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1.
Neurobiol Dis ; 199: 106603, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39002811

RESUMO

Caffeine consumption outcomes on Amyotrophic Lateral Sclerosis (ALS) including progression, survival and cognition remain poorly defined and may depend on its metabolization influenced by genetic variants. 378 ALS patients with a precise evaluation of their regular caffeine consumption were monitored as part of a prospective multicenter study. Demographic, clinical characteristics, functional disability as measured with revised ALS Functional Rating Scale (ALSFRS-R), cognitive deficits measured using Edinburgh Cognitive and Behavioural ALS Screen (ECAS), survival and riluzole treatment were recorded. 282 patients were genotyped for six single nucleotide polymorphisms tagging different genes involved in caffeine intake and/or metabolism: CYP1A1 (rs2472297), CYP1A2 (rs762551), AHR (rs4410790), POR (rs17685), XDH (rs206860) and ADORA2A (rs5751876) genes. Association between caffeine consumption and ALSFRS-R, ALSFRS-R rate, ECAS and survival were statistically analyzed to determine the outcome of regular caffeine consumption on ALS disease progression and cognition. No association was observed between caffeine consumption and survival (p = 0.25), functional disability (ALSFRS-R; p = 0.27) or progression of ALS (p = 0.076). However, a significant association was found with higher caffeine consumption and better cognitive performance on ECAS scores in patients carrying the C/T and T/T genotypes at rs2472297 (p-het = 0.004). Our results support the safety of regular caffeine consumption on ALS disease progression and survival and also show its beneficial impact on cognitive performance in patients carrying the minor allele T of rs2472297, considered as fast metabolizers, that would set the ground for a new pharmacogenetic therapeutic strategy.


Assuntos
Esclerose Lateral Amiotrófica , Cafeína , Citocromo P-450 CYP1A2 , Progressão da Doença , Polimorfismo de Nucleotídeo Único , Receptor A2A de Adenosina , Humanos , Esclerose Lateral Amiotrófica/genética , Esclerose Lateral Amiotrófica/tratamento farmacológico , Feminino , Masculino , Pessoa de Meia-Idade , Idoso , Receptor A2A de Adenosina/genética , Citocromo P-450 CYP1A2/genética , Cognição/fisiologia , Cognição/efeitos dos fármacos , Estudos Prospectivos , Citocromo P-450 CYP1A1/genética , Receptores de Hidrocarboneto Arílico/genética , Adulto , Disfunção Cognitiva/genética , Riluzol/uso terapêutico , Estimulantes do Sistema Nervoso Central/uso terapêutico , Fatores de Transcrição Hélice-Alça-Hélice Básicos
2.
Plant Cell ; 32(4): 833-852, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32086366

RESUMO

Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm, and maternal tissues). However, the complexity of the kernel makes it difficult to understand intercompartment interactions without access to spatially accurate information. Here, we took advantage of the large size of the maize (Zea mays) kernel to characterize genome-wide expression profiles of tissues at different embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared with whole seed compartments: the scutellar aleurone layer and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 d after pollination and persists for around 11 d, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated and to which additional endosperm cells are recruited as the embryo grows.


Assuntos
Endosperma/genética , Transcriptoma/genética , Zea mays/embriologia , Zea mays/genética , Morte Celular , Parede Celular/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Mutação/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Reprodutibilidade dos Testes , Transcrição Gênica , Regulação para Cima/genética
3.
Mol Biol Evol ; 38(8): 3445-3458, 2021 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-33878189

