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Circular rna

Josphat K Saina, Zhi-Zhong Li, Andrew W Gichira, Yi-Ying Liao
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence...
March 21, 2018: International Journal of Molecular Sciences
Zhu Kun-Peng, Ma Xiao-Long, Zhang Chun-Lin
Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs generated from back-splicing, with a circular loop structure. Many circRNAs have been reported to play essential roles in cancer development and have the potential to serve as a novel class of biomarkers for clinical diagnosis. However, the role of circRNA in osteosarcoma (OS) remains largely unknown. In the current study, we examined the expression level of circular RNA PVT1 (circPVT1), previously screened and identified the oncogenic role in gastric cancer, in OS and found that circPVT1 was significantly up-regulated in the OS tissues, serums and chemoresistant cell lines, correlated with poor prognosis of OS patients...
2018: International Journal of Biological Sciences
Thomas B Hansen
Non-coding RNA is an interesting class of gene regulators with diverse functionalities. One large subgroup of non-coding RNAs is the recently discovered class of circular RNAs (circRNAs). CircRNAs are conserved and expressed in a tissue and developmental specific manner, although for the vast majority, the functional relevance remains unclear. To identify and quantify circRNAs expression, several bioinformatic pipelines have been developed to assess the catalog of circRNAs in any given total RNA sequencing dataset...
2018: Frontiers in Cell and Developmental Biology
Miao Wang, Yuxi Yang, Jian Xu, Wen Bai, Xueli Ren, Huijian Wu
BACKGROUND: The expression of circular RNA (circRNA) may affect tumor progression. However, there have been no systemic meta-analysis for cancer diagnosis by using circRNAs in clinical till now. Herein, we aimed to collect and examined all the evidence on the potential role of circRNA as novel biomarker in human cancers. METHODS: A comprehensive search strategy was used to search relevant literatures in the databases of PubMed, Embase, and the Web of Science from 2015 to August 2017...
March 20, 2018: BMC Cancer
Tomasz Krzywkowski, Malte Kühnemund, Di Wu, Mats Nilsson
Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines...
March 15, 2018: Nucleic Acids Research
Naixiang Zhai, Yanqin Lu, Yanzhou Wang, Xiuzhi Ren, Jinxiang Han
Circular RNA (circRNA) is a non-linear form of RNA derived from exonic, intronic, and exon-intron gene regions. circRNAs are characterized by covalent closed loops, highly stable nuclease resistance, and specific expression in species and developmental stages. CircRNA molecules have been identified as playing roles in the regulation of cell transcription, transcriptional expression after translation, interactions with microRNAs, and protein coding. A high stability and tissue- and disease-specific expression allow circRNAs to serve as potential biomarkers both for diseases and prognosis...
February 2018: Intractable & Rare Diseases Research
Xuemei Ma, Xiaodong Yang, Wenhua Bao, Shumin Li, Shanshan Liang, Yunhui Sun, Yunwei Zhao, Jing Wang, Chenxu Zhao
Lung cancer remains a leading cause of cancer-related deaths worldwide. In the past years, increasing reports indicate that circular RNAs (circRNAs) exert a great important role in human cancers, including lung cancer. However, the knowledge about circRNA in lung cancer remains very little so far. In the present study, we screened out a highly expressed novel circRNA named circMAN2B2 in lung cancer tissues. We investigated the function of circMAN2B2 and found that circMAN2B2 knockdown significantly inhibited cell proliferation and invasion in both H1299 and A549 lung cancer cells...
March 16, 2018: Biochemical and Biophysical Research Communications
Kaixuan Zeng, Xiaoxiang Chen, Mu Xu, Xiangxiang Liu, Xiuxiu Hu, Tao Xu, Huiling Sun, Yuqin Pan, Bangshun He, Shukui Wang
Mounting evidences indicate that circular RNAs (circRNAs) have a vital role in human diseases, especially cancers. More recently, circHIPK3, a particularly abundant circRNA, was proposed to be involved in tumorigenesis. However, its role in colorectal cancer (CRC) has not been explored. In this study, we found circHIPK3 was significantly upregulated in CRC tissues and cell lines, at least in part, due to c-Myb overexpression and positively correlated with metastasis and advanced clinical stage. Moreover, Cox multivariate survival analysis showed that high-level expression of circHIPK3 was an independent prognostic factor of poor overall survival (OS) in CRC (hazard ratio [HR] = 2...
March 16, 2018: Cell Death & Disease
Giacomo Reina, Ngoc Do Quyen Chau, Yuta Nishina, Alberto Bianco
Several studies have demonstrated the ability of graphene oxide (GO) to efficiently adsorb small-interfering RNA (siRNA) on its surface and to transport it into cells. However, studies on whether and how siRNA interacts with GO are still inconclusive. In this context, understanding the interaction between GO and siRNA is fundamental to design new efficient gene silencing tools. In this work, the interactions between GO and siRNA molecules were systematically investigated. We focused on how the GO size, oxygenated groups present on the surface and chemical functionalization affect the double helix siRNA structure, using gel electrophoresis, UV-Vis spectroscopy, fluorescence resonance energy transfer (FRET) and circular dichroism (CD)...
March 15, 2018: Nanoscale
Shencun Fang, Huifang Guo, Yusi Cheng, Zewei Zhou, Wei Zhang, Bing Han, Wei Luo, Jing Wang, Weiping Xie, Jie Chao
Excessive proliferation and migration of fibroblasts contribute to pulmonary fibrosis in silicosis, and both epithelial cells and endothelial cells participate in the accumulation of fibroblasts via the epithelial-mesenchymal transition (EMT) and the endothelial-mesenchymal transition (EndMT), respectively. A mouse endothelial cell line (MML1) was exposed to silicon dioxide (SiO2 , 50 μg/cm2 ), and immunofluorescence and western blot analyses were performed to evaluate levels of specific endothelial and mesenchymal markers and to elucidate the mechanisms by which SiO2 induces the EndMT...
March 14, 2018: Cell Death & Disease
Mingsheng Yang, Lu Song, Jianhang Mao, Yuxia Shi, Changjing Wu, Yunxia Zhang, Li Huang, Weifeng Peng, Xiaomeng Liu
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367 bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced...
March 11, 2018: International Journal of Biological Macromolecules
Elizabeth Delve, Justin Parreno, Vivian Co, Po-Han Wu, Jasmine Chong, Matteo Di Scipio, Rita A Kandel
Osteoarthritis (OA) is a degenerative disease that initially manifests as loss of the superficial zone (SZ) of articular cartilage. SZ chondrocytes (SZC) differ in morphology from other chondrocytes as they are elongated and oriented parallel to the tissue surface. Proteoglycan 4 (PRG4) and tenascin C (TNC) are molecules expressed by SZC, which have been shown to be chondroprotective. Identification of the signalling pathway(s) regulating expression of SZ molecules may lead to a therapeutic target that can be used to delay or prevent the onset of OA...
March 14, 2018: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
Xingjie Bao, Shuying Zheng, Shuqi Mao, Tianlun Gu, Shike Liu, Jihan Sun, Lina Zhang
BACKGROUND: Essential hypertension (EH) is a high prevalence with multifactorial diseases. Human studies on the impact of genes on this disease are just in the initial stage, the mechanism of gene regulation is still remains unclear. Circular RNAs (circRNAs) as a continuous cycle of covalent closure, RNA molecules added to the 3'-5' end covalently bound by the formation of incidental event. CircRNAs may be an important biomolecule in revealing the molecule regulate mechanisms of EH. METHODS: The circRNAs were selected and validated with qRT-PCR followed...
March 8, 2018: Biochemical and Biophysical Research Communications
Linping Yan, Jie Feng, Feng Cheng, Xianwei Cui, Lingjuan Gao, Yajun Chen, Fei Wang, Tianying Zhong, Yun Li, Lan Liu
Circular RNAs (circRNAs) have recently been shown to exert their effects on multiple pathological processes by acting as microRNA (miRNA) sponges. However, the roles of circRNAs in gestational diabetes mellitus (GDM) are largely unknown. This study aimed to identify the circRNAs involved in GDM and predict their potential biological functions. We first performed next-generation sequencing (NGS) to generate unbiased placental villi circRNA expression profiles of GDM and normal controls. In total, 48,270 circRNAs from the placental villi of the two groups were sequenced...
