Regulatory Mechanisms Of miRNAs Research Articles

Expression and Function of MicroRNAs in Enamel Development.

MicroRNAs (miRNAs) are short (~21nt), noncoding, and single-stranded RNAs that can negatively regulate gene expression by binding to 3'UTRs of target mRNAs sequence-specifically to affect their translation and/or stability. MiRNAs are involved in multiple developmental events in various tissues and organs. Such events include dental enamel development. This review focuses on the expression and functions of miRNAs regulated in enamel development. This study further discusses the possible participation of signaling pathways affected by miRNAs during stem cell proliferation or renewal, cell differentiation, and cusp patterning formation. Research on the enamel developmental process and miRNA regulation mechanisms can facilitate better understanding of clinical enamel malformation and provide potential therapeutic schemes.

Requirement of MIR165A primary transcript sequence for its activity pattern in Arabidopsis leaf primordia

miRNAs might move cell to cell and act as mobile signals in plant development, while the regulatory mechanisms of miRNA cell-to-cell movement are still unclear. Recently, in Arabidopsis leaf primordia, we revealed that miR165 from the MIR165A gene, which is expressed in the abaxial epidermal cells of leaf primordia, acts non-cell-autonomously in inner cells on the abaxial side. We proposed that not only mature miR165 sequence but also the MIR165A primary transcript sequence are required for the confinement of miR165 activity to the abaxial side of leaf primordia. The deletion analysis of the MIR165A genomic fragment showed that with a lack of the 3' region of MIR165A its activity is not confined in leaf primordia, suggesting that the full-length primary transcript of MIR165A is important for the regulatory mechanism of miRNA activity confinement in leaf primordia. It has been reported that the MIR165A transcript is predicted to be translated into the short poly peptide, proposing that the MIR165A transcript may be exported to the cytoplasm. Considering these matters, we propose a hypothesis for the confinement of miR165 activity to the abaxial side in leaf primordia dependent on the MIR165A primary transcript.

Abstract 49: Mir-21 Contributes to Cardiac Aging by Targeting Pten

Background— Aging is among predominant risk factors for cardiovascular diseases and it also contributes to a significantly worse outcome in patients with acute myocardial infarction. MicroRNAs (miRNAs, miRs) have been indicated in aging. However, the regulatory mechanisms of miRNAs which govern the aging progress are poorly understood. Objective— To identify miRNAs responsible for cardiac aging besides miR-34 family members. Methods and Results— miRNA arrays were used to determine the dysregulated miRNAs in cardiac aging using cardiac ventricles from mice at 8 weeks and 15months of age. Besides miR-34 family members, miR-21 was also found to be elevated 3-fold in ventricles from mice aged 15 months compared to mice aged 8 weeks. Over-expression of miR-21 in the neonatal rat cardiomyocytes (NRCM) shortened the telomere length, attenuated and strengthened the activity of telomerase and senescence-related beta[[Unable to Display Character: –]]galactosidase, respectively, which was similar to the aging caused by doxorubicin (DOX). Using the quantitative PCRs and Western blotting, phosphatase and tensin homologue (PTEN) gene was found to be negatively regulated by miR-21 in NRCM. Moreover, knockdown of PTEN using siRNA mimics the effects of miR-21 in pro-aging in NRCM. Interestingly, knockdown of miR-21, as well as up-regulation of PTEN, repressed NRCM aging induced by DOX. Conclusions— These findings suggest that ectopic up- or down-modulation of miR-21 may be an important regulatory mechanism governing cardiac aging by targeting PTEN. Inhibition of miR-21 represent a novel therapy for cardiac aging.