RESUMO

The high mutational load of mitochondrial genomes combined with their uniparental inheritance and high polyploidy favors the maintenance of deleterious mutations within populations. How cells compose and adapt to the accumulation of disadvantageous mitochondrial alleles remains unclear. Most harmful changes are likely corrected by purifying selection, however, the intimate collaboration between mitochondria- and nuclear-encoded gene products offers theoretical potential for compensatory adaptive changes. In plants, cytoplasmic male sterilities are known examples of nucleo-mitochondrial coadaptation situations in which nuclear-encoded restorer of fertility (Rf) genes evolve to counteract the effect of mitochondria-encoded cytoplasmic male sterility (CMS) genes and restore fertility. Most cloned Rfs belong to a small monophyletic group, comprising 26 pentatricopeptide repeat genes in Arabidopsis, called Rf-like (RFL). In this analysis, we explored the functional diversity of RFL genes in Arabidopsis and found that the RFL8 gene is not related to CMS suppression but essential for plant embryo development. In vitro-rescued rfl8 plantlets are deficient in the production of the mitochondrial heme-lyase complex. A complete ensemble of molecular and genetic analyses allowed us to demonstrate that the RFL8 gene has been selected to permit the translation of the mitochondrial ccmFN2 gene encoding a heme-lyase complex subunit which derives from the split of the ccmFN gene, specifically in Brassicaceae plants. This study represents thus a clear case of nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants and demonstrates that RFL genes can be selected in response to other mitochondrial deviancies than CMS suppression.


Assuntos
Arabidopsis/genética , Genoma Mitocondrial , Seleção Genética , Arabidopsis/embriologia , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Grupo dos Citocromos c/metabolismo , Desenvolvimento Embrionário , Biossíntese de Proteínas , Splicing de RNA
4.
New Phytol ; 232(1): 80-97, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34128549

RESUMO

Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.


Assuntos
Populus , Metilação de DNA/genética , Secas , Regulação da Expressão Gênica de Plantas , Meristema , Populus/genética , Interferência de RNA
5.
BMC Genomics ; 21(1): 416, 2020 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-32571208

RESUMO

BACKGROUND: Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters for phenotype prediction remains to be studied. RESULTS: We measured 17 phenotypic traits for 241 cloned genotypes from a Populus nigra collection, covering growth, phenology, chemical and physical properties. We also sequenced RNA for each genotype and built co-expression networks to define core and peripheral genes. We found that cores were more differentiated between populations than peripherals while being less variable, suggesting that they have been constrained through potentially divergent selection. We also showed that while cores were overrepresented in a subset of genes statistically selected for their capacity to predict the phenotypes (by Boruta algorithm), they did not systematically predict better than peripherals or even random genes. CONCLUSION: Our work is the first attempt to assess the importance of co-expression network connectivity in phenotype prediction. While highly connected core genes appear to be important, they do not bear enough information to systematically predict better quantitative traits than other gene sets.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Redes Reguladoras de Genes , Populus/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Genótipo , Aprendizado de Máquina , Fenótipo , Proteínas de Plantas/genética , Populus/genética , Locos de Características Quantitativas , Análise de Sequência de RNA
6.
Brief Bioinform ; 19(1): 65-76, 2018 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-27742662

RESUMO

Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets. This framework is based on real data sets and allows the exploration of various scenarios differing in the proportion of non-differentially expressed genes. Hence, it provides an evaluation of the key ingredients of the differential analysis, free of the biases associated with the simulation of data using parametric models. Our results show the relevance of a proper modeling of the mean by using linear or generalized linear modeling. Once the mean is properly modeled, the impact of the other parameters on the performance of the test is much less important. Finally, we propose to use the simple visualization of the raw P-value histogram as a practical evaluation criterion of the performance of differential analysis methods on real data sets.


Assuntos
Proteínas de Arabidopsis/genética , Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA/genética , Análise de Sequência de RNA/métodos , Transcriptoma , Arabidopsis/genética , Simulação por Computador , Conjuntos de Dados como Assunto , Humanos , Modelos Estatísticos , Software
7.
BMC Plant Biol ; 19(1): 135, 2019 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-30971226

RESUMO

BACKGROUND: The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. RESULTS: We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. CONCLUSIONS: Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Reprogramação Celular/genética , Endorreduplicação/genética , Florígeno/metabolismo , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Arabidopsis/efeitos da radiação , Proteínas de Arabidopsis/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Flores/genética , Flores/crescimento & desenvolvimento , Flores/fisiologia , Flores/efeitos da radiação , Regulação da Expressão Gênica de Plantas , Meristema/genética , Meristema/crescimento & desenvolvimento , Meristema/fisiologia , Meristema/efeitos da radiação , Fotoperíodo , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/fisiologia , Folhas de Planta/efeitos da radiação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
8.
Planta ; 249(5): 1645-1651, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30820649

