title: Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.
abstract: Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.
authors.affiliation: Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway barah.pankaj@gmail.com.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Barah
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India.
authors.forename: Mahantesha Naika
authors.initials: MN
authors.lastname: B N
authors.affiliation: Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim N-7491, Norway.
authors.forename: Naresh Doni
authors.initials: ND
authors.lastname: Jayavelu
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India.
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India.
authors.forename: Khader
authors.initials: K
authors.lastname: Shameer
authors.affiliation: Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway atle.m.bones@ntnu.no.
authors.forename: Atle M
authors.initials: AM
authors.lastname: Bones
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects; D001665:Binding Sites; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008027:Light; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014157:Transcription Factors