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. machine learning | motif discovery | transcription factor binding site

Determinants of nucleosome positioning and their influence on plant gene expression

“…4C). In addition, many cis-regulatory elements are known to be responsible for dynamic changes of gene expression in various environments (Marcotte et al 1989;Mundy et al 1990;Baker et al 1994;Zou et al 2011;Hickman et al 2013;Benn et al 2014;Franco-Zorrilla et al 2014;Sullivan et al 2014). This raises the question of whether environmental stimuli may affect nucleosome occupancy on cis-regulatory elements and ultimately transcriptional response to environmental perturbation.…”

Introduction to a Special Issue on Genotype by Environment Interaction

“…More recently, genomewide transcriptional studies have also assessed the responses of contrasting genotypes when exposed to various types of environmental stresses. In those studies, numerous transcripts appear to be up or downregulated and the combination of that information has proven useful in terms of identifying relevant regulatory networks associated with that response (e.g., Zou et al, 2011). However, specific characteristics of the natural variants regulating those pathways is still largely unknown (Des Marais and Juenger, 2010;Juenger, 2013).…”

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…These CNSs are thought to be involved in diverse regulatory functions, including transcription initiation and transcript processing (for example, splicing or mRNA localization), as well as being implicated in complex patterning, such as embryonic development [9][10][11][12][13] . Plant CNSs have previously been identified on a genome-wide scale on the basis of the comparison of few or distant genomes (for example, maize versus rice [14][15][16] , Brachypodium distachyon versus rice 17 , A. thaliana versus Brassica oleracea 18,19 and sets of diverse angiosperms 20 ).…”