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

MicroRNAs (miRNAs) are small non-coding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Increasing evidence also supports that plant miRNAs contribute to immune responses to pathogens. Here, we used deep sequencing of small RNA libraries for global identification of rice miRNAs that are regulated by fungal elicitors. We also describe 9 previously uncharacterized miRNAs in rice. Combined small RNA and degradome analyses revealed regulatory networks enriched in elicitor-regulated miRNAs supported by the identification of their corresponding target genes. Specifically, we identified an important number of miRNA/target gene pairs involved in small RNA pathways, including miRNA, heterochromatic and trans-acting siRNA pathways. We present evidence for miRNA/target gene pairs implicated in hormone signaling and cross-talk among hormone pathways having great potential in regulating rice immunity. Furthermore, we describe miRNA-mediated regulation of Conserved-Peptide upstream Open Reading Frame (CPuORF)-containing genes in rice, which suggests the existence of a novel regulatory network that integrates miRNA and CPuORF functions in plants. The knowledge gained in this study will help in understanding the underlying regulatory mechanisms of miRNAs in rice immunity and develop appropriate strategies for rice protection.

Detection of miR-33 Expression and the Verification of Its Target Genes in the Fatty Liver of Geese.

Background: miRNAs are single-stranded, small RNA molecules with a length of 18–25 nucleotides. They bind to the 3′ untranslated regions of mRNA transcripts to reduce the translation of these transcripts or to cause their degradation. The roles of these molecules differ in biological processes, such as cell differentiation, proliferation, apoptosis and tumor genesis. miRNA-33 is encoded by the gene introns of proteins that bind sterol-regulatory elements. This molecule cooperates with these proteins to control cholesterol homeostasis, fatty acid levels and the genes that are related to the expression of fat metabolism. The examination of miR-33 expression and its target genes can promote the in-depth study of the miRNA regulation mechanism in the formation process of goose fatty liver and can lay a foundation for research into human fatty liver. Methodology/principal findings: (1) Through real-time fluorescent quantitative polymerase chain reaction (TaqMan MicroRNA Assay), we detected the expression of miR-33 during the feeding of Landes geese. The expression level of miR-33 increases significantly in the liver after 19 days in comparison with the control group; (2) By using the bioinformatics software programs TargetScan, miRDB and miRCosm to predict the target genes of miR-33 according to laboratory prophase transcriptome results and references, we screen nine target genes: adenosine triphosphate binding cassette transporters A1, adenosine triphosphate binding cassette transporters G1, Neimann Pick C, carnitine O-octanoyltransferase (CROT), cyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, beta subunit (HADHB), AMP-activated protein kinase, alpha subunit 1 (AMPKα1), insulin receptor substrate 2, glutamic pyruvate transaminase and adipose differentiation-related protein. The dual luciferase reporter gene system in the CHO cell line verifies that CROT, HADHB and NPC1 are the target genes of miR-33 in geese. The inhibition rate of CROT is highest and reaches 70%; (3) The seed sequence (5′ 2–8 bases) is the acting site of miR-33. The two predicted target sites of CROT are the target sites of miR-33. Moreover, the predicted target site of HADHB and NPC1 is the target site of miR-33. Conclusions/significance: (1) After 19 days of overfeeding, the expression level of miR-33 increases significantly in the livers of geese; (2) CROT, HADHB and NPC1 are the target genes of miR-33 in geese. These genes determine the combined target site.

Identification of miRNAs and Their Target Genes Associated with Sweet Corn Seed Vigor by Combined Small RNA and Degradome Sequencing.

High seed vigor is significant for agriculture. Low seed vigor of sweet corn hindered the popularization of sweet corn (Zea mays L. saccharata Sturt). To better understand the involvement and regulatory mechanism of miRNAs with seed vigor, small RNA libraries from seeds non-artificially aged and artificially aged for 2 days were generated by small RNA sequencing. A total of 27 differentially expressed miRNAs were discovered, of which 10 were further confirmed by real-time quantitative polymerase chain reaction. Furthermore, targets of miRNAs were identified by degradome sequencing. A total of 1142 targets that were potentially cleaved by 131 miRNAs were identified. Gene ontology (GO) annotations of target transcripts indicated that 26 target genes cleaved by 9 differentially expressed miRNAs might play roles in the regulation of seed vigor, such as peroxidase superfamily protein targeted by PC-5p-213179_17 playing a role in the oxidation-reduction process and response to oxidative stress. These findings provide valuable information to understand the involvement of miRNAs with seed vigor.

