真菌环状RNA鉴定及研究展望

环状RNA是一类具有丰富调节潜力的闭合环状单链RNA,其可以通过竞争性结合内源RNA、充当蛋白质支架以及翻译模板等方式,从而参与基因表达调控。本文综述了真菌环状RNA的鉴定流程和难点,为后续解析环状RNA在真菌发育与代谢等过程中的调节作用提供理论支持。     

Identification,characterization, and functional investigation of circular RNAs in subventricular zone of adult rat brain

Adult neural stem cells (NSCs) are able to self-renew and generate new neural cells. Identifying regulators of NSCs is significant for the development of NSC-based therapies for neurodegenerative diseases and brain injuries. Recently, circular RNAs (circRNAs) have been characterized in various cell lines and brain tissues, and found to participate in multiple biological processes. However, the expression pattern of circRNAs in adult NSCs is still unknown. Here, the subventricular zone (SVZ) of the lateral ventricle was isolated as the niche of NSCs in adult rat brain for RNA sequencing and the characteristics of circRNAs profiling in both SVZ and cerebral cortex were also investigated. As a result, 29 049 and 31 975 circRNAs were identified in SVZ and cortex, respectively. Among them, 41 were SVZ-specific and 48 were cortex-specific. 467 circRNAs were also found to express predominately in SVZ, while the cortex had other 423 circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the SVZ-specific circRNAs have close relationship with the regulation of NSC expansion and NSC-niche interaction, while the other differentially expressed circRNAs might be involved in neural cellular construction and nerve system function. Furthermore, the interactions between circRNAs and microRNAs were also explored, and the result showed that one SVZ-specific circRNA was capable to competitively bind miR-138-5p as a potential derepressive regulator in NSCs proliferation. Hence, our work has laid the foundations to decipher regulation mechanisms of circRNAs in adult NSCs and to develop circRNAs as novel biomarkers for adult NSCs.     

Overexpression of circ_0005198 sponges miR-1294 to regulate cell proliferation,apoptosis, migration,and invasion in glioma

Glioma (GM) is an aggressive malignancy with high mortality rate across the world. Mounting studies demonstrates that abnormally expressed circular RNAs (circRNAs) act as important roles in tumor progression. In the current work, a novel circRNA, circ_0005198, was explored. Circ_0005198 level in GM tissue samples and cells was detected. The clinical implication of circ_0005198 was analyzed by Fisher's test and Kaplan-Meier analysis. In vitro experiments were carried out to elucidate the influence of circ_0005198 on GM cell proliferation, apoptosis, and metastatic properties. Luciferase reporter and rescue experiments were conducted to clear the mechanism of circ_0005198. The expression of circ_0005198 was enhanced in GM tumors and cells. Its expression in tumor specimens was related to clinical severity and poor prognosis. Functionally, circ_0005198 could remarkably boost cell growth, clone-forming ability, and metastatic properties and attenuate cell apoptosis in GM cells. What's more, circ_0005198 could directly sponge miR-1294 to exert oncogenic functions. In summary, this study might provide an effective therapeutic target for GM.     

Circular RNA circ_001350 regulates glioma cell proliferation,apoptosis, and metastatic properties by acting as a miRNA sponge

Glioma is an aggressive malignancy with increasing incidence and threatens people's health worldwide. Accumulating evidence revealed that circular RNAs (circRNAs) play important functions in cancers. A previous study demonstrated that circ_001350 was elevated in glioma tissue samples than nontumorous tissue specimens screened by high-throughput microarray. The level of circ_001350 in glioma tissue specimens and cell lines was detected by quantitative real-time polymerase chain reaction. The Fisher exact test was carried out to estimate the correlation of circ_001350 level with clinical characteristics. Cell proliferation, apoptosis, and motility abilities were detected using cell counting kit-8, clonogenic, flow cytometry, and transwell experiments, respectively. The potential target of circ_001350 was identified by the luciferase assay. circ_001350 level was significantly enhanced in glioma tissue specimens and cells. Further, elevated expression of circ_001350 was closely linked to patients' clinical severity. Knockdown of circ_001350 could inhibit cell proliferation and metastatic properties and increase apoptotic cells. circ_001350 could directly bind to miR-1236 and regulate its expression to exert oncogenic functions. Collectively, circ_001350 directly sponges miR-1236, thus contributing to malignant progression of glioma.     

Insights into circular RNAs: Biogenesis,function and their regulatory roles in cardiovascular disease

As a distinctive member of the noncoding RNA family, circular RNAs (circRNAs) are generated from single-stranded, covalently closed structures and are ubiquitous in mammalian cells and tissues. Due to its atypical circular architecture, it was conventionally deemed insignificant dark matter for a prolonged duration. Nevertheless, studies conducted over the last decade have demonstrated that this abundant, structurally stable and tissue-specific RNA has been increasingly relevant in diverse diseases, including cancer, neurological disorders, diabetes mellitus and cardiovascular diseases (CVDs). Therefore, regulatory pathways controlled by circRNAs are widely involved in the occurrence and pathological processes of CVDs through their function as miRNA sponges, protein sponges and protein scaffolds. To better understand the role of circRNAs and their complex regulatory networks in CVDs, we summarize current knowledge of their biogenesis and function and the latest research on circRNAs in CVDs, with the hope of paving the way for the identification of promising biomarkers and therapeutic strategies for CVDs.     

Reduced contact order and RNA folding rates

We investigated the relationship between RNA structure and folding rates accounting for hierarchical structural formation. Folding rates of two-state folding proteins correlate well with relative contact order, a quantitative measure of the number and sequence distance between tertiary contacts. These proteins do not form stable structures prior to the rate-limiting step. In contrast, most secondary structures are stably formed prior to the rate-limiting step in RNA folding. Accordingly, we introduce "reduced contact order", a metric that reflects only the number of residues available to participate in the conformational search after the formation of secondary structure. Plotting the folding rates and the reduced contact order from ten different RNAs suggests that RNA folding can be divided into two classes. To examine this division, folding rates of circularly permutated isomers are compared for two RNAs, one from each class. Folding rates vary by tenfold for circularly permuted Bacillus subtilis RNase P RNA isomers, whereas folding rates vary by only 1.2-fold for circularly permuted catalytic domains. This difference is likely related to the dissimilar natures of their rate-limiting steps.     

环状RNA及其作为疾病标志物的潜能

环状RNA（circular RNA, circRNA）是一种共价闭合环状结构的内源性非编码RNA分子,不具有5′端帽子和3′端poly(A)尾巴结构,具有广泛性、保守性、组织特异性以及稳定性等特性;根据序列来源的不同可分为3种类型：外显子circRNA、内含子circRNA、外显子-内含子circRNA;随着生物信息学的快速发展和高通量测序技术的不断革新,目前已经在真核细胞中发现大量内源性circRNA,主要分布于细胞质中,其独特的序列结构,使它具有microRNA海绵、调节选择性剪接或转录、与RNA结合蛋白结合、滚动翻译和衍生假基因等功能;它参与癌症、糖尿病、神经系统疾病和动脉粥样硬化等疾病发生、发展过程。众多研究显示circRNA会成为新型的疾病临床诊断标志物或人类疾病治疗的潜在靶点,该评述较为详细地从circRNA的形成、特性、生物学功能、研究方法、研究数据库以及和疾病的关系等方面来阐述circRNA的最新研究进展,方便研究人员进行circRNA研究。     

数字PCR定量检测血浆中环状RNA方法的建立

生物标志物一直是医学领域的研究热点.目前主要以实时荧光定量PCR技术作为分子诊断的检测手段,用于大样本的核酸检测,但该技术具有限制性,会导致假阴性.作为第三代PCR的数字PCR技术,优化并提高了检测灵敏度,无需标准曲线实现绝对定量检测,大大提高了检测的精准度,尤其是对于低表达RNA的检测,显得更为出色.本研究以hsa_circ₀061276为例,利用微滴式数字PCR EvaGreen染料法对血浆中hsa_circ₀061276的拷贝数进行绝对定量地检测,成功检测出胃炎和胃癌患者血浆中hsa_circ₀061276的具体拷贝数.因此,数字PCR作为新型检测技术在临床实际应用中有较大推广价值.     

Selection and stabilization of the RNA aptamers against the human immunodeficiency virus type-1 nucleocapsid protein

The nucleocapsid (NC) protein of the human immunodeficiency virus-1 (HIV-1) plays an important role in the encapsidation of viral RNA and assembly of viral particle. Since the NC protein is resistant for mutation, it might be an excellent target for the anti-viral therapy. RNA aptamers that bind to the mature form of the NC protein were isolated from a RNA library. Surface plasmon resonance measurement and gel shift assay showed that the RNA aptamers specifically bind to the NC protein with high affinity and compete for the psi RNA binding to the NC protein. Mapping of the RNA aptamer showed at least two sites for the protein binding, suggesting a multiple and cooperative binding by the NC to RNA. In addition, the circular form of RNA avidly binds to the NC protein as a linear counter does. Stabilized RNA aptamer is expected to act as an inhibitor for the viral packaging.     

环状RNA：竞争性内源RNA新成员

环状RNA（circRNA）广泛存在于各种生物细胞中,具有结构稳定、丰度高和组织特异性表达等特征。最近的研究表明,一些circRNA作为竞争性内源NRNA（ceRNA）来发挥基因表达调控的作用。circRNA利用其microRNA（miRNA）应答元件结合miRNA,以阻断miRNA对其靶标表达的抑制作用,从而调控其他相关RNA的表达水平。circRNA在基因表达调控中重要作用的发现不仅丰富了人们对ceRNAiN控网络的认识,而且提示circRNA在药物开发和疾病诊治中具有良好的应用前景。     

Dysregulated circRNAs serve as prognostic and diagnostic markers in osteosarcoma by sponging microRNA to regulate the downstream signaling pathway

Circular RNAs (circRNAs) have been extensively studied in many tumors. The aim of this study was to demonstrate the relationship between circRNAs and clinical features, prognosis, and diagnosis of osteosarcoma patients. We mainly included studies about circRNAs expression and osteosarcoma. The odds ratio (ORs) and 95% confidence intervals (CIs) were used for clinical features, sensitivity, and specificity, while the hazard ratios (HRs) and 95% CIs were used to assess overall survival (OS). A number of 13 articles were included in this study, including 9 about clinical features, 11 about prognosis, and 5 about diagnosis. The results showed that increased circRNAs expression was significantly correlated with adverse clinical characteristics. In terms of prognosis, oncogenic circRNAs had adverse effects on overall survival (OS: HR = 2.54; 95%Cl: 2.05–3.03), and increased expression of cancer-suppressor circRNAs prolonged survival (OS: HR = 0.42; 95%Cl: 0.210.64). Our study further showed an AUC of 0.85, with an 80% sensitivity and 77% specificity to distinguish osteosarcoma patients from healthy controls. In conclusion, circRNAs may be new promising indicators for prognostic evaluation and early diagnosis of osteosarcoma patients.