Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

Maria Angels De Luis Balaguer, Adam P. Fisher, Natalie M. Clark, Maria Guadalupe Fernandez-Espinosa, Barbara K. Möller, Dolf Weijers, Jan U. Lohmann, Cranos Williams, Oscar Lorenzo, Rosangela Sozzani*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)

Abstract

Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells.
Original languageEnglish
Pages (from-to)E7632-E7640
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number36
DOIs
Publication statusPublished - 2017

Keywords

  • Cell-type expression profile
  • Gene regulatory network
  • Modeling
  • Root development
  • Root stem cell

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    Balaguer, M. A. D. L., Fisher, A. P., Clark, N. M., Fernandez-Espinosa, M. G., Möller, B. K., Weijers, D., Lohmann, J. U., Williams, C., Lorenzo, O., & Sozzani, R. (2017). Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. Proceedings of the National Academy of Sciences of the United States of America, 114(36), E7632-E7640. https://doi.org/10.1073/pnas.1707566114