The miRNA Transcriptome Directly Reflects the Physiological and Biochemical Differences between Red, White, and Intermediate Muscle Fiber Types.

MicroRNAs (miRNAs) are small non-coding RNAs that can regulate their target genes at the post-transcriptional level. Skeletal muscle comprises different fiber types that can be broadly classified as red, intermediate, and white. Recently, a set of miRNAs was found expressed in a fiber type-specific manner in red and white fiber types. However, an in-depth analysis of the miRNA transcriptome differences between all three fiber types has not been undertaken. Herein, we collected 15 porcine skeletal muscles from different anatomical locations, which were then clearly divided into red, white, and intermediate fiber type based on the ratios of myosin heavy chain isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e., red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. Furthermore, we constructed small RNA libraries for PL, PMM, and LDM using a deep sequencing approach. Results showed that the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism that achieves the phenotypic diversity of skeletal muscles.

MicroRNA Transcriptome Profile Analysis in Porcine Muscle and the Effect of miR-143 on the MYH7 Gene and Protein.

Porcine skeletal muscle fibres are classified based on their different physiological and biochemical properties. Muscle fibre phenotype is regulated by several independent signalling pathways, including the mitogen-activated protein kinase (MAPK), nuclear factor of activated T cells (NFAT), myocyte enhancer factor 2 (MEF2) and peroxisome proliferator-activated receptor (PPAR) signalling pathways. MicroRNAs are non-coding small RNAs that regulate many biological processes. However, their function in muscle fibre type regulation remains unclear. The aim of our study was to identify miRNAs that regulate muscle fibre type during porcine growth to help understand the miRNA regulation mechanism of fibre differentiation. We performed Solexa/Illumina deep sequencing for the microRNAome during 3 muscle growth stages (63, 98 and 161 d). In this study, 271 mature miRNAs and 243 pre-miRNAs were identified. We detected 472 novel miRNAs in the muscle samples. Among the mature miRNAs, there are 23 highest expression miRNAs (over 10000 RPM), account for 85.3% of the total counts of mature miRNAs., including 10 (43.5%) muscle-related miRNAs (ssc-miR-133a-3p, ssc-miR-486, ssc-miR-1, ssc-miR-143-3p, ssc-miR-30a-5p, ssc-miR-181a, ssc-miR-148a-3p, ssc-miR-92a, ssc-miR-21, ssc-miR-126-5p). Particularly, both ssc-miR-1 and ssc-miR-133 belong to the MyomiRs, which control muscle myosin content, myofibre identity and muscle performance. The involvement of these miRNAs in muscle fibre phenotype provides new insight into the mechanism of muscle fibre regulation underlying muscle development. Furthermore, we performed cell transfection experiment. Overexpression/inhibition of ssc-miR-143-3p in porcine skeletal muscle satellite cell induced an/a increase/reduction of the slow muscle fibre gene and protein (MYH7), indicating that miR-143 activity regulated muscle fibre differentiate in skeletal muscle. And it regulate MYH7 through the HDAC4-MEF2 pathway.

Polycomb repressive complex 2 regulates MiR-200b in retinal endothelial cells: potential relevance in diabetic retinopathy.

Glucose-induced augmented vascular endothelial growth factor (VEGF) production is a key event in diabetic retinopathy. We have previously demonstrated that downregulation of miR-200b increases VEGF, mediating structural and functional changes in the retina in diabetes. However, mechanisms regulating miR-200b in diabetes are not known. Histone methyltransferase complex, Polycomb Repressive Complex 2 (PRC2), has been shown to repress miRNAs in neoplastic process. We hypothesized that, in diabetes, PRC2 represses miR-200b through its histone H3 lysine-27 trimethylation mark. We show that human retinal microvascular endothelial cells exposed to high levels of glucose regulate miR-200b repression through histone methylation and that inhibition of PRC2 increases miR-200b while reducing VEGF. Furthermore, retinal tissue from animal models of diabetes showed increased expression of major PRC2 components, demonstrating in vivo relevance. This research established a repressive relationship between PRC2 and miR-200b, providing evidence of a novel mechanism of miRNA regulation through histone methylation.

