RESUMO
mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.
Assuntos
Arabidopsis/genética , Bases de Dados de Ácidos Nucleicos , MicroRNAs/metabolismo , RNA de Plantas/metabolismo , Mineração de Dados , Perfilação da Expressão Gênica , Internet , Software , Interface Usuário-ComputadorRESUMO
Arabidopsis thaliana HYL1 is a nuclear double-stranded RNA-binding protein involved in the maturation of pri-miRNAs. A quantitative real-time PCR platform for parallel quantification of 176 pri-miRNAs was used to reveal strong accumulation of 57 miRNA precursors in the hyl1 mutant that completely lacks HYL1 protein. This approach enabled us for the first time to pinpoint particular members of MIRNA family genes that require HYL1 activity for efficient maturation of their precursors. Moreover, the accumulation of miRNA precursors in the hyl1 mutant gave us the opportunity to carry out 3' and 5' RACE experiments which revealed that some of these precursors are of unexpected length. The alignment of HYL1-dependent miRNA precursors to A. thaliana genomic sequences indicated the presence of introns in 12 out of 20 genes studied. Some of the characterized intron-containing pri-miRNAs undergo alternative splicing such as exon skipping or usage of alternative 5' splice sites suggesting that this process plays a role in the regulation of miRNA biogenesis. In the hyl1 mutant intron-containing pri-miRNAs accumulate alongside spliced pri-miRNAs suggesting the recruitment of HYL1 into the miRNA precursor maturation pathway before their splicing occurs.
Assuntos
Processamento Alternativo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , MicroRNAs/genética , Proteínas de Ligação a RNA/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Genes de Plantas , Íntrons , MicroRNAs/química , MicroRNAs/metabolismo , Mutação , Precursores de RNA/química , Precursores de RNA/metabolismo , Processamento Pós-Transcricional do RNA , Proteínas de Ligação a RNA/genéticaRESUMO
HYL1 is a nuclear protein involved in the processing of miRNAs but its exact function remains unknown. Arabidopsis thaliana hyl1 mutants exhibit hypersensitivity to ABA. We decided to answer the question whether ABA affects the HYL1 protein localization within the cell and show that it does not. We also studied the expression of HYL1 in different tissues and organs. In this paper we show for the first time the expression profile of the HYL1 protein using anti-HYL1 antibodies. The protein is present in seedlings and mature plants in all organs studied, with the highest amount in inflorescences. A. thaliana HYL1 protein has several repetitions of a 28-amino-acid sequence at the C-terminus that confer protein instability. Our bioinformatic analysis of HYL1 homologs in different Brassica species shows that this repetition is typical only for Arabidopsis. This may suggest a relatively late evolutionary acquisition of the C-terminal domain.
Assuntos
Ácido Abscísico/farmacologia , Proteínas de Arabidopsis/metabolismo , Arabidopsis/efeitos dos fármacos , Arabidopsis/metabolismo , Proteínas de Ligação a RNA/metabolismo , Sequência de Aminoácidos , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Sequência de Bases , Brassica/genética , Primers do DNA/genética , DNA de Plantas/genética , Evolução Molecular , Perfilação da Expressão Gênica , MicroRNAs/biossíntese , MicroRNAs/genética , Dados de Sequência Molecular , Mutação , Plantas Geneticamente Modificadas , RNA de Plantas/biossíntese , RNA de Plantas/genética , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Homologia de Sequência de Aminoácidos , Frações Subcelulares/efeitos dos fármacos , Frações Subcelulares/metabolismoRESUMO
Micro RNAs are 21-24 nt long RNA molecules involved in the regulation of gene expression on mRNA level. Mature miRNA molecules associated with the RNA-induced silencing complex (RISC) guide specifically mRNA cleavage or inhibit the translation. In plants selective mRNA degradation in miRNA-dependent pathway is a widespread mechanism that occurs more frequently than translation inhibition. miRNA precursors, known as pri-miRNA, are processed in several steps to produce mature miRNA molecules. There are several plant proteins involved in miRNA processing: DCL1, HYL1, SE, HEN1 and HASTY. The role of these proteins is discussed.
Assuntos
Regulação da Expressão Gênica de Plantas , MicroRNAs/metabolismo , Proteínas de Plantas/metabolismo , Plantas/genética , Proteínas de Transporte/metabolismo , Metilação , Proteínas de Ligação a RNA/metabolismo , Complexo de Inativação Induzido por RNA/metabolismo , Análise de Sequência de ProteínaRESUMO
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375â Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
RESUMO
Phototropism enables plants to orient growth towards the direction of light and thereby maximizes photosynthesis in low-light environments. In angiosperms, blue-light photoreceptors called phototropins are primarily involved in sensing the direction of light. Phytochromes and cryptochromes (sensing red/far-red and blue light, respectively) also modulate asymmetric hypocotyl growth, leading to phototropism. Interactions between different light-signaling pathways regulating phototropism occur in cryptogams and angiosperms. In this review, we focus on the molecular mechanisms underlying the co-action between photosensory systems in the regulation of hypocotyl phototropism in Arabidopsis thaliana. Recent studies have shown that phytochromes and cryptochromes enhance phototropism by controlling the expression of important regulators of phototropin signaling. In addition, phytochromes may also regulate growth towards light via direct interaction with the phototropins.