CIBTech Journal of Biotechnology ISSN: 2319–3859 (Online) An Open Access, Online International Journal Available at http://www.cibtech.org/cjb.htm 2014 Vol. 3 (3) October-December, pp.1-10/Paul et al. Research Article © Copyright 2014 | Centre for Info Bio Technology (CIBTech) 1 IN SILICO PREDICTION OF THE RELATIONSHIP BETWEEN MIRNA AND DIFFERENTIALLY EXPRESSED GENES DURING SUBMERGENCE IN ORYZA SATIVA Prosenjit Paul 1 , *Supriyo Chakraborty 2 , Binata Halder 3 and Arup Kumar Malakar 4 Department of Biotechnology, Assam University, Silchar-788011, Assam, India *Author for Correspondence ABSTRACT Plant finely regulates the multifarious pattern of gene expression in response to submergence at the post- transcriptional level. To endure submergence plant genome induces several mRNA, miRNA and regulatory elements. MicroRNAs are short (20–27 nucleotides), non-coding RNA molecules. They play important role in regulation of gene expression. MicroRNAs are well-known as the negative regulator of gene expression via sequence specific recognition of their target mRNA. Here, we have predicted the relationship between the miRNA and mRNAs expressed differentially during submerged condition in Oryza sativa. The untranslated regions of the mRNAs are full of transcriptional factors and miRNA target site. Each anaerobically induced mRNA contains a unique combination of cis-acting regulatory elements in their UTRs. We have identified 10 conserved miRNAs families within the genome of Oryza sativa induced in response to submergence. The present study uncovers, notable propensity of these miRNAs to interact with the cis-acting regulatory element involved in many biological processes and stress response. These events may modulate the initial signal and produce a new signal and eventually lead to the increased expression of these genes. Keywords: Oryza Sativa; MicroRNA; Submergence; Gene Expression; Untranslated Region INTRODUCTION Crop productivity is strictly related to genome stability, an essential requisite for optimal plant growth and development (Macovei et al., 2012). In general there are numerous types of environmental stresses, often crop or location specific, which cause significant crop loses. Environmental stresses can cause severe effects on plant cells sufficient to cause cell death (Umeda and Uchimiya, 1994). Amongst all environmental stresses rice crops especially experience water stress (submergence) in the rainfed lowland of Northeast India. Submergence is considered to be one of the major constraints for crop production in many areas of the world (Kozlowski, 1984). According to FAO (2002) submergence adversely affects 10% of the global land area (Pradhan and Mohanty, 2013). It imposes several often concurrent challenges like starvation of oxygen / carbon-dioxide, hypoxia and anoxia and result in restricted plant growth, development and crop yield. The regulation of gene expression in response to environmental stress is an important factor in plant survival and adaptability. Gene expressional regulation is achieved through a series of complex mechanisms, generally in two distinct steps: firstly at transcriptional level mediated by cis-acting DNA elements such as promoters, enhancers, locus control regions and silencers to produce a mature mRNA (Pesole et al., 2001), secondly at the post-transcriptional control of mRNA nucleo- cytoplasmic transport, translation efficiency, subcellular localization and stability. Recently, miRNAs have been reported to control a variety of biological processes, such as plant development, differentiation, signal transduction or stress responses (Macovei et al., 2012). MicroRNAs (miRNAs) are a family of small endogenous non-protein coding RNA molecules especially ~20-27 nts, form Watson-Crick base pairs with different target mRNAs and are important post- transcriptional regulators of gene expression regulating various biological activities. Knowing the entire repertoire of these small molecules is the first step to gain a better understanding of their function. The number of miRNAs has expanded rapidly, shortly after the discovery of the first miRNA i.e.lin-4 & let-7 RNA in Caenorhabditis elegans (Ambros, 2004; Zhang et al., 2007; Sunkar and Jagadeeswaran, 2008). Sequencing data from several species further led to the discovery of many miRNAs, which in turn spurred