MicroRNAs(miRNAs) are a group of small non-coding RNAs of approximately 18 - 24 nucleotides that play a negative role in post-transcriptional changes in eukaryotes. The miRNAs are then loaded onto the argonate family proteins (AGO) to form a protein complex (RISC). The primary activity of the RISC complex is to direct the mature miRNA to the target RNA and to stop protein production (Megah et al., 2018). miRNAs are involved in response to abiotic stresses in plants such as drought; several miRNA families have been reported in response to drought stress in rice, tomato, Arabidopsis, Medicago truncatula, peach, barley and wheat (Akdogan et al., 2015). The purpose of this study was to identify new microRNAs and their role in suppressing and preventing expression of some of their target genes in rapeseed.

A total of 38589 known mature miRAN sequences were downloaded from the miRBase database. The miRNA sequences were used as known sequences to find conserved miRNAs based on homology search for miRNAs with rapeseed GSS sequences.103369 GSS for rapeseed was downloaded from NCBI database. Mature miRNA sequences were uploaded to the BLASTn algorithm to search for homology with rapeseed GSSs in Linux. The miRNA sequences as known sequences and the GSS sequences as sequences were compared with each other for homology search. GSSs with mature miRNA sequences up to four mismatches were selected as candidates (Zhang, 2005). GSS sequences were used instead of EST sequences because miRNAs can generate GSS sequences in addition to EST sequences. Consequently, GSSs were sequenced between the BLASTx miRNA sequences and the GSS coding sequences were deleted and only non-coding GSS sequences remained (Karimi et al., 2017). Mfold software was used to predict the secondary structure of candidate miRNAs (Vivek, 2018). ath-miR5021 and ath-miR8175 from Arabidopsis, bol-miR9410 and bol-miR9411 from wild cabbage and cas-miR11592 from Camelina sativa were selected from the psRNATarget website (Dai and Zhao, 2011.

For miR5021: The NST1 target gene encodes a protein called Stress response protein NST1, which plays a role in regulating secondary wall thickness in plants and preventing its destruction against a variety of stresses (Mitsuda et al., 2005). For miR9410: The HST gene is one of the target genes that encodes an enzyme called Shikimate O-hydroxycinnamoyltransferase in plants, which participates in the phenylpropanoid biosynthesis and heat stress control in plants, propanoids as secondary metabolites during developmental stages. The plant is synthesized in response to stress conditions (Lukasik et al., 2013).

Types of microRNAs and their role in suppressing target genes during live and abiotic stresses in barley, wheat, soybean, cucumber, alfalfa, olive, rice have been reported (Ozhuner et al., 2013). In this study, we tried to identify new microRNAs and their role in suppressing target genes for the first time in rapeseed. The results of this study showed that among the newly identified microRNAs, miR5021 and miR9410 families play an important role in suppressing NST1 and HST target genes, respectively, especially during stress in canola.. Therefore, identifying the molecular mechanism of these microRNAs and their target genes can help us in selecting drought and heat resistant varieties for rapeseed. A study of microRNAs for boron stress tolerance in leaves and roots of barley showed that of the four new microRNAs identified, miR408 was more involved in regulating cell signaling in leaves than the other three microRNAs (Ozhuner et al., 2013). Also, no response has been reported in hybrid and maize inbred lines for miR172 under drought and salt stress conditions (Kong et al., 2010). Therefore, understanding the cellular regulation mechanism for new microRNAs, including how to regulate the activity pathway of antioxidant enzymes such as superoxide dismutase in organs such as leaves, roots and shoots of canola, requires further investigation.

MicroRNAs can be used as a new molecular tool alongside existing classical breeding methods to improve the genetic status of plants to promote tolerance to a variety of biotic and abiotic stresses in plant breeding.

MicroRNAs are main groups of small, non-coding molecules that regulate gene expression in animals and plants. Ajwain (Trachyspermum ammi) is plants known for their medicinal properties. To date, no miRNAs have beenidentified in T. ammi. Therefore, in the present study, a computational approach based on homology search through Blastx algorithm against mirbase database was used to predict miRNA and their target genes. The parameters of GC percentage, minimum folding free energy, minimum folding free energy index and secondary structure were determined and the sequences of miRNA precursor candidate were identified. In order to investigate the expression of selected genes using Real time PCR, an experiment was performed in a completely randomized design on the ajwain Arak ecotype at three levels of 0, 12 and 24 hours after methyl jasmonate application. A total of nine miRNAs including miR156, miR160, miR166, miR168, miR171, miR172, miR396, miR477 and miR827 were identified. It was estimated that they regulate 931 of T. ammi genes, which belong to several gene families with different biological functions. Jasmonate and its derivatives are plant signaling molecules. Therefore, miR160 and miR166 expression was evaluated by Real time PCR technique. The results showed that pri-miR160 and pri-miR166 was up-regulated in response to methyl jasmonate treatment, that indicated pri-miR160 and pri-miR166 were associated with hormone transfer.

