic changes in the hippocampus, modified by aging and by tauopathy, an AD-related feature. We show that the cholesterol biosynthesis pathway is severely impaired in hippocampal neurons of tauopathic but not of aged mice pointing to vulnerability of these neurons in the disease. At the epigenomic level, histone hyperacetylation was observed at neuronal enhancers associated with glutamatergic regulations only in the tauopathy. Lastly, a treatment of tau mice with the CSP-TTK21 epi-drug that restored expression of key cholesterol biosynthesis genes counteracted hyperacetylation at neuronal enhancers and restored object memory. As acetyl-CoA is the primary substrate of both pathways, these data suggest that the rate of the cholesterol biosynthesis in hippocampal neurons may trigger epigenetic-driven changes, that may compromise the functions of hippocampal neurons in pathological conditions.
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Enfermedad de Alzheimer , Colesterol , Hipocampo , Ratones Transgénicos , Neuronas , Animales , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/genética , Hipocampo/metabolismo , Colesterol/biosíntesis , Colesterol/metabolismo , Neuronas/metabolismo , Ratones , Epigenómica , Epigénesis Genética , Ratones Endogámicos C57BL , Envejecimiento/metabolismo , Envejecimiento/genética , Masculino , Proteínas tau/metabolismo , Proteínas tau/genéticaRESUMEN
Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. Yet, the mechanisms linking FUS mislocalization to hippocampal function and memory formation are still not characterized. Herein, we show that in these mice, the hippocampus paradoxically displays nuclear FUS accumulation. Multi-omic analyses showed that FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in a hippocampal-dependent spatial memory task and displayed decreased dendritic spine density. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events. These data call for further investigation in the neurological phenotype of FUS-related diseases and open therapeutic strategies towards epigenetic drugs.
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Esclerosis Amiotrófica Lateral , Demencia Frontotemporal , Animales , Ratones , Esclerosis Amiotrófica Lateral/genética , Cromatina/metabolismo , Epigénesis Genética , Demencia Frontotemporal/genética , Hipocampo/metabolismo , Mutación , Proteína FUS de Unión a ARN/genética , Proteína FUS de Unión a ARN/metabolismoRESUMEN
Following an oil spill into water, bacteria can biodegrade petroleum hydrocarbons which could lead to petrogenic carbon assimilation by aquatic biota. We used changes in the isotope ratios of radio- (Δ14C) and stable (δ13C) carbon to examine the potential for assimilation of petrogenic carbon into a freshwater food web following experimental spills of diluted bitumen (dilbit) into a boreal lake in northwestern Ontario, Canada. Different volumes (1.5, 2.9, 5.5, 18, 42, 82, and 180 L) of Cold Lake Winter Blend (a heavy crude blend of bitumen and condensate) dilbit were applied to seven 10-m diameter littoral limnocorrals (approximate volume of 100 m3), and two additional limnocorrals had no added dilbit to serve as controls. Particulate organic matter (POM) and periphyton from oil-treated limnocorrals had lower δ13C (up to 3.2 and 2.1 for POM and periphyton, respectively) than the control at every sampled interval (3, 6 and 10 weeks for POM and 6, 8 and 10 weeks for periphyton). Dissolved organic and inorganic carbon (DOC and DIC, respectively) had lower Δ14C in the oil-treated limnocorrals relative to the control (up to 122 and 440 lower, respectively). Giant floater mussel (Pyganodon grandis) housed for 25 days in aquaria containing oil-contaminated water from the limnocorrals did not show significant changes in δ13C values of muscle tissue compared to mussels housed in control water. Overall, the changes in δ13C and Δ14C observed indicated small amounts (up to 11% in DIC) of oil carbon incorporation into the food web. The combined δ13C and Δ14C data provide evidence for minimal incorporation of dilbit into the food web of this oligotrophic lake, suggesting that microbial degradation and subsequent incorporation of oil C into the food web may play a relatively small role in the ultimate fate of oil in this type of ecosystem.
