Browsing by Author "Moyano Yugovic, Tomás Custodio"

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    Constructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants
    (Springer, 2015) Vidal Olate, Elena Alejandra; Contreras López, Luis Orlando; Gutiérrez Ilabaca, Rodrigo Antonio; Moyano Yugovic, Tomás Custodio; Stepanova, Anna N.
    Technological advances in the last decade have enabled biologists to produce increasing amounts of information for the transcriptome, proteome, interactome, and other -omics data sets in many model organisms. A major challenge is integration and biological interpretation of these massive data sets in order to generate testable hypotheses about gene regulatory networks or molecular mechanisms that govern system behaviors. Constructing gene networks requires bioinformatics skills to adequately manage, integrate, analyze and productively use the data to generate biological insights. In this chapter, we provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape platforms. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.
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    Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
    (2013) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio
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    Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots
    (2019) Álvarez, J. M.; Moyano Yugovic, Tomás Custodio; Zhang, T.; Gras, D.E.; Herrera, F.J.; Araus Caramori, Viviana; O'Brien, José; Carrillo, L.; Medina, J.; Vicente-Carbajosa, J.; Jiang, J.M.; Gutiérrez Ilabaca, Rodrigo Antonio
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    MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats : Relevance to Depression Pathophysiology
    (2018) Muñoz-Llanos, Mauricio; García-Pérez, María A.; Xu, Xiaojiang; Tejos-Bravo, Macarena; Vidal, Elena; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Aguayo, Felipe I.; Pacheco, Aníbal; García-Rojo, Gonzalo; Aliaga, Esteban; Rojas, Paulina S.; Cidlowski, John A.; Fiedler Temer, Jenny
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    Modelamiento de los estados del transcriptoma de A. thaliana frente a perturbaciones
    (2018) Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Pontificia Universidad Católica de Chile. Facultad de Ciencias Biológicas
    Hoy en día es habitual el análisis de cambios en la expresión génica para identificar genes relevantes en la respuesta a una perturbación o a una transición en el desarrollo. Sin embargo, muchos de los genes claves para la respuesta de un organismo, no están regulados a nivel de la expresión génica (por ejemplo, genes tempranos en las vías de señalización). Esos genes actualmente están ocultos a los enfoques tradicionales basados en transcriptomas. En este trabajo, abordamos el problema de identificar genes funcionalmente relevantes para una condición “A”, independiente si es que cambian sus niveles de expresión en una condición experimental contrastante. En esta tesis, proponemos un nuevo marco teórico basado en entropía para identificar estos genes. En primer lugar, determinamos los estados del transcriptoma y sus restricciones a partir de una gran cantidad de datos de expresión génica. Encontramos restricciones inherentes a la expresión génica a nivel global que revelan posibles nuevas relaciones funcionales para los genes, que no se obtienen por otros métodos ampliamente utilizados, tales como redes de correlación. Nuestro enfoque, además nos permitió encontrar nuevos genes relevantes en respuesta a perturbaciones, los cuales no necesariamente cambian su expresión en respuesta a dicha perturbación. Nuestro marco conceptual para analizar datos de transcriptomas fue evaluado en dos organismos modelos, Arabidopsis thaliana y Saccharomyces cerevisiae. Esta nueva metodología permite generar nuevas hipótesis acerca de redes regulatorias, las cuales no pueden ser alcanzadas con los métodos existentes. Adicionalmente, con el fin de contextualizar biológicamente listas de genes, se adaptó una metodología basada en análisis de texto que puede complementar la información de herramientas ya existentes, tales como Gene Ontology. Estas metodologías pueden ser fácilmente aplicadas a cualquier organismo que cuente con un número importante de datos transcriptómicos e información.
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    Nitrogen control of developmental phase transitions in Arabidopsis thaliana
    (2014) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Canales Carrasco, Javier; Gutiérrez Ilabaca, Rodrigo Antonio
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    Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments
    (2014) Canales, J.; Moyano Yugovic, Tomás Custodio; Villarroel Candia, Eva Mary; Gutiérrez Ilabaca, Rodrigo Antonio
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    TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis
    (2021) Herrera Vásquez, Ariel Esteban; Fonseca Cárdenas, Alejandro Alfredo; Ugalde Valdivia, José Manuel; Lamig Giannini, Liliana Andrea; Seguel Avello, Aldo Luis; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Salinas, Paula; Vidal, Elena A.; Holuigue Barros, Loreto
    Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription–PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
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    Transcription factor TGA2 is essential for UV-B stress tolerance controlling oxidative stress in Arabidopsis
    (2020) Herrera Vásquez, Ariel Esteban; Fonseca Cárdenas, Alejandro Alfredo; Ugalde Valdivia, José Manuel; Lamig Giannini, Liliana Andrea; Seguel Avello, Aldo Luis; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Salinas, Paula; Vidal, Elena A.; Holuigue Barros, Loreto
    Plants possess a diversity of Reactive Oxygen Species (ROS)-processing enzymes involved in sensing and controlling ROS levels under basal and stressful conditions. There is little information on the transcriptional regulators that control the expression of these ROS-processing enzymes, particularly at the onset of the defense response to abiotic stress. Filling this gap, this paper reports a critical role for Arabidopsis TGA class II factors (TGA2, TGA5, and TGA6) in the tolerance response to UV-B light and photooxidative stress, by activating the expression of genes with antioxidative roles. We identified two clusters of genes responsive to UV-B and activated by TGA2/5/6 were identified using RNAseq and clustering analysis. The GSTU gene family, which encodes glutathione transferase enzymes from the Tau subclass, was overrepresented in these clusters. We corroborated the TGA2-mediated activation in response to UV-B for three model genes (GSTU7, GSTU8, and GSTU25) using RT-qPCR and ChIP analyses. Interestingly, using tga256 mutant and TGA2- and GSTU7-complemented mutant plants, we demonstrated that TGA2-mediated induction of GSTU genes is essential to control ROS levels and oxidative damage after UV-B and MeV treatments. This evidence positions TGA class II factors, particularly TGA2, as a key players in the redox signaling network of Arabidopsis plants.
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    Whole genome sequence of Mapuche-Huilliche Native Americans
    (2018) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Bustos, Bernabé I.; Pérez-Palma, Eduardo; Moraga Marín, Carol Mabel; Montecinos López, Alejandro; Azócar López, Lorena Karina; Soto Wilder, Daniela Constanza; Riveras, Eleodoro; Vidal, Mabel; Genova, Alex Di; Puschel Illanes, Klaus; Nürnberg, Peter; Buch, Stephan; Hampe, Jochen; Eyheramendy Duerr, Susana; Miquel Poblete, Juan Francisco; Gutiérrez Ilabaca, Rodrigo Antonio
    Background Whole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant. Results Here we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96-97% high confidence calls. We found approximately 3.1x106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes. Conclusions Mapuche-Huilliche genomes contain a unique set of small- and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations