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3. The Botrytis cinerea Gene Expression Browser.

Author

Perez-Lara, Gabriel, primary, Moyano, Tomas C., additional, Vega, Andrea, additional, Larrondo, Luis, additional, Polanco, Ruben, additional, Alvarez, Jose M., additional, Aguayo, Daniel, additional, and Canessa, Paulo, additional

Published
2022
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6. Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

Author

Agencia Nacional de Investigación y Desarrollo (Chile), National Institute of General Medical Sciences (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Contreras-Lopez, Orlando [0000-0002-4048-6637], Vidal, Elena A. [0000-0002-8208-7327], Riveras, Eleodoro [0000-0001-8924-3954], Sparks, Erin E. [0000-0003-1543-6950], Medina, Joaquín [0000-0002-1735-330X], Contreras-Lopez, Orlando, Vidal, Elena A., Riveras, Eleodoro, Álvarez, José Miguel, Moyano, Tomas C., Sparks, Erin E., Medina, Joaquín, Pasquino, Angelo, Benfey, Philip N., Coruzzi, Gloria M., Gutierrez, Rodrigo A., Agencia Nacional de Investigación y Desarrollo (Chile), National Institute of General Medical Sciences (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Contreras-Lopez, Orlando [0000-0002-4048-6637], Vidal, Elena A. [0000-0002-8208-7327], Riveras, Eleodoro [0000-0001-8924-3954], Sparks, Erin E. [0000-0003-1543-6950], Medina, Joaquín [0000-0002-1735-330X], Contreras-Lopez, Orlando, Vidal, Elena A., Riveras, Eleodoro, Álvarez, José Miguel, Moyano, Tomas C., Sparks, Erin E., Medina, Joaquín, Pasquino, Angelo, Benfey, Philip N., Coruzzi, Gloria M., and Gutierrez, Rodrigo A.

Abstract

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type–specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type–specific transcription factor (TF)–target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF–target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.

Published
2022

8. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

Author

Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Science Foundation (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Agencia Estatal de Investigación (España), Álvarez, José Miguel [0000-0002-9826-085X], Moyano, Tomas C. [0000-0001-6495-4995], Gras, D. E. [0009-0000-0874-1995], Araus, Viviana [0000-0001-9457-431X], O'Brien, José Antonio [0000-0002-1788-1786], Carrillo, Laura [0000-0003-2215-322X], Medina, Joaquín [0000-0002-1735-330X], Vicente-Carbajosa, Jesús [0000-0002-6332-1712], Jiang, Jiming [0000-0002-6435-6140], Gutierrez, Rodrigo A. [0000-0002-5961-5005], Álvarez, José Miguel, Moyano, Tomas C., Zhang, Tao, Gras, D. E., Herrera, Francisco J., Araus, Viviana, O'Brien, José Antonio, Carrillo, Laura, Medina, Joaquín, Vicente-Carbajosa, Jesús, Jiang, Jiming, Gutierrez, Rodrigo A., Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Science Foundation (US), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Agencia Estatal de Investigación (España), Álvarez, José Miguel [0000-0002-9826-085X], Moyano, Tomas C. [0000-0001-6495-4995], Gras, D. E. [0009-0000-0874-1995], Araus, Viviana [0000-0001-9457-431X], O'Brien, José Antonio [0000-0002-1788-1786], Carrillo, Laura [0000-0003-2215-322X], Medina, Joaquín [0000-0002-1735-330X], Vicente-Carbajosa, Jesús [0000-0002-6332-1712], Jiang, Jiming [0000-0002-6435-6140], Gutierrez, Rodrigo A. [0000-0002-5961-5005], Álvarez, José Miguel, Moyano, Tomas C., Zhang, Tao, Gras, D. E., Herrera, Francisco J., Araus, Viviana, O'Brien, José Antonio, Carrillo, Laura, Medina, Joaquín, Vicente-Carbajosa, Jesús, Jiang, Jiming, and Gutierrez, Rodrigo A.

Abstract

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

Published
2019

9. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans

Author

Vidal, Elena A., Moyano, Tomas C., Bustos, Bernabe, I, Perez-Palma, Eduardo, Moraga, Carol, Riveras, Eleodoro, Montecinos, Alejandro, Azocar, Lorena, Soto, Daniela C., Vidal, Mabel, Di Genoval, Alex, Puschel, Klaus, Nurnberg, Peter, Buch, Stephan, Hampe, Jochen, Allende, Miguel L., Cambiazo, Veronica, Gonzalez, Mauricio, Hodar, Christian, Montecino, Martin, Munoz-Espinoza, Claudia, Orellana, Ariel, Reyes-Jara, Angelica, Travisanyl, Dante, Vizoso, Paula, Moraga, Mauricio, Eyheramendy, Susana, Maass, Alejandro, De Ferrari, Giancarlo, V, Mique, Juan Francisco, Gutierrez, Rodrigo A., Vidal, Elena A., Moyano, Tomas C., Bustos, Bernabe, I, Perez-Palma, Eduardo, Moraga, Carol, Riveras, Eleodoro, Montecinos, Alejandro, Azocar, Lorena, Soto, Daniela C., Vidal, Mabel, Di Genoval, Alex, Puschel, Klaus, Nurnberg, Peter, Buch, Stephan, Hampe, Jochen, Allende, Miguel L., Cambiazo, Veronica, Gonzalez, Mauricio, Hodar, Christian, Montecino, Martin, Munoz-Espinoza, Claudia, Orellana, Ariel, Reyes-Jara, Angelica, Travisanyl, Dante, Vizoso, Paula, Moraga, Mauricio, Eyheramendy, Susana, Maass, Alejandro, De Ferrari, Giancarlo, V, Mique, Juan Francisco, and Gutierrez, Rodrigo A.

Abstract

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 x 10(6) single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. 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 sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.

Published
2019

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