Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance

MicroRNA (miRNA)-target gene modules are essential components of plants’ abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module’s expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat’s drought tolerance

A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis

Abstract not availableRoohollah Shamloo-Dashtpagerdi, Hooman Razi, Massumeh Aliakbari, Angelica Lindlöf, Mahdi Ebrahimi, Esmaeil Ebrahimi

Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network

It is of great significance to understand the regulatory mechanisms by which plants deal with drought stress. Two EST libraries derived from rapeseed (Brassica napus) leaves in non-stressed and drought stress conditions were analyzed in order to obtain the transcriptomic landscape of drought-exposed B. napus plants, and also to identify and characterize significant drought responsive regulatory genes and microRNAs. The functional ontology analysis revealed a substantial shift in the B. napus transcriptome to govern cellular drought responsiveness via different stress-activated mechanisms. The activity of transcription factor and protein kinase modules generally increased in response to drought stress. The 26 regulatory genes consisting of 17 transcription factor genes, eight protein kinase genes and one protein phosphatase gene were identified showing significant alterations in their expressions in response to drought stress.We also found the six microRNAs which were differentially expressed during drought stress supporting the involvement of a posttranscriptional level of regulation for B. napus drought response. The drought responsive regulatory network shed light on the significance of some regulatory components involved in biosynthesis and signaling of various plant hormones (abscisic acid, auxin and brassinosteroids), ubiquitin proteasome system, and signaling through Reactive Oxygen Species (ROS). Our findings suggested a complex and multi-level regulatory system modulating response to drought stress in B. napus.Roohollah Shamloo-Dashtpagerdi, Hooman Razi, Esmaeil Ebrahimi

Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue

Adipose tissue plays important roles in whole body energy homeostasis and is now known to be a very important and active endocrine organ. The transcriptional regulatory network of adipose tissue metabolism is complex and much yet to be known. To identify transcriptional profile in adipose tissue, expressed sequence tag (EST) analysis using Digital Differential Display (DDD) was employed. The results of EST analysis were re-evaluated by microarray data using COXPRESdb (an available expression data repository). To uncover transcriptional regulatory mechanisms which play key roles in the adipose tissue metabolism, transcriptional regulatory network analysis was applied, using the promoter analysis and interaction network toolset. Sixty-five transcripts were found to be more frequent in adipose tissue in comparison to the other tissues. COXPRESdb result showed that 62 % of the identified over-expressed genes in adipose tissue by DDD had expression level greater than 1 (in base 2 logarithm). Based on coincidence of regulatory sites, candidate TFs were identified including TFs that previously known to be involved in adipose tissue metabolism (SP1, KROX, STAT1, LRF, VDR, LXR, SRF and HIF1) and TFs, such as CKROX, ZF5, ETF, AP-2, AP-2alpha, PAX-5, SPZ1, RBPJ and CACD, that had not been recognized previously. This work yielded several TF candidates activating in adipose tissue metabolism. These findings open a new avenue for future research on promoter occupancy and TF perturbation. © 2013 The Genetics Society of Korea.Mohammad Reza Bakhtiarizadeh, Mohammad Moradi-Shahrbabak, Esmaeil Ebrahimi