title: Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana.
abstract: Environmental stress leads to dramatic transcriptional reprogramming, which is central to plant survival. Although substantial knowledge has accumulated on how a few plant cis-regulatory elements (CREs) function in stress regulation, many more CREs remain to be discovered. In addition, the plant stress cis-regulatory code, i.e., how CREs work independently and/or in concert to specify stress-responsive transcription, is mostly unknown. On the basis of gene expression patterns under multiple stresses, we identified a large number of putative CREs (pCREs) in Arabidopsis thaliana with characteristics of authentic cis-elements. Surprisingly, biotic and abiotic responses are mostly mediated by two distinct pCRE superfamilies. In addition, we uncovered cis-regulatory codes specifying how pCRE presence and absence, combinatorial relationships, location, and copy number can be used to predict stress-responsive expression. Expression prediction models based on pCRE combinations perform significantly better than those based on simply pCRE presence and absence, location, and copy number. Furthermore, instead of a few master combinatorial rules for each stress condition, many rules were discovered, and each appears to control only a small subset of stress-responsive genes. Given there are very few documented interactions between plant CREs, the combinatorial rules we have uncovered significantly contribute to a better understanding of the cis-regulatory logic underlying plant stress response and provide prioritized targets for experimentation.
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zou
authors.forename: Kelian
authors.initials: K
authors.lastname: Sun
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Mackaluso
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Seddon
authors.forename: Rong
authors.initials: R
authors.lastname: Jin
authors.forename: Michael F
authors.initials: MF
authors.lastname: Thomashow
authors.forename: Shin-Han
authors.initials: SH
authors.lastname: Shiu
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D020218:Response Elements / Q000502:physiology*; D013312:Stress, Physiological / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors