Elucidating the functional role of predicted miRNAs in post-transcriptional gene regulation along with symbiosis inMedicago truncatula

Abstract

27Non-coding RNAs (ncRNAs) are found to be important regulator of gene expression because 28 of their ability to modulate post-transcriptional processes. microRNAs are small ncRNAs 29 which inhibit translational and post-transcriptional processes whereas long ncRNAs are 30 found to regulate both transcriptional and post-transcriptional gene expression. Medicago 31 truncatula is a well-known model plant for studying legume biology and is also used as a 32 forage crop. In spite of its importance in nitrogen fixation and soil fertility improvement, 33 little information is available about Medicago ncRNAs that play important role in symbiosis. 34To understand the role of Medicago ncRNAs in symbiosis and regulation of transcription 35 factors, we have identified novel miRNAs and tried to establish an interaction model with 36 their targets. 149 novel miRNAs are predicted along with their 770 target proteins. We have 37 shown that 51 of these novel miRNAs are targeting 282 lncRNAs. We have analyzed the 38 interactions between miRNAs and their target mRNAs as well as their targets on lncRNAs. 39Role of Medicago miRNAs in the regulation of various transcription factors were also 40 elucidated. Knowledge gained from this study will have a positive impact on the nitrogen 41 fixing ability of this important model plant, which in turn will improve the soil fertility. 42 transcription factor 44 45 46 47 50 51 Functional RNA molecules, encoded by non-coding RNA genes, play important roles in 52 regulating the expression of various genes (1). MicroRNAs (miRNAs), first discovered in 53 Caenorhabditis elegans (lin-4) (2) are 20-24 nucleotides long, endogenous, small non-coding 54 ribonucleic acids that regulate gene expression post-transcriptionally in plants, animals and 55 viruses (3,4). miRNAs regulate gene expression in various ways including cleavage, 56 degradation and decaying of mRNA and nascent polypeptide, inhibition of translation by 57 forming miRNA-mRNA complex, ribosome drop-off resulting in premature termination, 58 sequestration of target mRNAs in P-bodies that are distinct foci consisting enzymes involved 59 in mRNA turnover (5), transcriptional inhibition by miRNA mediated chromatin 60 reorganization, inhibition of translation initiation by suppressing the cap recognition by 61 elF4E and 60S-40S joining (6-16). Plant miRNAs can repress translation by binding in a 62 near-perfect manner with target mRNAs (17) where animal miRNAs can recognize target 63 mRNAs through six to eight nucleotides long seed region of the 5'end of the mRNA (18). 64 Various miRNAs have been discovered in animals, plants and viruses with the help of 65 conventional experimental strategies along with bioinformatics tools (19,20). In spite of 66 present state-of-the art technologies including high throughput sequencing, identification of 67 miRNAs in various organisms is still complex and need proper blending of experimental 68 strategies and computational approaches to get more accurate results. miRNAs can be 69 identified by computat...