title: EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.
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.
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225.
authors.forename: Olivia
authors.identifier: 0000-0001-9762-7069
authors.initials: O
authors.lastname: Wilkins
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225.
authors.forename: Christoph
authors.initials: C
authors.lastname: Hafemeister
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225.
authors.forename: Anne
authors.identifier: 0000-0002-1083-7459
authors.initials: A
authors.lastname: Plessis
authors.affiliation: Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia.
authors.forename: Meisha-Marika
authors.identifier: 0000-0002-8353-3536
authors.initials: MM
authors.lastname: Holloway-Phillips
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225.
authors.forename: Gina M
authors.identifier: 0000-0002-8058-7862
authors.initials: GM
authors.lastname: Pham
authors.affiliation: Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia.
authors.forename: Adrienne B
authors.initials: AB
authors.lastname: Nicotra
authors.affiliation: International Rice Research Institute, Metro Manila 1301, Philippines.
authors.forename: Glenn B
authors.identifier: 0000-0002-7512-9058
authors.initials: GB
authors.lastname: Gregorio
authors.affiliation: International Rice Research Institute, Metro Manila 1301, Philippines.
authors.forename: S V Krishna
authors.initials: SV
authors.lastname: Jagadish
authors.affiliation: International Rice Research Institute, Metro Manila 1301, Philippines.
authors.forename: Endang M
authors.identifier: 0000-0002-9481-304X
authors.initials: EM
authors.lastname: Septiningsih
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225 rb133@nyu.edu mp132@nyu.edu.|Simons Center for Data Analysis, Simons Foundation, New York, New York 10010.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.affiliation: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225 rb133@nyu.edu mp132@nyu.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Purugganan
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000502:physiology; D012275:Oryza / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism*; D013696:Temperature; D014157:Transcription Factors / Q000378:metabolism; D014867:Water / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors; D014867:Water