March 8, 2018: Biochemical and Biophysical Research Communications
Wei Lei, Tingting Feng, Xing Fang, You Yu, Junjie Yang, Zhen-Ao Zhao, Junwei Liu, Zhenya Shen, Wenbo Deng, Shijun Hu
BACKGROUND: Circular RNAs (circRNAs) are regarded as a novel class of noncoding RNA regulators. Although a number of circRNAs have been identified by bioinformatics analysis of RNA-seq data, tissue and disease-specific circRNAs are still to be uncovered to promote their application in basic research and clinical practice. The purpose of this study was to explore the circRNA profiles in human induced pluripotent stem cells (hiPSCs) and hiPSC-derived cardiomyocytes (hiPSC-CMs), and to identify cardiac or disease-specific circRNAs...
March 9, 2018: Stem Cell Research & Therapy
Xingfu Huang, Yanjia Chen, Junhui Xiao, Zheng Huang, Liwei He, Dingli Xu, Jian Peng
OBJECTIVE: Although differentially expressed circRNAs have been proposed to be closely associated with epithelial-mesenchymal transition (EMT), the roles of circRNAs remain unclear in endothelial-to-mesenchymal transition (EndMT), which is a subcategory of EMT. Herein, we characterized the expression and potential function of circRNAs during TGF-ß1-induced EndMT in rat coronary artery endothelial cells (CAEC). METHODS: High-throughput RNA sequencing was performed for unbiasedly profiling the expression of circRNAs...
March 2018: Anatolian Journal of Cardiology
Mitsunobu Nakamura, Fuyuki Ota, Tadao Takada, Kazuo Akagi, Kazushige Yamana
In this report, we describe the circularly polarized luminescence (CPL) of the RNA duplexes having one to four 2'-O-pyrene modified uridines (Upy) and the DNA duplexes having two, four, and six pyrene modified non-nucleosidic linkers (Py). Both the pyrene π-stack arrays formed on the RNA and DNA double helical structures exhibited pyrene excimer fluorescence. In the pyrene-modified RNA systems, the RNA duplex having four Upys gives CPL emission with glum value of <0.01 at 480 nm. The structure of pyrene stacks on the RNA duplex may be rigidly regulated with increase in the Upy domains, which resulted in the CPL emission...
March 9, 2018: Chirality
Han-Bo Ma, Yi-Nan Yao, Jin-Jun Yu, Xue-Xue Chen, Huai-Fang Li
Circular RNAs (circRNAs) are key regulators in the development and progression of human cancers, however its role in cervical cancer tumorigenesis is not well understood. The present study aims to investigate the expression profiles and potential modulation of circRNA on cervical cancer carcinogenesis. Human circRNA microarray was performed to screen for abnormally expressed circRNA in cervical cancer cells and circRNA-000284 was identified as one circRNA significantly upregulated in cervical cancer cells. Subsequent mechanistic investigations suggested that knockdown of circRNA-000284 suppressed cell proliferation and invasion, and caused G0/G1 phase cell cycle arrest...
2018: American Journal of Translational Research
Viktor Tokan, Janka Puterova, Matej Lexa, Eduard Kejnovsky
BACKGROUND: Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. RESULTS: In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast...
March 6, 2018: BMC Genomics
Aude Merdrignac, Gaëlle Angenard, Coralie Allain, Kilian Petitjean, Damien Bergeat, Pascale Bellaud, Allain Fautrel, Bruno Turlin, Bruno Clément, Steven Dooley, Laurent Sulpice, Karim Boudjema, Cédric Coulouarn
Intrahepatic cholangiocarcinoma (iCCA) is a deadly liver primary cancer associated with poor prognosis and limited therapeutic opportunities. Active transforming growth factor beta (TGFβ) signaling is a hallmark of the iCCA microenvironment. However, the impact of TGFβ on the transcriptome of iCCA tumor cells has been poorly investigated. Here, we have identified a specific TGFβ signature of genes commonly deregulated in iCCA cell lines, namely HuCCT1 and Huh28. Novel coding and noncoding TGFβ targets were identified, including a TGFβ-induced long noncoding RNA (TLINC), formerly known as cancer susceptibility candidate 15 (CASC15)...
March 2018: Hepatology Communications
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