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Carbono , Cadena Alimentaria , Hidrocarburos , Contaminantes Químicos del Agua , Isótopos de Carbono/análisis , Ecosistema , Lagos , Ontario , Agua , Contaminantes Químicos del Agua/análisisRESUMEN
The NFIA-ETO2 fusion is the product of a t(1;16)(p31;q24) chromosomal translocation, so far, exclusively found in pediatric patients with pure erythroid leukemia (PEL). To address the role for the pathogenesis of the disease, we facilitated the expression of the NFIA-ETO2 fusion in murine erythroblasts (EBs). We observed that NFIA-ETO2 significantly increased proliferation and impaired erythroid differentiation of murine erythroleukemia cells and of primary fetal liver-derived EBs. However, NFIA-ETO2-expressing EBs acquired neither aberrant in vitro clonogenic activity nor disease-inducing potential upon transplantation into irradiated syngenic mice. In contrast, in the presence of 1 of the most prevalent erythroleukemia-associated mutations, TP53R248Q, expression of NFIA-ETO2 resulted in aberrant clonogenic activity and induced a fully penetrant transplantable PEL-like disease in mice. Molecular studies support that NFIA-ETO2 interferes with erythroid differentiation by preferentially binding and repressing erythroid genes that contain NFI binding sites and/or are decorated by ETO2, resulting in a activity shift from GATA- to ETS-motif-containing target genes. In contrast, TP53R248Q does not affect erythroid differentiation but provides self-renewal and survival potential, mostly via downregulation of known TP53 targets. Collectively, our work indicates that NFIA-ETO2 initiates PEL by suppressing gene expression programs of terminal erythroid differentiation and cooperates with TP53 mutation to induce erythroleukemia.
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Leucemia Eritroblástica Aguda , Proteínas Represoras , Animales , Ratones , Proteínas Represoras/genética , Leucemia Eritroblástica Aguda/genética , Leucemia Eritroblástica Aguda/metabolismo , Diferenciación Celular/genética , Eritroblastos/metabolismo , Factores de Transcripción NFI/metabolismoRESUMEN
Oil spills constitute a major risk to the environment and the bioaccumulation potential of the derived oil constituents will influence their impact on aquatic biota. Here we determined the bioaccumulation potential and toxicokinetic parameters of polycyclic aromatic compounds (PACs) and various selected metals in the giant floater mussels (Pyganodon grandis) following experimental oil spills in a freshwater lake. Specifically, these mussels were exposed ex situ for 25 days to water contaminated with naturally weathered diluted bitumen (dilbit), a form of oil commonly transported through pipelines. We detected greater concentrations of total PAC in mussels (∑PAC44) exposed to dilbit-contaminated water (25.92-27.79 µg g-1 lipid, n = 9, at day 25 of the uptake phase) compared to mussels from a control with no exposure to dilbit (average of 2.62 ± 1.95 µg g-1 lipid; ±SD, n = 17). This study demonstrates the importance of including alkylated PACs when assessing the impacts of an oil spill as the concentration of alkylated PACs in mussel tissue were an order of magnitude higher than their parent counterparts. However, metal accumulation in dilbit-exposed mussels did not exceed the unexposed controls, suggesting no excess metal accumulation by mussels from a 25-day dilbit exposure. From first-order one-compartment models, mean uptake rate constants (0.78-18.11 L g-1 day-1, n = 29) and bioconcentration factors (log values from 4.02 to 5.92 L kg-1, n = 87) for the 29 individual PACs that accumulated in mussels demonstrated that some alkylated PACs had greater bioaccumulation potential compared to their parent PAC counterpart but for the most part, alkylated and parent PACs had comparable BCF values. Results from this study also demonstrated that giant floater mussels could be used to biomonitor PAC contamination following oil spills as PACs accumulated in mussel tissue and some were still detectable following the 16-day depuration phase. This study provides the largest, most comprehensive set of toxicokinetic and bioaccumulation parameters for PACs and their alkylated counterparts (44 analytes) in freshwater mussels obtained to date.