RESUMO

MAIN CONCLUSION: Modulation of gene expression in roots of Brassica napus by silicon (Si) supply could allow plants to cope with future stresses. The origin of the beneficial effects of silicon (Si) in plants, especially when they are subject to stress, remains poorly understood. Some authors have shown that Si alleviates plant stress and consider that this is mainly due to a mechanical effect on the cell wall. In addition, the other studies have shown that Si can also affect gene expression and modulate a number of metabolic pathways, especially in plants cultivated under stress conditions. Previously, Haddad et al. (Front Plant Sci 9:5-16, 2018) showed that a pretreatment of Brassica napus plants with Si (1.7 mM) for 1 week alleviated the stress induced by N privation. These results suggest that this improved resistance in Si-treated plants might be due to the establishment of defense mechanisms prior to exposure to the N stress. The aim of the current work was to test this assumption in Brassica napus roots (where Si is mainly stored) using a transcriptomic approach via the RNA sequencing. Our results indicated that the Si supply leads to a modulation of the expression of genes in Brassica napus roots. Functional categorization of the differentially expressed genes demonstrated that numerous genes are involved in different metabolic pathways and especially in cell wall synthesis, phytohormone metabolism, and stress responses. All these results show that Si modifies the root metabolism of B. napus, which could allow a better adaptation to future stresses.


Assuntos
Brassica napus/efeitos dos fármacos , Brassica napus/metabolismo , Silício/farmacologia , Brassica napus/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Regulação da Expressão Gênica de Plantas/genética , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Transcriptoma/efeitos dos fármacos , Transcriptoma/genética
9.
BMC Genomics ; 19(1): 909, 2018 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-30541448

RESUMO

BACKGROUD: Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra. RESULTS: We have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset. CONCLUSIONS: We demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies.


Assuntos
Genes de Plantas , Polimorfismo de Nucleotídeo Único , Populus/genética , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Mapeamento Cromossômico , Análise por Conglomerados , Éxons , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , RNA de Plantas/química , RNA de Plantas/isolamento & purificação , RNA de Plantas/metabolismo , Análise de Sequência de RNA
10.
Plant Biotechnol J ; 16(10): 1767-1777, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29510004

RESUMO

Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat-barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35 301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials.


Assuntos
Genoma de Planta , Hordeum/metabolismo , Transcriptoma , Triticum/metabolismo , Hordeum/genética , Deleção de Sequência , Triticum/genética
11.
Plant J ; 87(6): 583-96, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27227784

RESUMO

Light is a major regulator of plant growth and development by antagonizing gibberellins (GA), and we provide evidence for a role of light perception and GA in seed coat formation and seed tolerance to deterioration. We have identified two activation-tagging mutants of Arabidopsis thaliana, cog1-2D and cdf4-1D, with improved seed tolerance to deterioration linked to increased expression of COG1/DOF1.5 and CDF4/DOF2.3, respectively. These encode two homologous DOF transcription factors, with COG1 most highly expressed in seeds. Improved tolerance to seed deterioration was reproduced in transgenic plants overexpressing these genes, and loss of function from RNA interference resulted in opposite phenotypes. Overexpressions of COG1 and CDF4 have been described to attenuate various light responses mediated by phytochromes. Accordingly, we found that phyA and phyB mutants exhibit increased seed tolerance to deterioration. The phenotype of tolerance to deterioration conferred by gain of function of COG1 and by loss of function of phytochromes is of maternal origin, is also observed under natural aging conditions and correlates with a seed coat with increased suberin and reduced permeability. In developing siliques of the cog1-2D mutant the expression of the GA biosynthetic gene GA3OX3 and levels of GA1 are higher than in the wild type. These results explain the antagonism between phytochromes and COG1 in terms of the inhibition and the activation, respectively, of GA action.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Giberelinas/metabolismo , Sementes/fisiologia , Fatores de Transcrição/metabolismo , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Luz , Lipídeos/genética , Mutação , Fitocromo/genética , Fitocromo/metabolismo , Plantas Geneticamente Modificadas , Fatores de Transcrição/genética
12.
Plant Cell ; 26(9): 3519-37, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25194028