Various mutations in factor VIII locus are led to an X-linked bleeding disorder in hemophilia A. One of the leading causes of inefficient remedy for hemophilia A disease is the lack of specific and sensitive procedure for punctual diagnosis of the disease. miRNAs indicate that they have a great potential as diagnostic and prognostic biomarkers due to their stability in body fluids and their capability to identification. Furthermore, a relationship between alteration in expression levels of miRNAs and onset and progression of the hemophilia A disease has been reported.Prediction of new miRNAs and nomination as regulators of FVIII gene has been considered as the objective of this study. The ability to express new miRNAs in FVIII locus was studied via reliable bioinformatic databases such as SSCprofiler, RNAfold, miREval, FOMmiR, MaturBayes, miRFIND, UCSC genome browser, Deep Sequencing, and miRBase. Output data of previously mentioned databases were analyzed, and one stem-loop structure was qualified, and the region is predicted to express new miRNA. The presented stem-loop structure can be used as biomarker in diagnosis of the disease and regulation of factor VIII gene after subsequent experimental verification.

Cardiovascular diseases (CVDs) are globally the number 1 cause of death. Despite improvement in treatment strategies, heart disorders are strongly increasing. Therefore, identification of new regulatory factors involved in the cardiac differentiation is very important. TRKC receptor, part of the large family of receptor tyrosine kinases, is involved in development of the heart and central nervous system. There are many contradictory functions related to the TRKC gene which might be attributed to the non-coding RNAs located in it. Recently, a novel miRNA, hsa-miR-11181-5p located in TRKC gene, has been reported which is involved in nervous differentiation. MiRNAs are small non-coding RNAs regulating their target genes via mRNA degradation or protein inhibition. The goal of the present study was to investigate the expression pattern of hsa-miR-11181-5p during the course of cardiosphere-derived cells (CDCs) differentiation.

MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation and response to stresses in plants. Coriander or Coriandrum sativum L. is a plant of Apiaceae family with different nutritional and pharmaceutical applications. Up to now, the genome of this plant has not been sequenced and there is no report of miRNAs identification has been recorded for it. The present study was performed to identify the conserved miRNAs and their target genes in transcriptome of coriander plant. Firstly, Transcriptome of seed and leaf tissues was assembled and non-coding transcripts were identified and considered as miRNA precursor. Finally, among candidate sequences, three miRNAs named csa-miR162, csa-miR169 and csa-miR399 belong to three conserved families were identified after strict filtering. Identified miRNAs showed differential expression between seed and leaf tissues and also role of their target genes in different biological processes was confirmed. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of coriander plant in the present study, these miRNAs can be used as candidate genes to improve qualitative and quantitative yield and resistance to different stresses in this plant.

MicroRNAs (miRNAs) are endogenous, noncoding, small RNA molecules consisting of 18-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. Also, this group of RNAs play a crucial role in development of plant, biological processes, cell proliferation and stress response. To date, no miRNAs have been identified in the lentil species although there are several reports on miRNAs in other legume species. Therefore, in this study, in order to identify and analysis of potential miRNAs and their target genes in lentil, total RNA from leaf tissue was extracted using with TRIzol method and was sequenced. Non-protein coding unigenes were identified and considered for candidates of miRNA precursor. Finally five miRNAs belonging to 5 highly conserved families were identified following a range of strict filtering criteria, designated as, lcu-miR156, lcu-miR166, lcu-miR167, lcu-miR171 and lcu-miR391. In addition, we predicted target mRNA genes form complementary base pair in seed region of miRNAs. Totally, due to the regulatory role of the identified miRNA on changing the range of downstream genes in the gene networks, it may be possible to use the identified microRNA as candidate genes in breeding programs aimed at improving the quality and quantity of lentil.

