Extensive Natural Epigenetic Variation At A De Novo Originated Gene.

Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.9e100343

Analise probabilística da velocidade máxima do vento em Uruguaiana-RS, Brasil / Probabilistic analysis of maximum wind speed in Uruguayan-RS, Brazil

Dependendo da velocidade o vento tem potencial benéfico na polinização de plantas, na geração de energia, na manutenção da temperatura, mas ao ultrapassar certo patamar ele se torna perigoso e destrutivo, podendo causar danos a construções, plantações e a navegação. A teoria dos valores extremos desempenha um papel fundamental na modelagem de eventos associados a probabilidades muito pequenas ou eventos raros. Os modelos probabilísticos baseados nesta teoria visam predizer, a partir de um conjunto de valores máximos de um processo ambiental registrado num período relativamente curto, os valores máximos esperados em um período maior de tempo, que para o caso específico do vento, é de grande utilidade, por exemplo, na escolha da cultivar a ser semeada. Este trabalho consistiu no ajuste da distribuição generalizada de valores extremos (GVE) aos dados de velocidade máxima mensal de vento registrados durante um período de 54 anos (1961 a 1983 e 1989 a 2015) em Uruguaiana, Estado do Rio Grande do Sul. O ajuste aos dados foi avaliado por meio do teste de Kolmogorov-Smirnov. A distribuição generalizada de valores extremos com seus parâmetros estimados pelo método de máxima verossimilhança apresentou um ajuste satisfatório aos dados

Qua-Quine Starch Arabidopsis thaliana, a new gene regulated by DNA methylation and prone to epiallelic variation

Orientador: Michel Georges Albert VincentzTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: Modificações epigenéticas do DNA ou da cromatina atuam principalmente no controle da atividade de elementos de transposição, podendo também silenciar genes, geralmente quando estes estão associados a elementos de transposição ou sequências repetidas. Em plantas, alguns alelos epigenéticos afetando caracteres como morfologia floral, florescimento, estatura ou amadurecimento do fruto foram descritos, revelando o potencial deste tipo de regulação para gerar variabilidade fenotípica herdável não necessariamente vinculada a alterações da sequência de DNA. No entanto, o impacto de mecanismos epigenéticos em processos de evolução adaptativa é ainda bastante desconhecido, em parte, pela falta de informação sobre variação epigenética em populações naturais. Identificamos Qua-Quine Starch (QQS) de Arabidopsis thaliana como um gene sob um controle epigenético flexível e, portanto, particularmente propenso a variações epialélicas frequentes na natureza. QQS é um gene recente, que provavelmente originou-se de novo em Arabidopsis thaliana em uma região rica em elementos de transposição. Mostramos que QQS apresenta-se diferencialmente expresso entre acessos naturais assim como entre indivíduos diretamente coletados na natureza e que estas diferenças de expressão estão negativamente correlacionadas com o nível de metilação de sequências repetidas localizadas em sua região promotora e 5' UTR, não estando relacionadas a variação genética em cis ou trans. Mostramos ainda que variação epialélica em QQS é independente do nível de metilação de transposons vizinhos e que pode ser estavelmente herdada entre gerações. Considerando o impacto potencial de padrões de expressão contrastantes de QQS no metabolismo de amido, um importante componente para produção de biomassa e crescimento, sugerimos que variação epialélica em QQS possa ter implicações adaptativas. Nossos dados também apontam pela primeira vez uma ligação potencial entre mecanismos epigenéticos e o processo de evolução de genes novos. Propomos que genes novos, especialmente os de origem de novo, poderiam ser mais propensos a variar epigeneticamente, o que permite um ajuste fino de seu padrão de expressão até que o estado mais vantajoso seja fixado geneticamenteAbstract: Epigenetic modifications of DNA or chromatin control of the activity of transposable elements and can also silence genes which are associated to transposons or repetitive sequences. In plants, epigenetic alleles affecting characters such as floral morphology, flowering, stature or fruit ripening have been described, highlighting the potential of this type of regulation in generating heritable phenotypic diversity, not necessarily linked to DNA sequence alterations. However, the impact of epigenetic mechanisms in adaptative evolution is still largely unknown, in part, due to the lack of information about epiallelic variation in natural populations. We have identified Qua-Quine Starch (QQS) of Arabidopsis thaliana as a gene under flexible epigenetic control and thus particularly prone to epiallelic variation in nature. QQS is a recent gene that likely originated de novo in Arabidopsis thaliana in a transposon-rich region. We show that QQS is differentially expressed among natural accessions as well as among individuals directly sampled from the wild and that these expression differences are negatively correlated with the DNA methylation level of repeat sequences located on QQS promoter and 5'UTR region and are not correlated with cis or trans genetic variation. We also show that epiallelic variation at QQS is independent of the methylation status of nearby transposable elements and can be stably inherited across generations. Considering the potential impact of contrasting QQS expression patterns on starch accumulation, an important component of biomass production and growth, we suggest that epiallelic variation at QQS may have adaptative implications. Our data also points for the first time to a potential link between epigenetic mechanisms and the evolution of novel genes. We suggest that novel genes, more specifically those created de novo, could be endowed with an increased potential for epigenetic variation and thus for adjusting their expression pattern until the most adaptive state becomes genetically fixedDoutoradoGenetica Vegetal e MelhoramentoDoutor em Genetica e Biologia Molecula

Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture

International audienceTransposable elements (TEs) are repetitive DNA sequences that have the ability to mobilize in the genome and create major effect mutations. Despite the importance of transposition as a source of genetic novelty, we still know little about the rate, landscape, and consequences of TE mobilization. This situation stems in large part from the repetitive nature of TEs, which complicates their analysis. Moreover, TE mobilization is typically rare and therefore new TE (i.e., non-reference) insertions tend to be missed in small-scale population studies. This chapter describes a TE-sequence capture approach designed to identify transposition events for most of the TE families that are potentially active in Arabidopsis thaliana. We show that our TE-sequence capture design provides an efficient means to detect with high sensitivity and specificity insertions that are present at a frequency as low as 1/1000 within a DNA sample

Epigenetic diversity increases the productivity and stability of plant populations

Biological diversity within species can be an important driver of population and ecosystem functioning. Until now, such within-species diversity effects have been attributed to underlying variation in DNA sequence. However, within-species differences, and thus potentially functional biodiversity, can also be created by epigenetic variation. Here, we show that epigenetic diversity increases the productivity and stability of plant populations. Epigenetically diverse populations of Arabidopsis thaliana produce up to 40% more biomass than epigenetically uniform populations. The positive epigenetic diversity effects are strongest when populations are grown together with competitors and infected with pathogens, and they seem to be partly driven by complementarity among epigenotypes. Our study has two implications: first, we may need to re-evaluate previous within-species diversity studies where some effects could reflect epigenetic diversity; second, we need to incorporate epigenetics into basic ecological research, by quantifying natural epigenetic diversity and testing for its ecological consequences across many different species

Extensive natural epigenetic variation at a [i]De Novo[/i] originated gene

Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation

Mild drought in the vegetative stage induces phenotypic, gene expression and DNA methylation plasticity in Arabidopsis but no transgenerational effects

International audienceWhether environmentally-induced changes in phenotypes can be heritable is a topic with revived interest. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown if this other system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To obtain a comprehensive assessment of potential transgenerational effects induced by the environment, we subjected four natural accessions as well as the reference accession Col-0 of A. thaliana to mild drought in a multigenerational design. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of parental environments. However, after an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects and irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in the reference accession Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects

High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies

International audienceBackground: Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool.Methods: We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy.Results: The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response.Conclusions: This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses