A 360° view of circular RNAs: From biogenesis to functions

Size matters: conserved proteins function in length-dependent nuclear export of circular RNAs

This Outlook by Wan and Hopper discusses the study on circular RNAs (circRNAs) in this issue of Genes & Development by Huang et al. There, they show that nuclear export of circRNAs is length-dependent, and the length measurement mechanism is shown to be controlled by the four-amino-acid motifs in Hel25E and its homologs.

Circular RNAs (circRNAs) comprise a recently appreciated category of RNAs that are in high abundance and serve important biological functions. Although several discoveries have been made regarding the biogenesis and functions of circRNAs, their subcellular trafficking has remained largely unknown. In this issue of Genes & Development, Huang and colleagues (pp. 639–644) reported the first study of the nuclear export of circRNAs. Drosophila Hel25E and its human homologs, UAP56 and URH49, are required for nuclear export of circRNAs. Nuclear export of circRNAs is surprisingly length-dependent, and the length measurement mechanism was shown to be controlled by motifs in Hel25E and its homologs consisting of four amino acids.

Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control

Pepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy fruit ripening. Drastic visual changes and internal biochemical alterations are involved in fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper fruit ripening process. To explore the regulation of bell pepper fruit ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper fruit ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of fruit ripening.

RETRACTED: A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p

This article has been retracted at the request of the authors: please see Elsevier policy on article withdrawal (https://www.elsevier.com/locate/withdrawalpolicy). The authors claim that other members of their lab attempted to repeat the experiments in this study several times and found that the activation ability of snail on circ-znf652 was significantly lower than reported, indicating that this regulation loop does not exist. The authors' incorrect experimental method and lack of reasonable control, coupled with the lack of experimental experience of the first author, led to the mistakes and mean the results cannot be relied upon. In order not to mislead other scientists, they requested to retract their manuscript. The Editor-in-Chief has approved this retraction. The authors apologise to the readership of the journal for these errors.

Characterization and Cloning of Grape Circular RNAs Identified the Cold Resistance-Related Vv-circATS1

Circular RNAs (circRNAs) are widely distributed and play essential roles in a series of developmental processes, although none have been identified or characterized in grapevines (Vitis vinifera). In this study, we characterized the function of grape circRNA and uncovered thousands of putative back-splicing sites by global transcriptome analysis. Our results indicated that several reported circRNA prediction algorithms should be used simultaneously to obtain comprehensive and reliable circRNA predictions in plants. Furthermore, the length of introns flanking grape circRNAs was closely related to exon circularization. Although the longer introns flanking grape circRNAs appeared to circularize more efficiently, a 20- to 50-nt region seemed large enough to drive grape circRNA biogenesis. In addition, the endogenous introns flanking circularized exon(s) in conjunction with reverse complementary sequences could support the accurate and efficient circularization of various exons in grape, which constitutes a new tool for exploring the functional consequences caused by circRNA expression. Finally, we identified 475 differentially expressed circRNAs in grape leaves under cold stress. Overexpression of Vv-circATS1, a circRNA derived from glycerol-3-P acyltransferase, improved cold tolerance in Arabidopsis (Arabidopsis thaliana), while the linear RNA derived from the same sequence cannot. These results indicate the functional difference between circRNA and linear RNA, and provide new insight into plant abiotic stress resistance.

Circular RNAs in gynecological disease: promising biomarkers and diagnostic targets

Circular RNAs (circRNAs) are a category of RNA molecules with covalently closed circles lacking both a 5′ cap and a 3′ tail. In recent years, circRNAs have attracted much attention and become a research hotspot of the RNA field following miRNAs and lncRNAs. CircRNAs exhibit tissue specificity, structural stability, and evolutionary conservation. Although the biological effects of circRNAs are still underestimated, many studies have shown that circRNAs have functions including regulation of transcription, translation into proteins and miRNA sponges. In this review, we briefly described the biogenesis and function of circRNAs and present circular transcripts in gynecological disease.

Intriguing circles: Conflicts and controversies in circular RNA research

Circular RNAs (circRNAs) are covalently closed RNA circles without a 5' cap or 3' tail. Since the landmark discovery of ciRS-7/CDR1as functioning as a miR-7 sponge in 2013, circRNAs have become a hot topic in RNA research. CircRNAs have been found to play active roles in cancer, cardiovascular diseases, neurological disorders, and many other diseases. They can function as microRNA (miRNA) sponges, protein scaffolds, and even translation templates. However, as circRNA research expands, many divergent views have emerged. For example, are most circRNAs competent in serving as miRNA sponges? What kinds of circRNAs are most likely to sponge miRNAs? Apart from sponging miRNAs, what could the functions of most circRNAs be? What are the features of circRNAs that are translatable? Many researchers have claimed that circRNAs are abundant, stable, conserved, and specific molecules, which hold great potential in serving as biomarkers. However, circRNA abundance is variable and some circRNAs are abundant while others are not. In addition, their stability and conservation may vary under different circumstances. Furthermore, it is unclear whether circRNA biogenesis is more likely to be regulated by RNA binding proteins or transcription factors. All of these are open questions that remain to be answered by researchers in this field. Discussing and investigating these questions will advance the understanding of this class of novel molecules and may propel inspiring new ideas for future studies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

A novel role of U1 snRNP: Splice site selection from a distance

Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.

Biogenesis and Function of Circular RNAs in Health and in Disease

Circular RNAs (circRNAs) are a class of non-coding RNA that were previously thought to be insignificant byproducts of splicing errors. However, recent advances in RNA sequencing confirmed the presence of circRNAs in multiple cell lines and across different species suggesting a functional role of this RNA species. CircRNAs arise from back-splicing events resulting in a circular RNA that is stable, specific and conserved. They can be generated from exons, exon-introns, or introns. CircRNAs have multifaceted functions. They are likely part of the competing endogenous RNA class. They can regulate gene expression by sponging microRNAs, binding proteins or they can be translated into a protein themselves. CircRNAs have been associated with health and disease, some with disease protective effects, some with disease promoting functions. The widespread expression and disease regulatory mechanisms endow circRNAs to be used as functional biomarkers and therapeutic targets for a variety of different disorders. In this concise article we provide an overview of the association of circRNAs with various diseases including cancer, cardiovascular and kidney disease as well as cellular senescence. We conclude with an assessment of the current status and future outlook of this new field of research that carries immense potential with respect to diagnostic and therapeutic approaches of a variety of diseases.

Emerging Epigenetic Regulation of Circular RNAs in Human Cancer

Circular RNAs (circRNAs) are novel members of the noncoding RNA family. Their characteristic covalent closed-loop structure endows circRNAs that are much more stable than the corresponding linear transcript. circRNAs are ubiquitous in eukaryotic cells, and their functions are diverse and include adsorbing microRNAs (miRNAs; acting as miRNA sponges), regulating transcription, interacting with RNA-binding proteins, and translating and deriving pseudogenes. Moreover, circRNAs are associated with the occurrence and progression of a variety of cancers, acting as new biomarkers for early diagnosis to evaluate curative effects and patient prognosis. Here, this paper briefly describes the characteristics and functions of circRNAs, and it further concludes the relationship between circRNAs and human cancer.

Increasing Upstream Chromatin Long-Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells

Circular RNAs (circRNAs) are non-coding RNAs that form covalently closed continuous loops, and act as gene regulators in physiological and disease conditions. To test our hypothesis that proatherogenic lipid lysophosphatidylcholine (LPC) induce a set of circRNAs in human aortic endothelial cell (HAEC) activation, we performed circRNA analysis by searching our RNA-Seq data from LPC-activated HAECs, and found: (1) LPC induces significant modulation of 77 newly characterized cirRNAs, among which 47 circRNAs (61%) are upregulated; (2) 34 (72%) out of 47 upregulated circRNAs are upregulated when the corresponding mRNAs are downregulated, suggesting that the majority of circRNAs are upregulated presumably via LPC-induced “abnormal splicing” when the canonical splicing for generation of corresponding mRNAs is suppressed; (3) Upregulation of 47 circRNAs is temporally associated with mRNAs-mediated LPC-upregulated cholesterol synthesis-SREBP2 pathway and LPC-downregulated TGF-β pathway; (4) Increase in upstream chromatin long-range interaction sites to circRNA related genes is associated with preferred circRNA generation over canonical splicing for mRNAs, suggesting that shifting chromatin long-range interaction sites from downstream to upstream may promote induction of a list of circRNAs in lysoPC-activated HAECs; (5) Six significantly changed circRNAs may have sponge functions for miRNAs; and (6) 74% significantly changed circRNAs contain open reading frames, suggesting that putative short proteins may interfere with the protein interaction-based signaling. Our findings have demonstrated for the first time that a new set of LPC-induced circRNAs may contribute to homeostasis in LPC-induced HAEC activation. These novel insights may lead to identifications of new therapeutic targets for treating metabolic cardiovascular diseases, inflammations, and cancers.

A regulatory circuit of circ-MTO1/miR-17/QKI-5 inhibits the proliferation of lung adenocarcinoma

Circular RNA (circRNA) is a new class of non-coding RNA that plays a pivotal role in carcinogenesis. Recently, circ-MTO1 (hsa_circ_0007874) was shown to be a cancer-related circRNA. However, its role in lung adenocarcinoma (LUAD) has not been reported. Here, we found that circ-MTO1 was significantly down-regulated in LUAD, which was closely associated with malignant features and dismal prognosis. Enforced expression of circ-MTO1 suppressed the growth of LUAD cells both in vitro and in vivo. Subsequent mechanism experiments showed that circ-MTO1 served as a sponge of oncogenic miR-17 to increase the expression of RNA-binding protein QKI-5, leading to the inactivation of Notch signaling pathway, thereby restraining the growth of LUAD. Importantly, increased QKI-5 expression caused by circ-MTO1 overexpression in turn promoted circ-MTO1 expression. Clinically, circ-MTO1 expression was strongly positively correlated with QKI-5 expression, but negatively correlated with miR-17 expression. Taken together, our data suggest that circ-MTO1 is a critical negative regulator of LUAD and elucidate the potential molecular mechanism of a novel circ-MTO1/miR-17/QKI-5 feedback loop in inhibiting LUAD progression.

Exo-circRNAs: a new paradigm for anticancer therapy

CircRNAs, as new members of long noncoding RNAs, have been the focus of recent investigation. CircRNAs feature a closed continuous loop structure without 5′-3′ polarity or a poly A tail. Many studies have reported the potential application of circRNAs in the clinic as new biomarkers and therapeutic targets in different diseases, especially for cancer. Additionally, the exosomes are important vehicles in cell-to-cell communication. And exo-circRNAs are circRNAs in exosomes which can be detected to provide additional evidence for conventional diagnostic methods and can be applied to suppress the malignant progress in cancer. In this review, we describe the biogenesis, characteristics, and functions of circRNAs and exosomes. Specifically, we present a comprehensive update of the promising role of exo-circRNAs in anticancer therapy.

Circular RNAs and their roles in head and neck cancers

Circular RNAs are abundant endogenous non-coding RNA with no 5′ cap and 3′ polyadenylation tail that modify liner mRNAs and have no terminal structures. Our knowledge of the biogenesis of circular RNAs has been expanded, and circular RNAs were shown to be key regulators of various diseases, especially cancers. Head and neck cancers are the sixth most popular cancers worldwide, and the overall survival rates remain unsatisfactory. Recent studies have indicated that circular RNAs are involved in the tumorigenesis, progression, invasion and chemosensitivity of head and neck cancers and that some circular RNAs could serve as diagnostic and prognostic biomarkers. In this study, we summarize research advances in the regulation of circular RNA biogenesis, their characteristics and functions, the involvement of circular RNAs in the pathophysiology of head and neck cancers and their potential clinical utilization, as well as the likely directions of future studies.

Regulatory Non-coding RNAs Network in Non-alcoholic Fatty Liver Disease

Non-alcoholic fatty liver disease (NAFLD) spectrum comprises simple steatosis and non-alcoholic steatohepatitis (NASH) that can lead to fibrosis and cirrhosis. The patients usually have no history of excessive alcohol consumption and other etiologies that can cause fatty liver. Understanding of the pathophysiology of NAFLD has revealed that non-coding RNAs (ncRNAs) play significant roles in modulating the disease susceptibility, pathogenesis and progression. Currently, the ncRNAs are grouped according to their sizes and their regulatory or housekeeping functions. Each of these ncRNAs has a wide range of involvement in the regulation of the genes and biological pathways. Here, we briefly review the current literature the regulatory ncRNAs in NAFLD pathogenesis and progression, mainly the microRNAs, long non-coding RNAs and circular RNAs. We also discuss the co-regulatory functions and interactions between these ncRNAs in modulating the disease pathogenesis. Elucidation of ncRNAs in NAFLD may facilitate the identification of early diagnostic biomarkers and development of therapeutic strategies for NAFLD.