Reduction in crops yield due to global warming threatens food security. Response of plants to heat stress is a complex prosses. MicroRNAs play an essential role in heat stress response regulatory network with post-translational modification of transcript, specially transcription factors. Lentil is one of the most important legumes cultivated in Iran. The role of microRNAs, in response to biotic and abiotic stresses in lentil plant, has not been studied so far. In this study, in order to identify conserved miRNAs and their target genes in lentil under heat stress, the total RNA was extracted using Trizol reagent and the RNA samples were sequenced. Then, transcripts which did not code any protein were examined to identification of miRNA precursors. Finally, seven miRNAs were identified which belonged to six conserved miRNA families including miR408, miR172, miR169, miR167, miR166 and miR156 that miR408, miR169 and miR166 were downregulated and miR156 was upregulated in response to heat stress. Study of these miRNAs targets showed that, most of these miRNAs involved in regulation of heat stress-responsive transcription factors including of HSF, NF-Y subunits, ARR-B, WRKY, MYB, AP2 and C3H. This result can help to better understanding of gene expression regulatory network in response to heat stress.

Gall oak (Quercus infectoria) is one of the extraordinary tree species with functional medicinal properties within the oak family. Various studies have confirmed the presence of numerous secondary metabolites with therapeutic properties in this plant. Despite the significance of gall oak, its genetic structure remains elusive. Therefore, unraveling the genetic structure of gall ok may provide valuable insights into its potential applications across diverse industries. MicroRNAs emerge as pivotal genetic elements implicated in the biosynthesis of crucial metabolites across a wide range of different plant species. Despite the significant role of miRNAs in plants, as of yet, no miRNAs have been reported in Q. infectoria.. Therefore, in the present study, after assembling the transcriptome of Q. infectoria, the conserved microRNAs were identified.  Leaf and root samples of Q. infectoria were collected from trees in the Shineh region, and 2-year-old seedlings were grown from mature oaks in Khorramabad (Lorestan Province, Iran). Total RNA was extracted from roots and leaves using the Djami-Tchatchou method. After sequencing by the Illumina HiSeq 2500 platform and checking the quality of all the generated reads, the adapter sequences were removed, and the high-quality reads were assembled using Trinity package. To identify miRNAs and their target genes, all plant miRNAs sequences were downloaded from the miRbase database. The BLASTn algorithm was employed to identify the highest similarity between unigenes and mature plant miRNAs. Furthermore, BLASTx was used to search against the non-redundant proteins (NR) database to remove protein-coding unigenes. The investigation of miRNA second-structure prediction involved assessing the similarity between potential unigenes and mature miRNA sequences using the mfold web tool. Identification of miRNA target genes and gene ontology (GO) was performed using the psRNAtarget web-tool and OmicsBox software, respectively. Following a range of strict filtering criteria, four miRNAs belonging to conserved miRNAs families were identified, including qin-miR156, qin-miR399, qin-miR160, and qin-miR172. KEGG pathway analysis showed the target genes were involved in the citrate cycle pathway. Examining miRNA target genes in Q. infectoria and analyzing their interaction network, finally led to the identification of three hub genes. Identified miRNA target genes were associated with the biosynthesis of various enzyme groups, suggesting that most of miRNAs regulating hydrolases, transferases, and oxidoreductases. Given the role of microRNAs in regulating transcription factors and their impact on genes involved in secondary metabolite biosynthesis, future breeding programs in Q. infectoria may benefit from the potential of such regulatory elements as a guide and key.

Multiple Sclerosis (MS) is a neurodegenerative disease in the central nervous system with an unknown etiology. The prevalence of MS increased worldwide including Iran. The association of rs243324 SNP of SOCS1 gene with MS was evaluated by Vandenbroeck. Also many studies evaluated the role of miRNAs in the pathogenesis of MS. Since miRNAs are small functional units، single base changes in the precursor elements، the mature miRNA sequence and their target gene sequences may drive alteration in their biological function. In this study، the sequence of rs243324 SNP obtained from NCBI database. The analysis of the sequence of SNP in the presence and absence of the risk allele evaluated via miRBase algorithm. Our results revealed that، the sequence of rs243324 SNP is homologous with the sequence of some miRNAs including: hsamiR- 4732-5p، hsa-miR-3976، hsa-miR-4727-3p and hsa-miR- 4793-5p and can change their binding sites and this homology affected by alternation of C to T allele of SNP miRNAs regulate the gene expression at the posttranscriptional level by repression or degradation of their mRNA targets. rs243324 SNP can change the binding sites of some miRNAs and may be effective in the pathogenesis of MS through the change of SOCS1 expression. After demonstration in expression level، SOCS1 can be proposed as a new potential therapeutic target for MS.

Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection.. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew.. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing.. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction.. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research..