A new method for discovering disease-specific MiRNA-target regulatory networks.

Genes and their expression regulation are among the key factors in the comprehension of the genesis and development of complex diseases. In this context, microRNAs (miRNAs) are post-transcriptional regulators that play an important role in gene expression since they are frequently deregulated in pathologies like cardiovascular disease and cancer. In vitro validation of miRNA - targets regulation is often too expensive and time consuming to be carried out for every possible alternative. As a result, a tool able to provide some criteria to prioritize trials is becoming a pressing need. Moreover, before planning in vitro experiments, the scientist needs to evaluate the miRNA-target genes interaction network. In this paper we describe the miRable method whose purpose is to identify new potentially relevant genes and their interaction networks associate to a specific pathology. To achieve this goal miRable follows a system biology approach integrating together general-purpose medical knowledge (literature, Protein-Protein Interaction networks, prediction tools) and pathology specific data (gene expression data). A case study on Prostate Cancer has shown that miRable is able to: 1) find new potential miRNA-targets pairs, 2) highlight novel genes potentially involved in a disease but never or little studied before, 3) reconstruct all possible regulatory subnetworks starting from the literature to expand the knowledge on the regulation of miRNA regulatory mechanisms.

MicroRNAs in tumor stem cells

Abstract MicroRNAs (miRNAs) are a class of non-coding RNAs that are believed to have a significant role in tumorigenesis and cancer metastasis. Cancer stem cells play a major role in tumor recurrence, metastasis, and drug resistance. Research has shown that miRNAs can promote or inhibit the stemness of cancer stem cells and regulate the differentiation and self-renewal of cancer stem cells. In this article, the phenotype and regulatory mechanisms of miRNAs in cancer stem cells will be described, together with an explanation of their potential role in tumor diagnosis and treatment.

Dietary walnut suppression of colorectal cancer in mice: Mediation by miRNA patterns and fatty acid incorporation

Colorectal cancer, unlike many other malignancies, may be preventable. Recent studies have demonstrated an inverse association between nut consumption and incidence of colon cancer; however, the underlying mechanisms are not fully understood. An emerging concept suggests that microribonucleic acids (miRNAs) may help explain the relationship between walnut consumption and decreased colorectal neoplasia risk.Seven days after HT-29 colon cancer cell injection, mice were randomized to either control or walnut diets for 25days of diet treatment. Thirty samples of tumor and of omental adipose were analyzed to determine changes in lipid composition in each dietary group. In the tumors of the walnut-containing diet, we found significant increases in α-linolenic, eicosapentaenoic, docosahexaenoic and total omega-3 acids, and a decrease in arachidonic acid, as compared to the control diet. Final tumor size measured at sacrifice was negatively associated with percentage of total omega-3 fatty acid composition (r=−0.641, P=.001). MicroRNA expression analysis of colorectal tumor tissue revealed decreased expression of miRNAs 1903, 467c and 3068 (P<.05) and increased expression of miRNA 297a* (P=.0059) in the walnut-treated group as compared to control diet.Our results indicate that changes in the miRNA expression profiles likely affect target gene transcripts involved in pathways of anti-inflammation, antivascularization, antiproliferation and apoptosis. We also demonstrate the incorporation of protective fatty acids into colonic epithelium of walnut-fed mice, which may independently alter miRNA expression profiles itself. Future studies of the mechanism of widespread miRNA regulation by walnut consumption are needed to offer potential prognostic and therapeutic targets.

The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection.

Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases.

Promiscuous Gene Expression in the Thymus: A Matter of Epigenetics, miRNA, and More?

