José Miguel Álvarez, PhD.

Principal Investigator and Assistant Professor

Laboratorio de Regulación del Genoma Vegetal

PhD in Biological Sciences, Pontificia Universidad Católica de Chile, Chile.

Líneas de Investigación

  • Regulación de la transcripción en plantas
  • Biología de sistemas y genómica

Laboratorio de Regulación del Genoma Vegetal

Our lab studies the regulatory mechanisms that drive plant adaptation to environmental cues, with a specific interest in drought and changes in nutrient availability. Plant adaptation to environmental signals relies on variations in chromatin accessibility, transcriptional regulation, and changes in gene expression. To understand these processes, we use an array of advanced molecular techniques including transcriptomics, Chromatin Immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitivity sequencing (DNAse-seq), Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). By integrating these approaches using bioinformatic tools, we have built significant knowledge of the underlying mechanism that regulates the plant's adaptation to changes in the environment.

We apply principles of genomics and systems biology to challenges in agricultural sustainability with an emphasis on drought effects, which is poised to intensify in the coming years due to climate change.

Selected publications

Transient genome-wide interactions of the master transcription factor NLP7 initiates a rapid nitrogen-response cascade. Alvarez, J.M., Schinke, A., Brooks, M.D., Pasquino, A., Leonelli, L., Varala, K., Safi A., Krouk, G., Krapp, A., Coruzzi, G.M. Nature Communications (2020). (11): 1157.

Nutrient dose-responsive transcriptome changes driven by Michaelis-Menten kinetics underlie plant growth rates. Swift, J.*, Alvarez, J.M.*, Araus, V., Gutiérrez, R.A., Coruzzi, G.M. *These authors contributed equally to this work. Proceedings of the National Academy of Sciences (2020). In press.

A balancing act: How nitrogen and drought signaling combine to regulate plant responses. Araus, V*., Swift, J.*, Alvarez., J.M.*, Henry., A., Coruzzi., G.M. *These authors contributed equally to this work. Journal of Experimental Botany (2020). doi: 10.1093/jxb/eraa054. [Epub ahead of print].

Local changes in chromatin accessibility and transcriptional networks underlying the nitrate response in Arabidopsis roots. Alvarez, J.M., Moyano, T.C., Zhang, T., Gras, D.E., Herrera, F.J., Araus, V., O’Brien, J., Carrillo, L., Medina, J., Vicente-Carbajosa, J., Jiang, J., Gutiérrez, R.A. Molecular Plant (2019). 12 (12): 1545-1560.

Systems approaches identify TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. Alvarez, J.M., Riveras, E., Vidal, E.A., Gras, D.E., Contreras-López, O., Tamayo, K.P., Aceituno, F., Gómez, I., Ruffel, S., Lejay, L., Jordana, X., and Gutiérrez, R.A. The Plant Journal (2014). 80: 1-13.



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