Aug 19, 2011

Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana

Proceedings of the National Academy of Sciences of the United States of America
Cheng ZouShin-Han Shiu

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 ...Continue Reading

Mentioned in this Paper

Transcription, Genetic
Gene Expression
Arabidopsis thaliana Proteins
Response Elements
Transcription Factor
Arabidopsis thaliana <plant>
CST8 gene

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