The induction of central tolerance in the course of T cell development crucially depends on promiscuous gene expression (pGE) in medullary thymic epithelial cells (mTECs). mTECs express a genome-wide variety of tissue-restricted antigens (TRAs), preventing the escape of autoreactive T cells to the periphery, and the development of severe autoimmunity. Most of our knowledge of how pGE is controlled comes from studies on the autoimmune regulator (Aire). Aire activates the expression of a large subset of TRAs by interacting with the general transcriptional machinery and promoting transcript elongation. However, further factors regulating Aire-independent TRAs must be at play. Recent studies demonstrated that pGE in general and the function of Aire in particular are controlled by epigenetic and post-transcriptional mechanisms. This mini-review summarizes current knowledge of the regulation of pGE by miRNA and epigenetic regulatory mechanisms such as DNA methylation, histone modifications, and chromosomal topology.

Expression profiling analysis of the microRNA response of Cynoglossus semilaevis to Vibrio anguillarum and other stimuli.

To investigate the roles of microRNAs (miRNA) of Cynoglossus semilaevis in response to Vibrio anguillarum that were previously identified using high-throughput sequencing, microarray analyses was performed on three small RNA libraries (CG, NOSG, and HOSG) prepared from C. semilaevis immune tissues. In total, of 1279 designed probes, 739 (57.78 %) were detectable. The expression levels of these miRNAs were analyzed using pairwise comparisons among the three libraries, and a total of 99 miRNAs were observed to be significantly differentially expressed. The expression patterns of 10 differentially expressed miRNAs were validated by real-time quantitative PCR (RT-qPCR). In addition, expression of miR-142-5p, miR-223, and miR-181a in response to V. anguillarum at numerous time-points in four tissues, as well as the responses to lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly I:C), peptidoglycan (PGN), and red-spotted grouper nervous necrosis virus (RGNNV) in head kidney cells, were studied by qRT-PCR. Taken together, all of the expression profiles showed significant differences compared to the control group; both similarities and differences in the expression responses to the same pathogen were observed. Collectively, these findings highlighted the putative roles for miRNAs in the context of the innate immune response of C. semilaevis exposing to pathogens and that further studies are needed to understand the molecular mechanisms of miRNA regulation in C. semilaevis host-pathogen interactions.

Integrative analysis of differentially expressed microRNAs of pulmonary alveolar macrophages from piglets during H1N1 swine influenza A virus infection.

H1N1 swine influenza A virus (H1N1 SwIV) is one key subtype of influenza viruses with pandemic potential. MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression. MiRNAs relevant with H1N1 SwIV have rarely been reported. To understand the biological functions of miRNAs during H1N1 SwIV infection, this study profiled differentially expressed (DE) miRNAs in pulmonary alveolar macrophages from piglets during the H1N1 SwIV infection using a deep sequencing approach, which was validated by quantitative real-time PCR. Compared to control group, 70 and 16 DE miRNAs were respectively identified on post-infection day (PID) 4 and PID 7. 56 DE miRNAs were identified between PID 4 and PID 7. Our results suggest that most host miRNAs are down-regulated to defend the H1N1 SwIV infection during the acute phase of swine influenza whereas their expression levels gradually return to normal during the recovery phase to avoid the occurrence of too severe porcine lung damage. In addition, targets of DE miRNAs were also obtained, for which bioinformatics analyses were performed. Our results would be useful for investigating the functions and regulatory mechanisms of miRNAs in human influenza because pig serves as an excellent animal model to study the pathogenesis of human influenza.

The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA–mRNA interaction network

BackgroundDNA damage transactivates tumour protein p53 (TP53)-regulated surveillance, crucial in suppressing tumorigenesis. TP53 mediates this process directly by transcriptionally modulating gene and microRNA (miRNA) expression and indirectly by regulating miRNA biogenesis. However, the role of TP53 in regulating miRNA-AGO2 loading and global changes in AGO2 binding to its gene targets in response to DNA damage are unknown. These processes might be novel mechanisms by which TP53 regulates miRNAs in response to DNA damage. MethodsTo show the network of miRNA–mRNA interactions that occur in response to DNA damage, we stimulated TP53 wild-type and null cell-lines with doxorubicin and performed RNA sequencing from total RNA (RNA-Seq) and AGO2-immunoprecipitated RNA (AGO2-RIP-Seq). We used a combined AGO2 RIP-seq and AGO2 PAR-CLIP-seq (photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation) approach to determine the exact sites of interaction between the AGO2-bound miRNAs and their mRNA targets. FindingsTP53 directly associated with AGO2, and induced and reduced loading of a subset of miRNAs, including the lethal 7 (let-7) miRNA family members, onto AGO2 in response to DNA damage. Although mutated TP53 maintained its capacity to interact with AGO2, it mediated unloading instead of loading of let-7 family miRNAs, thereby reducing their activity. We determined the miRNA–mRNA interaction networks involved in the response to DNA damage both in the presence and absence of TP53. Furthermore, we showed that miRNAs whose cellular abundance or differential loading onto AGO2 was regulated by TP53 were involved in an intricate network of regulatory feedback and feedforward circuits that fine-tuned gene expression levels in response to DNA damage to permit the repair of DNA damage or initiation of programmed cell death. InterpretationControl of AGO2 loading by TP53 is a new mechanism of miRNA regulation in carcinogenesis. FundingUK Medical Research Council, Action Against Cancer.

MicroRNAs: New players in cancer prevention targeting Nrf2, oxidative stress and inflammatory pathways.

miRNAs are endogenous small non-coding RNAs of 20-22 nucleotides that repress gene expression at the post-transcriptional level. There is growing interest in the role of miRNAs in cancer chemoprevention, and several naturally occurring chemopreventive agents have been found to be modulators of miRNA expression both in vitro and in vivo. Moreover, these chemopreventive phytochemicals commonly possess anti-oxidative and/or anti-inflammatory properties, and Nrf2 has been extensively studied as a molecular target in cancer prevention. The crosstalk between miRNAs and the traditional cellular signaling pathways of chemoprevention remain to be fully elucidated. This review summarizes the data regarding the potential interactions between miRNAs and anti-oxidative and anti-inflammatory pathways. Cellular redox homeostasis can affect the biogenesis and processing of miRNAs, which in turn regulate the Nrf2 pathway of detoxifying/anti-oxidative genes. We also discuss the miRNA regulatory mechanisms in relation to inflammation-related cancer signaling pathways.

MicroRNAs: emerging novel targets of cancer therapies.