RNA-seq of circular RNAs identified circPTPN22 as a potential new activity indicator in systemic lupus erythematosus

Background

Circular RNAs (circRNAs) are possible biomarkers for many diseases, but the knowledge of circRNAs in the peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE) remains limited. This study aimed to assess the expression of circRNAs in PBMCs from patients with SLE and healthy individuals by RNA sequencing (RNA-seq).

Methods

In total, 128 circRNAs were significantly differentially expressed including 39 upregulated and 89 downregulated circRNAs in four new-onset SLE patients compared with three healthy controls. After verification of the four candidate circRNAs in 49 patients with SLE and 37 controls using quantitative real-time polymerase chain reaction (qRT-PCR) assays, a previously undescribed circRNA with potential translation activity, circPTPN22, was selected to confirm its clinical significance.

Results

Bioinformatics analysis demonstrated that the parent gene of circPTPN22 was protein tyrosine phosphatase non-receptor type 22 (PTPN22), a potent regulator of T cell activation. The downregulation of circPTPN22 in patients with SLE was strongly negatively correlated with their Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) scores. circRNA-miRNA-mRNA co-expression network analysis indicated a correlation between circPTPN22 and the miRNAs and mRNAs related to immunological regulation including the development of SLE. Patients with higher SLEDAI scores had lower circPTPN22 expression levels, and long-term hormone treatment significantly increased circPTPN22 levels. Receiver operating characteristic curve analysis indicated that circPTPN22 has good diagnostic value for SLE.

Conclusion

Our data demonstrated the aberrant expression of circRNAs in patients with SLE compared with healthy controls; circPTPN22 might function as a diagnostic and disease severity indicator in SLE.

Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control

Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.

Identification of circular RNAs in the immature and mature rat anterior pituitary

Circular RNAs (circRNAs) are a new class of RNA that have a stable structure characterized by covalently closed circular molecules and are involved in invasive pituitary adenomas and recurrent clinically nonfunctioning pituitary adenomas. However, information on circRNAs in the normal pituitary, especially in rats, is limited. In this study, we identified 4123 circRNAs in the immature (D15) and mature (D120) rat anterior pituitary using the Illumina platform, and 32 differentially expressed circRNAs were found. A total of 150 Gene Ontology terms were significantly enriched, and 16 KEGG pathways were found to contain differentially expressed genes. Moreover, we randomly selected eight highly expressed circRNAs and detected their relative expression levels in the mature and immature rat pituitary by qPCR. In addition, we predicted 90 interactions between 53 circRNAs and 57 miRNAs using miRanda. Notably, circ_0000964 and circ_0001303 are potential miRNA sponges that may regulate the Fshb gene. The expression profile of circRNAs in the immature and mature rat anterior pituitary may provide more information about the roles of circRNAs in the development and reproduction in mammals.

Insights into the biogenesis and potential functions of exonic circular RNA

Circular RNAs (circRNAs) exhibit unique properties due to their covalently closed nature. Models of circRNAs synthesis and function are emerging but much remains undefined about this surprisingly prevalent class of RNA. Here, we identified exonic circRNAs from human and mouse RNA-sequencing datasets, documenting multiple new examples. Addressing function, we found that many circRNAs co-sediment with ribosomes, indicative of their translation potential. By contrast, circRNAs with potential to act as microRNA sponges were scarce, with some support for a collective sponge function by groups of circRNAs. Addressing circRNA biogenesis, we delineated several features commonly associated with circRNA occurrence. CircRNA-producing genes tend to be longer and to contain more exons than average. Back-splice acceptor exons are strongly enriched at ordinal position 2 within genes, and circRNAs typically have a short exon span with two exons being the most prevalent. The flanking introns either side of circRNA loci are exceptionally long. Of note also, single-exon circRNAs derive from unusually long exons while multi-exon circRNAs are mostly generated from exons of regular length. These findings independently validate and extend similar observations made in a number of prior studies. Furthermore, we analysed high-resolution RNA polymerase II occupancy data from two separate human cell lines to reveal distinctive transcription dynamics at circRNA-producing genes. Specifically, RNA polymerase II traverses the introns of these genes at above average speed concomitant with an accentuated slow-down at exons. Collectively, these features indicate how a perturbed balance between transcription and linear splicing creates important preconditions for circRNA production. We speculate that these preconditions need to be in place so that looping interactions between flanking introns can promote back-splicing to raise circRNA production to appreciable levels.

CircFunBase: a database for functional circular RNAs

Increasing evidence reveals that circular RNAs (circRNAs) are widespread in eukaryotes and play important roles in diverse biological processes. However, a comprehensive functionally annotated circRNA database is still lacking. CircFunBase is a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. The current version of CircFunBase documents more than 7000 manually curated functional circRNA entries, mainly including Homo sapiens, Mus musculus etc. CircFunBase provides visualized circRNA-miRNA interaction networks. In addition, a genome browser is provided to visualize the genome context of circRNAs. As a biological information platform for circRNAs, CircFunBase will contribute for circRNA studies and bridge the gap between circRNAs and their functions.

Circular RNAs and Their Emerging Roles in Immune Regulation

Circular ribonucleic acid (RNA) molecules (circRNAs) are covalently closed loop RNA molecules with no 5' end caps or 3' poly (A) tails, which are generated by back-splicing. Originally, circRNAs were considered to be byproducts of aberrant splicing. However, in recent years, development of high-throughput sequencing has led to gradual recognition of functional circRNAs, and increasing numbers of studies have elucidated their roles in cancer, neurologic diseases, and cardiovascular disorders. Nevertheless, studies of the functions of circRNAs in the immune system are relatively scarce. In this review, we detail relevant research on the biogenesis and classification of circRNAs, describe their functional mechanisms and approaches to their investigation, and summarize recent studies of circRNA function in the immune system.

Circular RNAs are abundantly expressed and upregulated during repair of the damaged endometrium by Wharton's jelly-derived mesenchymal stem cells

BACKGROUND

Wharton's jelly-derived mesenchymal stem cells (WJ-MSCs) exhibit strong and powerful potential in repairing different diseases. The expression profile of circular RNA (circRNA) provides valuable insight for regulation of the repair process and exploration of reparative effect mechanisms.

METHODS

Human endometrial stromal cells (ESCs) were cultured with mifepristone to obtain damaged ESCs, which were then cocultured with or without WJ-MSCs (cocultured group versus non-cocultured group) to observe the reparative effect upon damaged ESCs by WJ-MSCs. CircRNA microarray was performed between the two groups. Based on the transcriptomics data, the differential gene expression profiles of the two groups were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and network analysis methods. Screening of a circRNA database was performed, and the results were confirmed by quantitative polymerase chain reaction (qPCR).

RESULTS

WJ-MSCs exerted a reparative effect upon damaged ESCs in the cocultured group such as improved cell morphology, higher proliferative ability, and lower apoptosis rate. CircRNA array showed that 7757 circRNAs were differentially expressed in ESCs from the cocultured group. Mitotic cell cycle, cell cycle process, and nuclear division ranked top in the GO upregulated list of the two groups, while DNA replication and cell cycle ranked top in the KEGG pathway analysis upregulated list of the two groups. The nine most aberrantly expressed circRNAs were selected for further verification in the same cohort of samples by microarray analysis. Seven of the nine most aberrantly circRNAs were confirmed to be significantly upregulated in the cocultured group. And four of the seven circRNAs (hsa_circ_0015825, hsa-circRNA4049-38, hsa-circRNA5028-15, and hsa_circ_0111659) expression both in ESCs and WJ-MSCs tended to decrease with time by qPCR. The levels of the remaining three circRNAs (hsa-circRNA8881-21, hsa_circ_0020492 and hsa_circ_ 0026141) did not change significantly over time in either ESCs or WJ-MSCs. Moreover, we focused on hsa_circRNA_0111659 and predicted its miRNAs and targeted mRNA. The association of circRNA-miRNA-mRNA is likely to be involved in regulating the repair of endometrial damage.