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Bivalvos , Hidrocarburos Policíclicos Aromáticos , Compuestos Policíclicos , Unionidae , Contaminantes Químicos del Agua , Animales , Bioacumulación , Toxicocinética , Contaminantes Químicos del Agua/toxicidad , Hidrocarburos , Lagos , Metales , Agua , Lípidos , Hidrocarburos Policíclicos Aromáticos/toxicidadRESUMEN
Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are reported as disease-associated. Thus, 10%-30% of most frequent cord blood TCRs are associated with common pathogens and autoantigens. TDT-dependent TCRs present distinct structural features and are less shared among subjects. TDT-dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.
RESUMEN
Molecular mechanisms underlying cognitive deficits in Huntington's disease (HD), a striatal neurodegenerative disorder, are unknown. Here, we generated ChIPseq, 4Cseq and RNAseq data on striatal tissue of HD and control mice during striatum-dependent egocentric memory process. Multi-omics analyses showed altered activity-dependent epigenetic gene reprogramming of neuronal and glial genes regulating striatal plasticity in HD mice, which correlated with memory deficit. First, our data reveal that spatial chromatin re-organization and transcriptional induction of BDNF-related markers, regulating neuronal plasticity, were reduced since memory acquisition in the striatum of HD mice. Second, our data show that epigenetic memory implicating H3K9 acetylation, which established during late phase of memory process (e.g. during consolidation/recall) and contributed to glia-mediated, TGFß-dependent plasticity, was compromised in HD mouse striatum. Specifically, memory-dependent regulation of H3K9 acetylation was impaired at genes controlling extracellular matrix and myelination. Our study investigating the interplay between epigenetics and memory identifies H3K9 acetylation and TGFß signaling as new targets of striatal plasticity, which might offer innovative leads to improve HD.
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Enfermedad de Huntington , Ratones , Animales , Enfermedad de Huntington/genética , Acetilación , Modelos Animales de Enfermedad , Cuerpo Estriado , Factor de Crecimiento Transformador betaRESUMEN
Caffeine is the most widely consumed psychoactive substance in the world. Strikingly, the molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus at the epigenomic, proteomic, and metabolomic levels. Caffeine lowered metabolism-related processes (e.g., at the level of metabolomics and gene expression) in bulk tissue, while it induced neuron-specific epigenetic changes at synaptic transmission/plasticity-related genes and increased experience-driven transcriptional activity. Altogether, these findings suggest that regular caffeine intake improves the signal-to-noise ratio during information encoding, in part through fine-tuning of metabolic genes, while boosting the salience of information processing during learning in neuronal circuits.
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Cafeína , Proteómica , Animales , Cafeína/metabolismo , Cafeína/farmacología , Hipocampo/metabolismo , Aprendizaje , Ratones , Plasticidad Neuronal/fisiologíaRESUMEN
Large-scale, in-lake enclosures (limnocorrals) were used to simulate spills of diluted bitumen (dilbit) in a boreal lake. In this study we use these simulated spills, which covered a range of sizes (oil:water ratio) representative of the upper 25% of onshore crude oil spills in North America (2008-2019), to assess the fate of dilbit-derived hydrocarbons and metals as well as the impacts of the spills on standard water quality parameters. The systems were monitored over 70 days following the application of dilbit amounts ranging between 1.5 and 179.8 L into 10-m diameter, ~100 m3 limnocorrals. The concentration of total petroleum hydrocarbons (TPH) in the water column increased rapidly over the first two weeks reaching a plateau that ranged between 200 µg/L and 2200 µg/L for the lowest and highest treatment respectively. The concentration of total polycyclic aromatic compounds (PACs) also increased over the first two weeks, prior to a slow decrease until day 70. The maximum measured concentrations in the highest treatment were 2858 ng/L for the sum of all 46 quantified PACs, 2716 ng/L for alkylated PACs and 154 ng/L for the 16 EPA priority PAHs. The concentrations of PACs in the sediment increased continuously over the study in the three highest treatments with maximum observed concentrations of 189 ng/g for ΣPAC46, 169 ng/g for ΣPACalk. No significant treatment-related changes in the 16 EPA priority PAHs were observed in the sediment. Of the 25 metals quantified in the water column, only manganese, molybdenum, and vanadium displayed a significant treatment effect with increases of 280, 76 and 25% respectively in the total fraction. These results can help us understand and predict the fate of oil-derived contaminants following a spill and characterize the exposure of freshwater organisms living within them. These results should help inform the risk assessment of future dilbit transportation projects.