RESUMO

In the exalbuminous species Arabidopsis thaliana, seed maturation is accompanied by the deposition of oil and storage proteins and the reduction of the endosperm to one cell layer. Here, we consider reserve partitioning between embryo and endosperm compartments. The pattern of deposition, final amount, and composition of these reserves differ between the two compartments, with the embryo representing the principal storage tissue in mature seeds. Complex regulatory mechanisms are known to prevent activation of maturation-related programs during embryo morphogenesis and, later, during vegetative growth. Here, we describe a regulator that represses the expression of maturation-related genes during maturation within the endosperm. MYB118 is transcriptionally induced in the maturing endosperm, and seeds of myb118 mutants exhibit an endosperm-specific derepression of maturation-related genes associated with a partial relocation of storage compounds from the embryo to the endosperm. Moreover, MYB118 activates endosperm-induced genes through the recognition of TAACGG elements. These results demonstrate that the differential partitioning of reserves between the embryo and endosperm in exalbuminous Arabidopsis seeds does not only result from developmental programs that establish the embryo as the preponderant tissue within seeds. This differential partitioning is also regulated by MYB118, which regulates the biosynthesis of reserves at the spatial level during maturation.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/embriologia , Arabidopsis/metabolismo , Endosperma/embriologia , Endosperma/metabolismo , Fatores de Transcrição/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Sequência de Bases , Endosperma/genética , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Dados de Sequência Molecular , Mutação/genética , Ligação Proteica/genética , Fatores de Transcrição/genética , Ativação Transcricional/genética
13.
Nucleic Acids Res ; 43(Database issue): D1010-7, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25392409

RESUMO

CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein-protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.


Assuntos
Arabidopsis/genética , Bases de Dados Genéticas , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Estresse Fisiológico/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Perfilação da Expressão Gênica , Internet , Modelos Genéticos , Mapeamento de Interação de Proteínas
14.
PLoS Genet ; 10(8): e1004564, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25144737

RESUMO

The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.


Assuntos
Arabidopsis/genética , Exossomos/metabolismo , RNA Helicases/genética , Estabilidade de RNA/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Núcleo Celular/genética , Exossomos/genética , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , RNA Helicases/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Nucleolar Pequeno/genética , RNA Nucleolar Pequeno/metabolismo
15.
EMBO J ; 30(10): 1928-38, 2011 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-21487388

RESUMO

Post-translational modification of histones and DNA methylation are important components of chromatin-level control of genome activity in eukaryotes. However, principles governing the combinatorial association of chromatin marks along the genome remain poorly understood. Here, we have generated epigenomic maps for eight histone modifications (H3K4me2 and 3, H3K27me1 and 2, H3K36me3, H3K56ac, H4K20me1 and H2Bub) in the model plant Arabidopsis and we have combined these maps with others, produced under identical conditions, for H3K9me2, H3K9me3, H3K27me3 and DNA methylation. Integrative analysis indicates that these 12 chromatin marks, which collectively cover ∼90% of the genome, are present at any given position in a very limited number of combinations. Moreover, we show that the distribution of the 12 marks along the genomic sequence defines four main chromatin states, which preferentially index active genes, repressed genes, silent repeat elements and intergenic regions. Given the compact nature of the Arabidopsis genome, these four indexing states typically translate into short chromatin domains interspersed with each other. This first combinatorial view of the Arabidopsis epigenome points to simple principles of organization as in metazoans and provides a framework for further studies of chromatin-based regulatory mechanisms in plants.


