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.     

Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus)

Circular RNAs (circRNAs) are a new class of non-coding RNAs in animals and are a novel target of non-coding RNA (ncRNA) regulation. The mechanism and function of circRNAs have been reported in some species and tissues. However, there is little available information on the functions of circRNAs in the goat reproductive system. In the present study, we deeply sequenced and analyzed circRNAs through bioinformatics to reveal the expression profiles, and predicted 13,950 circRNAs in the pre-ovulatory ovarian follicles of goats for the first time. Thirty-seven circRNAs were differentially expressed in the Boer goat compared with the Macheng black goat. The chi_circ_0008219 was involved in a vast circRNA-miRNA-mRNA co-expression network. Via a luciferase activity assay, chi_circ_0008219 is observed to sponge to 3 ovarian follicle-related miRNAs. These findings demonstrate that circRNAs have potential effects in the ovarian follicles of ewes and may represent a promising new research field in ovarian follicular development.     

Identification and characterization of N6-methyladenosine modification of circRNAs in glioblastoma

This research systematically profiled the global N6-methyladenosine modification pattern of circular RNAs (circRNAs) in glioblastoma (GBM). Based on RNA methylation sequencing (MeRIP sequencing or N6-methyladenosine sequencing) and RNA sequencing, we described the N6-methyladenosine modification status and gene expression of circRNAs in GBM and normal brain tissues. N6-methyladenosine–related circRNAs were immunoprecipitated and validated by real-time quantitative PCR. Bioinformatics analysis and related screening were carried out. Compared with those of the NC group, the circRNAs from GBM exhibited 1370 new N6-methyladenosine peaks and 1322 missing N6-methyladenosine peaks. Among the loci associated with altered N6-methyladenosine peaks, 1298 were up-regulated and 1905 were down-regulated. The N6-methyladenosine level tended to be positively correlated with circRNA expression. Bioinformatics analysis was used to predict the biological function of N6-methyladenosine–modified circRNAs and the corresponding signalling pathways. In addition, through PCR validation combined with clinical data mining, we identified five molecules of interest (BUB1, C1S, DTHD1, F13A1 and NDC80) that could be initial candidates for further study of the function and mechanism of N6-methyladenosine–mediated GBM development. In conclusion, our findings demonstrated the N6-methyladenosine modification pattern of circRNAs in human GBM, revealing the possible roles of N6-methyladenosine–mediated novel noncoding RNAs in the origin and progression of GBM.     

CircITGA7对缺血性心律失常大鼠心肌细胞凋亡的影响

研究环状RNA ITGA7(circITGA7)在心律失常大鼠心肌细胞中的表达,并探讨其对心律失常大鼠心肌细胞凋亡的影响及机制。40只SPF级SD雄性大鼠,分为4组,分别为假手术组、心律失常组、circITGA7干扰心律失常组和对照干扰心律失常组,尾静脉注射circITGA7干扰腺相关病毒构建circITGA7干扰大鼠模型,并通过手术结扎冠状动脉前降支建立缺血性心律失常大鼠模型。通过荧光定量PCR法(Q-PCR)检测circITGA7在心律失常大鼠心肌组织中的表达水平。分别检测circITGA7对心律失常大鼠心肌氧化应激和凋亡的影响;Western blotting检测circITGA7对心律失常大鼠心肌细胞p-AKT和ITGA7蛋白表达的影响。Q-PCR结果显示circITGA7在心律失常大鼠心肌组织中的表达显着高于假手术组大鼠;与对照干扰心律失常组比较,circITGA7干扰心律失常组大鼠心律失常评分显著降低,差异具有统计学意义(p<0.01)。与假手术组比较,心律失常组大鼠心肌细胞SOD活力显著降低,MDA含量显著升高;与对照干扰心律失常组比较,circITGA7干扰心律失常组大鼠心律失常组大鼠心肌细胞SOD活力显著升高,MDA含量显著降低,差异具有统计学意义(p<0.01)。TUNEL检测结果显示,与假手术组比较,心律失常大鼠心肌细胞凋亡程度显著升高;与对照干扰心律失常组大鼠比较,circITGA7干扰心律失常组大鼠心肌细胞凋亡率为显著降低(p<0.01);Western blotting结果显示,与假手术组比较,心律失常大鼠心肌细胞p-AKT和ITGA7的蛋白表达水平均显著升高;与对照干扰心律失常组比较,circITGA7干扰心律失常组大鼠心肌细胞p-AKT和ITGA7的蛋白表达水平均显著下降(p<0.01)。干扰circITGA7能够抑制AKT路径,抑制心律失常大鼠心肌细胞氧化应激和细胞凋亡,缓解大鼠心律失常。     

