title: Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp.
abstract: BACKGROUND
  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 insights into the abiotic and biotic stresses. However, the interaction between miRNAs and TFs in a gene regulatory network (GRN) still remains uncovered. Previous research has been mostly directed at inferring either miRNA or TF regulatory networks from data. However, networks involving a single type of regulator may not fully reveal the complex gene regulatory mechanisms, therefore study of interplay among these two regulators in gene regulation is important towards explaining the mechanism of different abiotic stresses.
  
  
  RESULTS
  Oligonucleotide microarrays containing 51,279 transcripts were used to identify total 133 salt responsive target genes regulated by 11 TFs that are also differentially regulated by miRNA under salinity, heat and drought stresses in Oryza sativa. TF's-target interactions which are most enriched in their downstream regulation were also identified. Many genes whose encoded proteins are implicated in response to light and radiation stimulus, hormone stimuli, oxidative stress, copper ion binding and electron transport were found to be enriched. However the majority were novel for the combined abiotic stress, which indicates that there are a great number of genes induced after the exposure these abiotic stresses and regulated by miRNA.
  
  
  CONCLUSIONS
  Analysis of the expression profile data of Oryza provides clues regarding some putative cellular and molecular processes that are undertaken in response to these stresses. The study also identified a large number of candidate functional genes that appear to be constitutively involved in salt, drought and heat stresses tolerance. Further examination of these genes may enable the molecular basis of abiotic stress tolerance in Oryza, to be elucidated.
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India.
authors.forename: Deepti
authors.initials: D
authors.lastname: Nigam
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India. Electronic address: sanjeevk@iasri.res.in.
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India.
authors.forename: D C
authors.initials: DC
authors.lastname: Mishra
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Rai
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India.
authors.forename: Shuchi
authors.initials: S
authors.lastname: Smita
authors.affiliation: Centre for Agricultural Bio-Informatics (CAB-in), Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, PUSA Campus, New Delhi, India.
authors.forename: Arijit
authors.initials: A
authors.lastname: Saha
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D006358:Hot Temperature; D035683:MicroRNAs / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D018384:Oxidative Stress; D012965:Sodium Chloride / Q000737:chemistry; D013312:Stress, Physiological; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors; D012965:Sodium Chloride
keywords: Algorithm for the reconstruction of accurate cellular networks; Gene regulatory network; Transcription factors; miRNA