EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments

Olivia Wilkins, Christoph Hafemeister, Anne Plessis, Meisha Marika Holloway-Phillips, Gina M. Pham, Adrienne B. Nicotra, Glenn B. Gregorio, S. V. Krishna Jagadish, Endang M. Septiningsih, Richard Bonneau, Michael Purugganan

Research output: Contribution to journalArticle

Abstract

Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental signals. EGRINs encompass many layers of regulation, which culminate in changes in accumulated transcript levels. Here, we inferred EGRINs for the response of five tropical Asian rice (Oryza sativa) cultivars to high temperatures, water deficit, and agricultural field conditions by systematically integrating time-series transcriptome data, patterns of nucleosome-free chromatin, and the occurrence of known cis-regulatory elements. First, we identified 5447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes harboring known cis-regulatory motifs in nucleosome free regions proximal to their transcriptional start sites. We then used network component analysis to estimate the regulatory activity for each TF based on the expression of its putative target genes. Finally, we inferred an EGRIN using the estimated transcription factor activity (TFA) as the regulator. The EGRINs include regulatory interactions between 4052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of the heat shock factor family, including a putative regulatory connection between abiotic stress and the circadian clock. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference.

Original languageEnglish (US)
Pages (from-to)2365-2384
Number of pages20
JournalPlant Cell
Volume28
Issue number10
DOIs
StatePublished - Oct 1 2016

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Gene Regulatory Networks
regulator genes
Transcription Factors
transcription factors
rice
Temperature
Water
temperature
nucleosomes
Nucleosomes
water
Genes
genes
regulatory sequences
Circadian Clocks
Transcriptome
transcriptome
circadian rhythm
abiotic stress
Chromatin

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

Cite this

EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments. / Wilkins, Olivia; Hafemeister, Christoph; Plessis, Anne; Holloway-Phillips, Meisha Marika; Pham, Gina M.; Nicotra, Adrienne B.; Gregorio, Glenn B.; Krishna Jagadish, S. V.; Septiningsih, Endang M.; Bonneau, Richard; Purugganan, Michael.

In: Plant Cell, Vol. 28, No. 10, 01.10.2016, p. 2365-2384.

Research output: Contribution to journalArticle

Wilkins, O, Hafemeister, C, Plessis, A, Holloway-Phillips, MM, Pham, GM, Nicotra, AB, Gregorio, GB, Krishna Jagadish, SV, Septiningsih, EM, Bonneau, R & Purugganan, M 2016, 'EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments', Plant Cell, vol. 28, no. 10, pp. 2365-2384. https://doi.org/10.1105/tpc.16.00158
Wilkins, Olivia ; Hafemeister, Christoph ; Plessis, Anne ; Holloway-Phillips, Meisha Marika ; Pham, Gina M. ; Nicotra, Adrienne B. ; Gregorio, Glenn B. ; Krishna Jagadish, S. V. ; Septiningsih, Endang M. ; Bonneau, Richard ; Purugganan, Michael. / EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments. In: Plant Cell. 2016 ; Vol. 28, No. 10. pp. 2365-2384.
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