For a long time, researchers have been working on unravelling the role of genes which are responsible for the expression of proteins. Researchers were curious to know the reason that why the non-coding sequences are conserved through evolutionary selection. New light was shed on this problem in 1993 when the first miRNA was identified from the junk DNA of the nematode C. elegans named as lin-4 (1). The first plant miRNA was discovered in the year 2002 from the Arabodipsis thaliana, after that total of 4014 miRNAs from 52 different plant species have been identified and deposited miRBASE database which is availabe in public domain and freely accessible (2). miRNAs are 20–25 nucleotide in length, endogenous in origin, small, and noncoding RNA molecules found in all the eukaryotic organism. miRNA takes part in the regulation of gene expression at the post-transcriptional level by leading to the target degaradation or translational repression with the sequence specific interactions to complementary sites of target mRNA (3).
The transcription of MIR genes takes place similar to mRNA coding genes by the enzyme RNA polymerase II (4) (5). Once MIR genes are transcribed, they produce long pri-miRNA transcripts with characteristic features similar to mRNAs. The stabiliaztion of pri-miRNA takes place through the addition of a 5' 7-methylguanosine cap, and a 3' poly A tail (6). pri-miRNA transcripts fold back due to their internal sequence complementarity into an imperfect stem-loop structure and are recognized by the members of a ribonuclease enzyme Dicer-like1 (DCL) family which belongs to RNAse III endoribonuclease protein family. Inside the nucleus the pri-miRNA sliced in two steps by the DCL1 complex. In the first step the base of the stem is trimmed and remaining structure is called as pre-miRNA. In the second step the loop of pre-miRNA is removed and the duplex of miRNA:miRNA* is left for further processing (2). The enzyme methytransferase HEN1, 2’-O-methylates the 3’ terminus of miRNA:miRNA* duplexes (7). 2’-O-methylation of miRNA-3p/5p duplex is essential to protect the 3’ termini of unwound mature miRNA from the action of exonucleases, such as SDN proteins(8). Previously it was assumed that after the maturation of miRNA:miRNA*, only miRNA was loaded to RISC and proceeds for binding with the target mRNA. But now it is reported that miRNA* also may load on the RISC and can regulate the target genes. So considering this point now the miRNA : miRNA* duplex is named as miRNA-5p and miRNA-3p (9). The miRNA strand of the miRNA 5p/3p is loaded into the RNA inducing silencing complex (RISC) led by a protein AGO thereby directing miRNA towards its complementary target mRNA sequence (10). In the RNA induced silencing complex (RISC), miRNAs bind to target mRNA, based on the perfect or near-perfect complementarity between the miRNA and the mRNA either transcript cleavage or translation repression takes place.
The role of plant miRNA have been established in the regulation of several developmental processes such as leaf morphogenesis and polarity, root development, vascular development, phase transition from somatic to reproductive, flower and seed development (11). The role of miRNAs are also well established in diverse responses to stresses such as abiotic stresses like drought, salt, cold, oxidative, nutrient deficiency and biotic stresses (12). Most of the protein coding genes which are targetted by miRNAs, coding for transcription factor, which act in key biological processes like responding to abiotic and biotic stresses, performing metabolic functions, and regulating developmental processess.
Jatropha curcas L. is a monoecious and perennial shrub which is extensively grown throughout the tropical countries. It grows in any unfavorable agro-climatic conditions due to its low moisture demand, low fertility requirement, tolerance to excessive temperature, pest and disease resistance. Due to ever inflating fuel prices and increasing concern over the greenhouse gas emissions such as CO2, has led researchers to search for potential renewable biofuels. Jatropha curcas L. oil has drawn attention as one of the most potential biofuels that can be a substitute of never-ending fuel crisis. The crude seed oil of Jatropha curcas have the potential to be converted into biodiesel which can qualify the European and United State standards (13). A major constraint to high quality oil yield from Jatropha curcas is the lack of knowledge about its genetic regulation. To elucidate the role of miRNAs in the Jatropha curcas many studies has been conducted for the miRNA’s identification in Jatropha curcas. The first of its kind for the miRNA identification study was reported by using small RNA cloning methodology but researchers did not provide the precursor sequences (14). In the second study, the conserved miRNAs of Jatropha curcas were predicted by using the available Expressed sequence tags and Genome survey sequences in the publicly available databases by using comparative genomics approach (15). In the third study, conserved and novel miRNAs from J. curcas were identified through the deep sequencing of small RNAs (sRNA) from mature seeds (16). In the latest study, conserved and novel miRNAs from J. curcas were identified through the deep sequencing of small RNAs (sRNA) from the leaves tissue of Jatropha curcas (17). In a strategy to predict the conserved miRNAs from the different plant species by exploiting the whole genome shot gun sequences many reports have been published. At present, the miRNA prediction from the available whole genome shotgun assembly sequences of J. curcas is not reported from any researcher. This is an in-silico approach for the screening of potential conserved miRNAs by using homolog search of model plant Arabidopsis thaliana miRNAs against the genome of Jatropha curcas L. To identify the role of J. curcas miRNAs, the target genes of predicted miRNA is also identified.