Synergistic regulatory networks mediated bymicroRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp

Abstract

Transcription factors (TFs) and microRNAs (miRNAs) are primary gene regulators within the cell.Regulatory mechanisms of these two main regulators are of great interest to biologists and may provide insightsinto the abiotic and biotic stresses. However, the interaction between miRNAs and TFs in a gene regulatory net-work (GRN) still remains uncovered. Previous research has been mostly directed at inferring either miRNA or TFregulatory networks from data. However, networks involving a single type of regulator may not fully reveal thecomplex gene regulatory mechanisms, therefore study of interplay among these two regulators in gene regula-tion is important towards explaining the mechanism of different abiotic stresses.Result:Oligonucleotide microarrays containing 51,279 transcripts were used to identify total 133 salt responsivetarget genes regulated by 11 TFs that are also differentially regulated by miRNA under salinity, heat and droughtstresses inOryza sativa. TF's-target interactions which are most enriched in their downstream regulation werealso identified. Many genes whose encoded proteins are implicated in response to light and radiation stimulus,hormone stimuli, oxidative stress,copperion binding and electron transportwere found to beenriched. Howeverthe majority were novel for the combined abiotic stress, which indicates that there are a great number of genesinduced after the exposure these abiotic stresses and regulated by miRNA.Conclusion:Analysis of the expression profile data ofOryzaprovides clues regarding some putative cellular andmolecular processes that are undertaken in response to these stresses. The study also identified a large numberof candidate functional genes that appear to be constitutively involved in salt, drought and heat stresses toler-ance. Further examination of these genes may enable the molecular basis of abiotic stress tolerance inOryza,to be elucidated.© 2014 Elsevier B.V. All rights reserved.1. IntroductionAbiotic stress causes substantial loss to agricultural production glob-ally. Rice(Oryza sativa) is a staple food crop that is cultivated worldwideand constitutes a primary source of food especially in Asia. Abioticstresses basically drought, extreme temperatures and salinity are themajor limiting factor in rice cultivation. Reflecting the diminishing envi-ronmental conditions, more often than not crops are exposed simulta-neously to multiple stresses resulting in vast changes in the molecularscene within the cell. Therefore, comprehensive understanding of theregulatory networks that govern the dynamic adaptive changes in aplant responding to stress is critical to meet future energy needs. Be-sides high agricultural importance, rice is model plant organismsrepresenting monocots and has extensive biological resources includingcomplete genome sequence, highest number of microarray and tran-scriptome studies. Therefore it is important to study the molecularmechanism of different kinds of abiotic stress within rice as it may re-veal a number of pivotal attributes that may behave similarly for othercrops of the same family.MicroRNAs (miRNAs) are approximately 21-nucleotide (nt) non-coding RNAs that play critical roles in gene expression regulation atthe post-transcriptional level. In plants, cleavage of the target mRNA ap-pears to be the prevalent method of posttranscriptional regulation.Brodersen et al. (2008)provided evidence that plant miRNA-guided si-lencing has a widespread translational inhibitory component. PlantmiRNA-guided gene regulation has been shown to be involved in mul-tiple developmental processes including organ polarity (Bowman,2004), leaf growth (Chuck et al., 2007), and male or female sterility(Millar and Gubler, 2005). ,Transcription factorbinding sites; CRMs,Cis-regulatory modules.