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Petróleo , Hidrocarburos Policíclicos Aromáticos , Contaminantes Químicos del Agua , Hidrocarburos , Lagos , Petróleo/análisis , Proyectos de Investigación , Contaminantes Químicos del Agua/análisis , Calidad del AguaRESUMEN
Temporal dynamics and mechanisms underlying epigenetic changes in Huntington's disease (HD), a neurodegenerative disease primarily affecting the striatum, remain unclear. Using a slowly progressing knockin mouse model, we profile the HD striatal chromatin landscape at two early disease stages. Data integration with cell type-specific striatal enhancer and transcriptomic databases demonstrates acceleration of age-related epigenetic remodelling and transcriptional changes at neuronal- and glial-specific genes from prodromal stage, before the onset of motor deficits. We also find that 3D chromatin architecture, while generally preserved at neuronal enhancers, is altered at the disease locus. Specifically, we find that the HD mutation, a CAG expansion in the Htt gene, locally impairs the spatial chromatin organization and proximal gene regulation. Thus, our data provide evidence for two early and distinct mechanisms underlying chromatin structure changes in the HD striatum, correlating with transcriptional changes: the HD mutation globally accelerates age-dependent epigenetic and transcriptional reprogramming of brain cell identities, and locally affects 3D chromatin organization.
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Envejecimiento , Ensamble y Desensamble de Cromatina/genética , Cuerpo Estriado/metabolismo , Modelos Animales de Enfermedad , Enfermedad de Huntington/genética , Enfermedades Neurodegenerativas/genética , Animales , Conducta Animal/fisiología , Cromatina/genética , Cuerpo Estriado/citología , Cuerpo Estriado/fisiopatología , Epigenómica/métodos , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica , Humanos , Proteína Huntingtina/genética , Enfermedad de Huntington/diagnóstico , Enfermedad de Huntington/fisiopatología , Ratones Endogámicos C57BL , Enfermedades Neurodegenerativas/diagnóstico , Enfermedades Neurodegenerativas/fisiopatología , Neuronas/metabolismo , Expansión de Repetición de Trinucleótido/genéticaRESUMEN
The role of brain cell-type-specific functions and profiles in pathological and non-pathological contexts is still poorly defined. Such cell-type-specific gene expression profiles in solid, adult tissues would benefit from approaches that avoid cellular stress during isolation. Here, we developed such an approach and identified highly selective transcriptomic signatures in adult mouse striatal direct and indirect spiny projection neurons, astrocytes, and microglia. Integrating transcriptomic and epigenetic data, we obtained a comprehensive model for cell-type-specific regulation of gene expression in the mouse striatum. A cross-analysis with transcriptomic and epigenomic data generated from mouse and human Huntington's disease (HD) brains shows that opposite epigenetic mechanisms govern the transcriptional regulation of striatal neurons and glial cells and may contribute to pathogenic and compensatory mechanisms. Overall, these data validate this less stressful method for the investigation of cellular specificity in the adult mouse brain and demonstrate the potential of integrative studies using multiple databases.
