Integrative transcriptomic analysis uncovers novel gene modules that underlie the sulfate response in Arabidopsis thaliana

Henríquez Valencia, Carlos and Arenas, Anita and Medina Alcazar, Joaquin and Canales, Javier (2018). Integrative transcriptomic analysis uncovers novel gene modules that underlie the sulfate response in Arabidopsis thaliana. "Frontiers in Plant Science", v. 9 ; pp.. ISSN 1664-462X. https://doi.org/10.3389/fpls.2018.00470.

Description

Title: Integrative transcriptomic analysis uncovers novel gene modules that underlie the sulfate response in Arabidopsis thaliana
Author/s:
  • Henríquez Valencia, Carlos
  • Arenas, Anita
  • Medina Alcazar, Joaquin
  • Canales, Javier
Item Type: Article
Título de Revista/Publicación: Frontiers in Plant Science
Date: January 2018
ISSN: 1664-462X
Volume: 9
Subjects:
Freetext Keywords: gene co-expression analysis; sulfur; sulfate assimilation; microarray analysis; network analysis; transcription factors
Faculty: Centro de Investigación en Biotecnología y Genómica de Plantas (CBGP) (UPM)
Department: Otro
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.

Funding Projects

TypeCodeAcronymLeaderTitle
Government of SpainRTA2015-00014-C02-01UnspecifiedUnspecifiedUnspecified

More information

Item ID: 55044
DC Identifier: http://oa.upm.es/55044/
OAI Identifier: oai:oa.upm.es:55044
DOI: 10.3389/fpls.2018.00470
Official URL: https://www.frontiersin.org/articles/10.3389/fpls.2018.00470/full
Deposited by: Memoria Investigacion
Deposited on: 15 Jul 2019 11:48
Last Modified: 15 Jul 2019 11:48
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