Assuntos
Arabidopsis/fisiologia , Cromatina/metabolismo , Epigênese Genética , Regulação da Expressão Gênica de Plantas , Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cromossomos/metabolismo , Metilação de DNA , Histonas/metabolismo , Processamento de Proteína Pós-Traducional
16.
Planta ; 242(1): 39-52, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25809153

RESUMO

MAIN CONCLUSION: A fungal gene encoding a transcription factor is expressed from its own promoter in Arabidopsis phloem and improves drought tolerance by reducing transpiration and increasing osmotic potential. Horizontal gene transfer from unrelated organisms has occurred in the course of plant evolution, suggesting that some foreign genes may be useful to plants. The CtHSR1 gene, previously isolated from the halophytic yeast Candida tropicalis, encodes a heat-shock transcription factor-related protein. CtHSR1, with expression driven by its own promoter or by the Arabidopsis UBQ10 promoter, was introduced into the model plant Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation and the resulting transgenic plants were more tolerant to drought than controls. Fusions of the CtHSR1 promoter with ß-glucuronidase reporter gene indicated that this fungal promoter drives expression to phloem tissues. A chimera of CtHSR1 and green fluorescence protein is localized at the cell nucleus. The physiological mechanism of drought tolerance in transgenic plants is based on reduced transpiration (which correlates with decreased opening of stomata and increased levels of jasmonic acid) and increased osmotic potential (which correlates with increased proline accumulation). Transcriptomic analysis indicates that the CtHSR1 transgenic plants overexpressed a hundred of genes, including many relevant to stress defense such as LOX4 (involved in jasmonic acid synthesis) and P5CS1 (involved in proline biosynthesis). The promoters of the induced genes were enriched in upstream activating sequences for water stress induction. These results demonstrate that genes from unrelated organisms can have functional expression in plants from its own promoter and expand the possibilities of useful transgenes for plant biotechnology.


Assuntos
Adaptação Fisiológica , Arabidopsis/fisiologia , Candida/genética , Secas , Proteínas Fúngicas/genética , Regiões Promotoras Genéticas , Fatores de Transcrição/genética , Arabidopsis/genética , Núcleo Celular/metabolismo , Proteínas Fúngicas/metabolismo , Regulação da Expressão Gênica de Plantas , Genes Fúngicos , Proteínas de Fluorescência Verde/metabolismo , Motivos de Nucleotídeos/genética , Floema/genética , Fotossíntese , Estômatos de Plantas/fisiologia , Plantas Geneticamente Modificadas , Prolina/metabolismo , Nicotiana/metabolismo , Fatores de Transcrição/metabolismo , Transcriptoma/genética
17.
Plant Physiol ; 164(2): 999-1010, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24335333

RESUMO

Seed longevity is crucial for agriculture and plant genetic diversity, but it is limited by cellular damage during storage. Seeds are protected against aging by cellular defenses and by structures such as the seed coat. We have screened an activation-tagging mutant collection of Arabidopsis (Arabidopsis thaliana) and selected four dominant mutants with improved seed longevity (isl1-1D to isl4-1D) under both natural and accelerated aging conditions. In the isl1-1D mutant, characterized in this work, overexpression of the transcription factor ARABIDOPSIS THALIANA HOMEOBOX25 (ATHB25; At5g65410) increases the expression of GIBBERELLIC ACID3-OXIDASE2, encoding a gibberellin (GA) biosynthetic enzyme, and the levels of GA1 and GA4 are higher (3.2- and 1.4-fold, respectively) in the mutant than in the wild type. The morphological and seed longevity phenotypes of the athb25-1D mutant were recapitulated in transgenic plants with moderate (4- to 6-fold) overexpression of ATHB25. Simultaneous knockdown of ATHB25, ATHB22, and ATHB31 expression decreases seed longevity, as does loss of ATHB25 and ATHB22 function in a double mutant line. Seeds from wild-type plants treated with GA and from a quintuple DELLA mutant (with constitutive GA signaling) are more tolerant to aging, providing additional evidence for a role of GA in seed longevity. A correlation was observed in several genotypes between seed longevity and mucilage formation at the seed surface, suggesting that GA may act by reinforcing the seed coat. This mechanism was supported by the observation of a maternal effect in reciprocal crosses between the wild type and the athb25-1D mutant.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Giberelinas/farmacologia , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas/genética , Genótipo , Germinação/efeitos dos fármacos , Mutação/genética , Motivos de Nucleotídeos/genética , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo , Mucilagem Vegetal/metabolismo , Plantas Geneticamente Modificadas , Regiões Promotoras Genéticas/genética , Sementes/efeitos dos fármacos , Coloração e Rotulagem , Triazóis/farmacologia
18.
BMC Plant Biol ; 13: 159, 2013 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-24128060