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Encéfalo/metabolismo , Enfermedad de Huntington/genética , Animales , ADN/química , Epigénesis Genética , Perfilación de la Expresión Génica/métodos , Humanos , Enfermedad de Huntington/metabolismo , Captura por Microdisección con Láser/métodos , Masculino , Ratones , Ratones Transgénicos , MicroARNs/metabolismo , Conformación de Ácido Nucleico , ARN Mensajero/metabolismo , Factores de Transcripción/metabolismoRESUMEN
In plants, RNA silencing-based antiviral defense generates viral small RNAs (sRNAs) faithfully representing the viral genomes. We employed sRNA sequencing and bioinformatics (sRNA-omics) to characterize antiviral defense and to reconstruct the full genomic sequences and their variants in the evolving viral quasispecies in cultivated solanaceous plants carrying mixed infections. In naturally infected Solanum tuberosum (potato), one case study revealed a virome comprising Potato virus Y (genus Potyvirus) and Potato virus X (genus Potexvirus), which was reconstructed by de novo-assembling separate genome-size sRNA contigs. Another case study revealed a virome comprising NTN and O strains of Potato virus Y, whose sRNAs assembled in chimeric contigs, which could be disentangled on the basis of reference genome sequences. Both viromes were stable in vegetative potato progeny. In a cross-protection trial of Solanum lycopersicum (tomato), the supposedly protective mild strain CH2 of Pepino mosaic virus (genus Potexvirus) was tested for protection against strain LP of the same virus. Reciprocal mechanical inoculations eventually resulted in co-infection of all individual plants with CH2 and LP strains, reconstructed as separate sRNA contigs. LP invasions into CH2-preinfected plants and vice versa were accompanied by alterations of consensus genome sequences in viral quasispecies, indicating a potential risk of cross-protection measures. Additionally, the study also revealed, by reconstruction from sRNAs, the presence of the mechanically nontransmissible Southern tomato virus (genus Amalgavirus) in some plants. Our in-depth analysis of sRNA sizes, 5'-nucleotide frequencies and hotspot maps revealed similarities in sRNA-generating mechanisms in potato and tomato, differential silencing responses to virome components and potential for sRNA-directed cross-targeting between viral strains which could not, however, prevent the formation of stable viromes.
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Genoma Viral , Enfermedades de las Plantas/virología , Potexvirus/genética , Potyvirus/genética , Solanum , Coinfección , Potexvirus/aislamiento & purificación , Potyvirus/aislamiento & purificación , Interferencia de ARN , ARN Viral , Solanum/virologíaRESUMEN
Tobamoviral replicase possesses an RNA-dependent RNA polymerase (RDR) domain and is translated from genomic (g)RNA via a stop codon readthrough mechanism at a one-to-ten ratio relative to a shorter protein lacking the RDR domain. The two proteins share methyltransferase and helicase domains and form a heterodimer implicated in gRNA replication. The shorter protein is also implicated in suppressing RNA silencing-based antiviral defenses. Using a stop codon mutant of Oilseed rape mosaic tobamovirus (ORMV), we demonstrate that the readthrough replicase (p182) is sufficient for gRNA replication and for subgenomic RNA transcription during systemic infection in Nicotiana benthamiana and Arabidopsis thaliana. However, the mutant virus displays milder symptoms and does not interfere with HEN1-mediated methylation of viral short interfering (si)RNAs or plant small (s)RNAs. The mutant virus tends to revert the stop codon, thereby restoring expression of the shorter protein (p125), even in the absence of plant Dicer-like activities that generate viral siRNAs. Plant RDR activities that generate endogenous siRNA precursors do not prevent replication or movement of the mutant virus, and double-stranded precursors of viral siRNAs representing the entire virus genome are likely synthesized by p182. Transgenic expression of p125 partially recapitulates the ORMV disease symptoms associated with overaccumulation of plant sRNAs. Taken together, the readthrough replicase p182 is sufficient for viral replication and transcription but not for silencing suppression. By contrast, the shorter p125 protein suppresses silencing, provokes severe disease symptoms, causes overaccumulation of unmethylated viral and plant sRNAs but it is not an essential component of the viral replicase complex.
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Interferencia de ARN , ARN Polimerasa Dependiente del ARN/metabolismo , Tobamovirus/enzimología , Tobamovirus/fisiología , Replicación Viral , Arabidopsis/genética , Arabidopsis/virología , Metilación de ADN/genética , Enfermedades de las Plantas/virología , Plantas Modificadas Genéticamente , ARN Interferente Pequeño/metabolismo , Ribonucleasa III/metabolismo , Análisis de Secuencia de ARN , Proteínas Virales/metabolismoRESUMEN
MOTIVATIONS: Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, often rely on a computationally intensive tree space search which forecloses an application to large genomic databases. RESULTS: We propose a new method, called ProfileNJ, that takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of information from a species tree and a distance matrix. Its low running time enabled us to use it on the whole Ensembl Compara database, for which we propose an alternative, arguably more plausible set of gene trees. This allowed us to perform a genome-wide analysis of duplication and loss patterns on the history of 63 eukaryote species, and predict ancestral gene content and order for all ancestors along the phylogeny. AVAILABILITY: A web interface called RefineTree, including ProfileNJ as well as a other gene tree correction methods, which we also test on the Ensembl gene families, is available at: http://www-ens.iro.umontreal.ca/~adbit/polytomysolver.html. The code of ProfileNJ as well as the set of gene trees corrected by ProfileNJ from Ensembl Compara version 73 families are also made available.