CONCLUSIONS

Our results presented the abundant and upregulated circRNAs profile during repair of the damaged endometrium by WJ-MSCs and provided a novel perspective for circRNAs in the regulation of WJ-MSCs for endometrial repair.

Upregulation of circ-UBAP2 predicts poor prognosis and promotes triple-negative breast cancer progression through the miR-661/MTA1 pathway

Recently, a large number of studies have shown that circular RNA (circRNA) is involved in the development and progression of human cancer. However, its role in triple-negative breast cancer (TNBC) remains largely unknown. In this study, a novel circRNA, circ-UBAP2 (hsa_circ_0001846), was shown to be markedly upregulated in TNBC. Moreover, high circ-UBAP2 expression was closely associated with larger tumour size (p = 0.003), advanced TNM stage (p = 0.005), lymph node metastasis (p = 0.002), and unfavourable prognosis (p = 0.0256). Functionally, lentivirus-mediated stable knockdown of circ-UBAP2 dramatically weakened the ability of TNBC cells to proliferate and migrate and induced apoptosis in vitro and in vivo. Regarding the mechanism, we found that circ-UBAP2 was mainly observed in the cytoplasm and was capable of sponging miRNA-661 to increase the expression of the oncogene MTA1. Additionally, silencing of miRNA-661 or overexpression of MTA1 could partially rescue the attenuated malignant phenotype caused by circ-UBAP2 knockdown. Taken together, our data reveal that circ-UBAP2 plays a vital regulatory role in TNBC via the miR-661/MTA1 axis and may serve as a promising therapeutic target for TNBC patients.

Noncoding RNAs: potential regulators in cardioncology

Cancer is the leading cause of morbidity and mortality in the United States and globally. Owing to improved early diagnosis and advances in oncological therapeutic options, the number of cancer survivors has steadily increased. Such efficient cancer therapies have also lead to alarming increase in cardiovascular complications in a significant proportion of cancer survivors, due to adverse cardiovascular effects such as cardiotoxicity, cardiac atrophy, and myocarditis. This has emerged as a notable concern in healthcare and given rise to the new field of cardioncology, which aims at understanding the processes that occur in the two distinct disorders and how they interact to influence the progression of each other. A key player in both cancer and heart failure is the genome, which is predominantly transcribed to noncoding RNAs (ncRNAs). Since the emergence of ncRNAs as master regulators of gene expression, several reports have shown the relevance of ncRNAs in cancer and cardiovascular disorders. However, the knowledge is quite limited regarding the relevance of ncRNAs in cardioncology. The objective of this review is to summarize the current knowledge of ncRNAs in the context of cardioncology. Furthermore, the therapeutic strategies as well as the prospective translational applications of these ncRNA molecules to the clinics are also discussed.

Identification and characterization of a conservative W chromosome-linked circRNA in half-smooth tongue sole (Cynoglossus semilaevis) reveal its female-biased expression in immune organs

Circular RNAs (CircRNAs) represent an important class of noncoding RNAs to regulate biological and development processes. In the present study, the cDNA library was constructed and sequenced using Illumina Hiseq 2000 platform to identify circRNAs in half-smooth tongue sole. In the sequencing library, we validated a conservatively expressed circRNA with 363 nucleotides on W chromosome (termed as Wcirc5284614), which was spliced with the exon3, exon4, and exon5 of CNOT6L. Reverse transcription polymerase chain reaction indicated that Wcirc5284614 was mainly expressed in female's immune tissues, especially in the head kidney and spleen of the female. Comparative analysis showed that circRNA was highly conservative in vertebrate. These circRNA profiles provide new valuable resources for further study on the function and mechanism of circRNAs in half-smooth tongue sole, especially in immune organs.