RESUMO

BACKGROUND: Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. RESULTS: A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. CONCLUSIONS: We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax.


Assuntos
Linho/genética , Genoma de Planta/genética , Mutagênese/genética , Mutação/genética , Genética Reversa/métodos , Pareamento de Bases/genética , Metanossulfonato de Etila , Flores/genética , Genes de Plantas/genética , Genótipo , Lignina/genética , Taxa de Mutação , Motivos de Nucleotídeos/genética , Fenótipo , Filogenia , Sementes/genética
19.
J Med Genet ; 49(4): 258-63, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22499346

RESUMO

BACKGROUND: Expanded GGGGCC hexanucleotide repeats in the promoter of the C9ORF72 gene have recently been identified in frontotemporal dementia (FTD), Amyotrophic Lateral Sclerosis (ALS) and ALS-FTD and appear as the most common genetic cause of familial (FALS) and sporadic (SALS) forms of ALS. METHODS: We searched for the C9ORF72 repeat expansion in 950 French ALS patients (225 FALS and 725 SALS) and 580 control subjects and performed genotype-phenotype correlations. RESULTS: The repeat expansion was present in 46% of FALS, 8% of SALS and 0% of controls. Phenotype comparisons were made between FALS patients with expanded C9ORF72 repeats and patients carrying another ALS-related gene (SOD1, TARDBP, FUS) or a yet unidentified genetic defect. SALS patients with and without C9ORF72 repeat expansions were also compared. The C9ORF72 group presented more frequent bulbar onset both in FALS (p<0.0001 vs SOD1, p=0.002 vs TARDBP, p=0.011 vs FUS, p=0.0153 vs other FALS) and SALS (p=0.047). FALS patients with C9ORF72 expansions had more frequent association with FTD than the other FALS patients (p<0.0001 vs SOD1, p=0.04 vs TARDBP, p=0.004 vs FUS, p=0.03 vs other FALS). C9ORF72-linked FALS patients presented an older age of onset than SOD1 (p=0.0139) or FUS mutation (p<0.0001) carriers. Disease duration was shorter for C9ORF72 expansion carriers than for SOD1 (p<0.0001) and TARDBP (p=0.0242) carriers, other FALS (p<0.0001) and C9ORF72-negative SALS (p=0.0006). CONCLUSIONS: Our results confirm the major role of expanded repeats in C9ORF72 as causative for ALS and provide evidence for specific phenotypic aspects compared to patients with other ALS-related genes.


Assuntos
Esclerose Lateral Amiotrófica/diagnóstico , Esclerose Lateral Amiotrófica/genética , Expansão das Repetições de DNA , Mutação , Fenótipo , Proteínas/genética , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Proteína C9orf72 , Proteínas de Ligação a DNA/genética , Feminino , Estudos de Associação Genética , Humanos , Masculino , Pessoa de Meia-Idade , Proteína FUS de Ligação a RNA/genética , Superóxido Dismutase/genética , Superóxido Dismutase-1 , Adulto Jovem
20.
Science ; 381(6661): eadg0995, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37651534

RESUMO

Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that "mitochondrial translation factors" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal "small" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.


Assuntos
Mitocôndrias , Iniciação Traducional da Cadeia Peptídica , Proteínas de Plantas , RNA Mensageiro , Animais , Sítios de Ligação , Mitocôndrias/genética , Mitocôndrias/metabolismo , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Mitocondrial/genética , RNA Mitocondrial/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Sequência Conservada
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