结节性甲状腺肿circRNA-miRNA-mRNA调控网络的构建

基于生物信息分析筛选结节性甲状腺肿中差异表达的环状RNA(circRNA),并揭示circRNA-miRNA-mRNA调控网络在结节性甲状腺肿中的作用。从GEO数据库中检索结节性甲状腺肿组织基因芯片数据,利用R软件筛选出差异表达的circRNA。联合多个生物信息数据库预测差异表达circRNA下游的miRNA及mRNA, 并对靶mRNA进行GO及KEGG富集分析。利用STRING在线数据库及Cytoscape软件筛选核心基因。确定了2个circRNA,42个miRNA及546个mRNA。GO及KEGG富集分析表明靶mRNA主要涉及细胞生长及基因表达调控过程。基于Cytoscape软件筛选出了14个核心基因(SP1、IGF1R、RPS6KB1、SMAD2、SMAD3、SMAD4、VEGFA、CCND1、CDK2、HSPA4、HIF1A、CREB1,NR3C1和STAT5A)。最终基于2个circRNA、11个miRNA和14个核心mRNA构建了circRNA-miRNA-mRNA调控网络。结节性甲状腺肿组织中异常表达的circRNA及相关的circRNA-miRNA-mRNA调控网络可能成为结节性甲状腺肿诊断与治疗的新靶点。     

circ_0000267靶向miR-198对急性淋巴细胞白血病细胞KOCL44增殖和凋亡的影响

目的探讨circ_0000267对急性淋巴细胞白血病（ALL）KOCL44细胞增殖和凋亡的影响及其作用机制。 方法选择ALL细胞株KOCL44为研究对象,分别将小干扰RNA （siRNA）阴性对照（si-NC）、circ_0000267 siRNA （si-circ_0000267）、微小RNA （miRNA）阴性对照（miR-NC）、miR-198模拟物（miR-198）、circ_0000267 siRNA+miRNA抑制剂阴性对照（si-circ_0000267+anti-miR-NC）和circ_0000267 siRNA+miR-198抑制剂（si-circ_0000267+anti-miR-198）转染细胞,48 h后通过RT-qPCR检测细胞circ_0000267和miR-198相对表达水平,采用CCK-8法检测KOCL44细胞的增殖水平,流式细胞术实验检测KOCL44细胞的凋亡水平,Western blot检测KOCL44细胞Ki-67、Bcl-2和Bax蛋白表达水平,通过双荧光素酶报告实验验证circ_0000267和miR-198靶向关系。两组间比较采用独立样本t检验。 结果与健康志愿者比较,ALL患者circ_0000267表达水平（1.00±0.06比3.19±0.21）上调,miR-198表达水平（1.00±0.07比0.41±0.03）下调,差异有统计学意义（P < 0.05）。敲低circ_0000267或者过表达miR-198可抑制KOCL44细胞增殖（0.68±0.05比0.32±0.02、0.69±0.06比0.39±0.03）、Ki-67 （0.84±0.06比0.37±0.03、0.85±0.06比0.45±0.04）和Bcl-2蛋白表达（0.63±0.05比0.22±0.02、0.65±0.04比0.29±0.02）,促进细胞凋亡[（6.53±0.51）﹪比（24.29±2.06）﹪、（7.38±0.57）﹪比（20.03±1.66）﹪]和Bax蛋白表达（0.31±0.03比0.77±0.04、0.30±0.02比0.71±0.04）,差异有统计学意义（P < 0.05）。双荧光素酶报告实验验证circ_0000267可以靶向miR-198表达,干扰miR-198表达可以逆转抑制circ_0000267表达对KOCL44细胞的增殖和凋亡的作用,差异有统计学意义（P < 0.05）。 结论circ_0000267通过调控miR-198抑制ALL细胞增殖,并促进凋亡,为临床治疗ALL提供新的依据。