MicroRNAs (miRNAs) are a large family of small noncoding RNAs (~22 nucleotide long) that negatively regulate protein-coding gene expression posttranscriptionally by interacting with messenger RNAs (mRNAs), causing either their degradation or translation inhibition. While miRNAs were first discovered as important regulators of developmental timing, subsequent studies have shown that their deregulations are critically involved in various diseases, including cancer. This is evident from the crucial roles they play in regulating a wide range of cellular processes such as cell survival, apoptosis, cell cycle progression and proliferation, cell-cell interaction, differentiation, and motility. It has been found that miRNA expression levels are altered in all types of cancer and they play important roles in almost all aspects of cancer pathogenesis such as initiation, promotion, metastasis, and responses to drug treatment. These recognitions and other accumulating evidences clearly suggest that miRNAs can serve as novel targets for cancer therapies. Indeed, targeting abnormally-expressed miRNAs has been shown to have great potential in suppressing primary tumor growth, reducing tumor metastasis, and overcoming anticancer drug resistance. It is anticipated that miRNAs can be valuable cancer-specific targets and novel miRNA-based targeted therapies can be formulated to provide effective treatments for cancer. The purpose of this special issue is to provide readers with an overview of research findings on the roles of miRNAs in cancer development, progression, diagnosis and treatment, and how miRNA expression may be regulated. This issue will also update the readers about the challenges and possibilities of miRNAs to emerge as future cancer therapeutics. A. L. Oom et al. first briefly review the potential value of miRNAs as cancer diagnostic markers, which is followed by the detailed discussion on the potential role of miRNAs in cancer therapy. The authors review literatures reporting the role of miRNAs in sensitizing of or mediating resistance to traditional and targeted cancer therapies. A nice summary about studies on miRNAs in combination with traditional cancer therapies is provided in a table. The authors also discuss the current studies on miRNA delivery systems. This review ends with discussion on challenges and perspectives of developing miRNAs as effective cancer therapies. The review paper, authored by K. Otsuka and T. Ochiya, discusses the role of miRNAs in tumor development by uniquely focusing on the interplay between the classic tumor suppressor p53 and the emerging tumor regulatory miRNAs. The authors review recent findings showing both the regulation of expression of various miRNAs by p53 and the direct targeting of p53 by miRNAs. Particularly, this review summarizes up to date research findings about the critical roles of various miRNAs in regulation of cell cycle and apoptosis in the p53 pathways. Y. Fujita, K. Kuwano, T. Ochiya, and F. Takeshita provide an in-depth review of current findings showing the potential of circulating miRNAs as diagnostic biomarkers for lung cancer. This review discusses the general mechanism of miRNA release into extracellular spaces and the impact of extracellular vesicle-encapsulated circulating miRNAs on cancer progression. Moreover, this review also summarizes current studies in detail showing the potential of miRNAs as circulating biomarkers in cancer diagnosis, particularly for lung cancer. N. H. Phuah and N. H. Nagoor review the regulation of miRNAs by natural compounds. Recent studies have shown that natural agents such as curcumin, resveratrol, genistein, epigallocatechin-3-gallate, indole-3-carbinol, and 3,3′-diindolylmethane exert their antiproliferative and/or proapoptotic effects through the regulation of one or more miRNAs. This review summarizes current research findings about the regulation of miRNAs by above natural compounds. The review also discusses the potential of integrating natural agents with conventional chemotherapeutic drugs, thus, enhancing their efficacy. The review article by S. K. Srivastava, S. Arora, C. Averett, S. Singh, and A. P. Singh discusses the effect of naturally occurring phytochemicals on miRNA expression. Particularly, the authors focus on the underlying molecular mechanisms of miRNA regulation by phytochemicals and their functional significance in cancer development and progression. Moreover, the translational potential of the relevant research findings is also discussed. In closing, the guest editors of this special issue would like to thank all the reviewers for their timely and excellent review and journal management team for efficient processing of papers from submission through publication. Chengfeng Yang Yiguo Jiang Ajay P. Singh Fumitaka Takeshita

Prediction and functional analysis of lincRNAs targeted by miRNAs.

Long intergenic non-coding RNAs (lincRNAs) located between protein-coding genes are non-coding RNAs longer than 200 nucleotides in length. LincRNAs are involved in a variety of biological processes such as cell cycle regulation, immune surveillance and embryonic stem cells differentiation in animals; however, the function of lincRNAs in plants is largely unclear. MicroRNAs (miRNAs) are a class of endogenous, single-stranded, non-coding small (~21 nt) RNAs, which can regulate gene expression at transcriptional or post-transcriptional level in eukaryotes by means of sequence complementation. Now, intensive studies on protein-coding genes targeted by miRNAs have been carried out, but the research on non-coding RNAs targeted by miRNAs is seldom explored, especially in plants. In order to uncover the potential function of lincRNAs, the data including miRNAs, cDNAs and degradomes were firstly collected and integrated, followed by bioinformatics methods to predict the potential binding sites of 337 mature miRNAs at 2708 lincRNAs in Arabidopsis thaliana. The regulatory networks of miRNAs-mRNAs-lincRNAs were constructed and the function of lincRNAs was predicted according to the competing endogenous RNA (ceRNA) hypothesis. This study may lay a solid foundation for elucidating the regulatory mechanism of miRNAs on lincRNAs as well as the function of lincRNAs in plants.