Alternative mechanisms of translation initiation: An emerging dynamic regulator of the proteome in health and disease

Eukaryotic mRNAs were historically thought to rely exclusively on recognition and binding of their 5' cap by initiation factors to effect protein translation. While internal ribosome entry sites (IRESs) are well accepted as necessary for the cap-independent translation of many viral genomes, there is now recognition that eukaryotic mRNAs also undergo non-canonical modes of translation initiation. Recently, high-throughput assays have identified thousands of mammalian transcripts with translation initiation occurring at non-canonical start codons, upstream of and within protein coding regions. In addition to IRES-mediated events, regulatory mechanisms of translation initiation have been described involving alternate 5' cap recognition, mRNA sequence elements, and ribosome selection. These mechanisms ensure translation of specific mRNAs under conditions where cap-dependent translation is shut down and contribute to pathological states including cardiac hypertrophy and cancer. Such global and gene-specific dynamic regulation of translation presents us with an increasing number of novel therapeutic targets. While these newly discovered modes of translation initiation have been largely studied in isolation, it is likely that several act on the same mRNA and exquisite coordination is necessary to maintain 'normal' translation. In this short review, we summarize the current state of knowledge of these alternative mechanisms of eukaryotic protein translation, their contribution to normal and pathological cell biology, and the potential of targeting translation initiation therapeutically in human disease.

Processing and roles of snoRNA-ended long noncoding RNAs

Small nucleolar RNAs (snoRNAs) are a family of conserved nuclear RNAs that function in the modification of small nuclear RNAs (snRNAs) or ribosomal RNAs (rRNAs), or participate in the processing of rRNAs during ribosome subunit maturation. Eukaryotic DNA transcription and RNA processing produce many long noncoding RNA (lncRNA) species. Although most lncRNAs are processed like typical mRNAs to be 5' capped and 3' polyadenylated, other types of lncRNAs are stabilized from primary Pol II transcripts by alternative mechanisms. One way to generate stable lncRNAs is to co-operate with snoRNA processing to produce snoRNA-ended lncRNAs (sno-lncRNAs) and 5' snoRNA-ended and 3'-polyadenylated lncRNAs (SPAs). Rather than silently accumulating in the nucleus, some sno-lncRNAs and SPAs are involved in the regulation of pre-rRNA transcription and alternative splicing of pre-mRNAs. Here we provide a mini-review to discuss the biogenesis and functions of these unusually processed lncRNAs.

CircBA9.3 supports the survival of leukaemic cells by up-regulating c-ABL1 or BCR-ABL1 protein levels

The unchecked tyrosine kinase activity of BCR-ABL1 contributes to the immortality of leukaemic cells. Therefore, this oncogene is a highly important therapeutic target for chronic myelogenous leukaemia (CML). Tyrosine kinase inhibitors (TKIs) are an excellent drug treatment for CML patients. However, there are still some patients who are not responsive to TKIs. We found that a novel circular RNA (circRNA), named circBA9.3, is derived from BCR-ABL1. CircBA9.3 can efficiently promote the proliferation and inhibit apoptosis of cancer cells. In addition, some patients with TKI resistance have elevated circBA9.3 expression, which is positively correlated with the level of BCR-ABL1. Furthermore, circBA9.3 is predominantly located in the cytoplasm and enhances c-ABL1 and BCR-ABL1 oncoprotein expression. Thus, circBA9.3 is a molecule associated with increased tyrosine kinase activity that promotes resistance against TKI therapy. In this study, we provided a new potential target for the treatment of TKI-resistant CML patients.

A novel circulating hsa_circ_0081001 act as a potential biomarker for diagnosis and prognosis of osteosarcoma

Chemo-resistance and lung metastasis have been the two obstacles in the osteosarcoma (OS) treatment, which is still lack of effective biomarkers for prediction, diagnosis and treatment. Circular RNA (circRNA) is a new type of endogenous noncoding RNA that could serve as ideal biomarkers in cancer because of its stable loop structure. However, little is known about the diagnostic value of circRNAs in OS as well as their associations with clinicopathologic characteristics of OS patients. In the current study, we identified a novel circRNA, hsa_circ_0081001, screened by the RNA sequencing in the three paired chemo-resistant and chemo-sensitive OS cell lines (MG63/DXR vs MG63, KHOS/DXR vs KHOS, U2OS/DXR vs U2OS), and found that hsa_circ_0081001 was significantly up-regulated in the OS cell lines, tissues and serums, associated with poor overall survival and cox multivariate analysis showed that hsa_circ_0081001 was a novel independent prognostic factor for OS patients. Then, receiver operating characteristic (ROC) curve analysis revealed that hsa_circ_0081001 could act as a biomarker for the OS diagnosis and prognosis prediction, better than alkaline phosphatase (ALP) and lactate dehydrogenase (LDH). In addition, we preliminarily found that hsa_circ_0081001 expression level may dynamically monitor and reflect the condition changes of OS patients in a small-scale prospective clinical pretest. In conclusion, our study suggested that circulating hsa_circ_0081001 could serve as a potential biomarker and therapeutic target for OS patients.

CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http://www.picb.ac.cn/rnomics/circpedia.

Downregulation of hsa_circ_0007534 suppresses breast cancer cell proliferation and invasion by targeting miR-593/MUC19 signal pathway

Circular RNAs (circRNAs) are important non-coding RNAs that are reportedly involved in the progression of diverse human cancers through their action as a microRNA (miRNA) sponge. However, the exact roles of circRNAs in breast cancer (BC) remain largely unknown. The present data demonstrate the significantly upregulated expression of hsa_circ_0007534 circRNA in BC tissues and cell lines. In contrast, miR-593 expression was significantly downregulated. Knockdown of hsa_circ_0007534 inhibited BC cell proliferation, colony formation, and invasion, and promoted apoptosis in BC cells. Moreover, hsa_circ_0007534 was demonstrated to be a sponge of miR-593, and expression of miR-593 in BC cells was negatively correlated with hsa_circ_0007534. MUC19 expression was markedly increased in BC tissues and cell lines, and the 3'-UTR of MUC19 was targeted by miR-593. The expression of MUC19 was negatively regulated by miR-593 in BC cells. Our findings suggest an oncogenic role for hsa_circ_0007534 in BC by acting as a miR-593 sponge to promote MUC19 expression.

Characteristics of circular RNA expression in lung tissues from mice with hypoxia‑induced pulmonary hypertension

Pulmonary hypertension (PH) is a life-threatening lung disease, characterized by an increase in pulmonary arterial pressure caused by vasoconstriction and vascular remodeling. The pathogenesis of PH is not fully understood, and there is a lack of potential biomarkers for the diagnosis and treatment of patients with PH. Non-coding RNAs with a characteristic covalently closed loop structure, termed circular RNAs (circRNAs), are present in a number of pulmonary diseases. To the best of our knowledge, the present study is the first to use microarray analysis to determine the expression profile of circRNAs in lung tissues from mice with hypoxia-induced PH. In total, 23 significantly upregulated and 41 significantly down-regulated circRNAs were identified. Of these, 12 differentially expressed circRNAs were selected for further validation using reverse transcription-quantitative polymerase chain reaction. Putative microRNAs (miRNAs) that bind to the dysregulated circRNAs were predicted. Subsequently, bioinformatics tools were used to construct circRNA-miRNA-mRNA networks for the two most promising circRNAs, namely mmu_circRNA_004592 and mmu_circRNA_018351. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of target genes of the dysregulated circRNAs revealed that these dysregulated circRNAs may serve an important role in the pathogenesis of hypoxia-induced PH. Therefore, these dysregulated circRNAs are candidate diagnostic biomarkers and potential therapeutic targets for PH.

A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs

Here, Huang et al. investigated how circRNA localization or nuclear export is controlled and, using RNAi screening, found that depletion of the Drosophila DExH/D-box helicase Hel25E results in nuclear accumulation of long (>800-nt), but not short, circRNAs. Their findings suggest that the lengths of mature circRNAs are measured to dictate the mode of nuclear export.

Circular RNAs (circRNAs) are generated from many protein-coding genes. Most accumulate in the cytoplasm, but how circRNA localization or nuclear export is controlled remains unclear. Using RNAi screening, we found that depletion of the Drosophila DExH/D-box helicase Hel25E results in nuclear accumulation of long (>800-nucleotide), but not short, circRNAs. The human homologs of Hel25E similarly regulate circRNA localization, as depletion of UAP56 (DDX39B) or URH49 (DDX39A) causes long and short circRNAs, respectively, to become enriched in the nucleus. These data suggest that the lengths of mature circRNAs are measured to dictate the mode of nuclear export.