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Algoritmos , Biología Computacional/métodos , Evolución Molecular , Genes/genética , Genoma/genética , Filogenia , Animales , Humanos , Análisis de Secuencia de ADNRESUMEN
In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a consensus sequence and count sRNAs of any chosen sizes and 5'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps.
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Biología Computacional/métodos , Genoma Viral , ARN Pequeño no Traducido , ARN Viral , Programas Informáticos , Virus de Plantas/genética , Polimorfismo de Nucleótido SimpleRESUMEN
RNA interference (RNAi) is a widely used approach to generate virus-resistant transgenic crops. However, issues of agricultural importance like the long-term durability of RNAi-mediated resistance under field conditions and the potential side effects provoked in the plant by the stable RNAi expression remain poorly investigated. Here, we performed field trials and molecular characterization studies of two homozygous transgenic tomato lines, with different selection markers, expressing an intron-hairpin RNA cognate to the Tomato yellow leaf curl virus (TYLCV) C1 gene. The tested F6 and F4 progenies of the respective kanamycin- and basta-resistant plants exhibited unchanged field resistance to TYLCV and stably expressed the transgene-derived short interfering RNA (siRNAs) to represent 6 to 8% of the total plant small RNAs. This value outnumbered the average percentage of viral siRNAs in the nontransformed plants exposed to TYLCV-infested whiteflies. As a result of the RNAi transgene expression, a common set of up- and downregulated genes was revealed in the transcriptome profile of the plants selected from either of the two transgenic events. A previously unidentified geminivirus causing no symptoms of viral disease was detected in some of the transgenic plants. The novel virus acquired V1 and V2 genes from TYLCV and C1, C2, C3, and C4 genes from a distantly related geminivirus and, thereby, it could evade the repressive sequence-specific action of transgene-derived siRNAs. Our findings shed light on the mechanisms of siRNA-directed antiviral silencing in transgenic plants and highlight the applicability limitations of this technology as it may alter the transcriptional pattern of nontarget genes.
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Geminiviridae/fisiología , Enfermedades de las Plantas/virología , Plantas Modificadas Genéticamente , Interferencia de ARN , Solanum lycopersicum/genética , Solanum lycopersicum/fisiología , Regulación de la Expresión Génica de las Plantas , Predisposición Genética a la Enfermedad , Datos de Secuencia Molecular , Enfermedades de las Plantas/genética , ARN Interferente Pequeño , TranscriptomaRESUMEN
Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.
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Genoma Viral/genética , Oryza/virología , Enfermedades de las Plantas/virología , ARN Bicatenario/genética , Tungrovirus/genética , Proteínas Virales/metabolismo , ADN Complementario/química , ADN Complementario/genética , Expresión Génica , Biblioteca de Genes , Oryza/genética , Hojas de la Planta , Interferencia de ARN , ARN de Planta/genética , ARN Interferente Pequeño/genética , ARN Viral/genética , Análisis de Secuencia de ADN , Nicotiana/virología , Sitio de Iniciación de la Transcripción , Tungrovirus/fisiología , Proteínas Virales/genética , Replicación ViralRESUMEN
UNLABELLED: Vegetatively propagated crop plants often suffer from infections with persistent RNA and DNA viruses. Such viruses appear to evade the plant defenses that normally restrict viral replication and spread. The major antiviral defense mechanism is based on RNA silencing generating viral short interfering RNAs (siRNAs) that can potentially repress viral genes posttranscriptionally through RNA cleavage and transcriptionally through DNA cytosine methylation. Here we examined the RNA silencing machinery of banana plants persistently infected with six pararetroviruses after many years of vegetative propagation. Using deep sequencing, we reconstructed consensus master genomes of the viruses and characterized virus-derived and endogenous small RNAs. Consistent with the presence of endogenous siRNAs that can potentially establish and maintain DNA methylation, the banana genomic DNA was extensively methylated in both healthy and virus-infected plants. A novel class of abundant 20-nucleotide (nt) endogenous small RNAs with 5'-terminal guanosine was identified. In all virus-infected plants, 21- to 24-nt viral siRNAs accumulated at relatively high levels (up to 22% of the total small RNA population) and covered the entire circular viral DNA genomes in both orientations. The hotspots of 21-nt and 22-nt siRNAs occurred within open reading frame (ORF) I and II and the 5' portion of ORF III, while 24-nt siRNAs were more evenly distributed along the viral genome. Despite the presence of abundant viral siRNAs of different size classes, the viral DNA was largely free of cytosine methylation. Thus, the virus is able to evade siRNA-directed DNA methylation and thereby avoid transcriptional silencing. This evasion of silencing likely contributes to the persistence of pararetroviruses in banana plants. IMPORTANCE: We report that DNA pararetroviruses in Musa acuminata banana plants are able to evade DNA cytosine methylation and transcriptional gene silencing, despite being targeted by the host silencing machinery generating abundant 21- to 24-nucleotide short interfering RNAs. At the same time, the banana genomic DNA is extensively methylated in both healthy and virus-infected plants. Our findings shed light on the siRNA-generating gene silencing machinery of banana and provide a possible explanation why episomal pararetroviruses can persist in plants whereas true retroviruses with an obligatory genome-integration step in their replication cycle do not exist in plants.
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Regulación Viral de la Expresión Génica , Evasión Inmune/genética , Musa/genética , Virus de Plantas/genética , ARN Interferente Pequeño/inmunología , Retroviridae/genética , Metilación de ADN , Regulación de la Expresión Génica de las Plantas/inmunología , Silenciador del Gen , Genoma Viral , Musa/inmunología , Musa/virología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/inmunología , Enfermedades de las Plantas/virología , Inmunidad de la Planta/genética , Virus de Plantas/patogenicidad , ARN Interferente Pequeño/genética , ARN Viral/genética , ARN Viral/inmunología , Retroviridae/patogenicidad , Transcripción GenéticaRESUMEN
Virus-infected plants accumulate abundant, 21-24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this 'siRNA omics' approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.
Asunto(s)
Virus ADN/genética , Virus de Plantas/genética , Plantas/virología , Virus ARN/genética , ARN Interferente Pequeño/genética , Mapeo Contig , Secuenciación de Nucleótidos de Alto Rendimiento , Datos de Secuencia Molecular , Virus del Mosaico/genética , Enfermedades de las Plantas/virología , Hojas de la Planta/virología , Polimorfismo de Nucleótido Simple , Interferencia de ARN , ARN Bicatenario , ARN Interferente Pequeño/metabolismo , Análisis de Secuencia de ADN , Viroides/genética , Vitis/virologíaRESUMEN
In eukaryotes, diverse small RNA (sRNA) populations including miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons, transgenes and viruses. Functional sRNAs are associated with effector proteins based on their size and nucleotide composition. The sRNA populations are currently analyzed by deep sequencing that generates millions of reads which are then mapped to a reference sequence or database. Here we developed a tool called MISIS to view and analyze sRNA maps of genomic loci and viruses which spawn multiple sRNAs. MISIS displays sRNA reads as a histogram where the x-axis indicates positions of the 5'- or 3'-terminal nucleotide of sense and antisense sRNAs, respectively, along a given reference sequence or its selected region and the y-axis the number of reads starting (for sense sRNA) or ending (for antisense sRNA) at each position. Size-classes of sRNAs can be visualized and compared separately or in combination. Thus, MISIS gives an overview of sRNA distribution along the reference sequence as well as detailed information on single sRNA species of different size-classes and abundances. MISIS reads standard BAM/SAM files outputted by mapping tools and generates table files containing counts of sRNA reads at each position of the reference sequence forward and reverse strand and for each of the chosen size-classes of sRNAs. These table files can be used by other tools such as Excel for further quantitative analysis and visualization. MISIS is a Java standalone program. It is freely available along with the source code at the following website: http://www.fasteris.com/apps.