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https://www.readbyqxmd.com/read/28346469/computational-identifying-and-characterizing-circular-rnas-and-their-associated-genes-in-hepatocellular-carcinoma
#1
Yan Li, Yongcheng Dong, Ziyan Huang, Qifan Kuang, Yiming Wu, Yizhou Li, Menglong Li
Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT...
2017: PloS One
https://www.readbyqxmd.com/read/28344082/circ-znf609-is-a-circular-rna-that-can-be-translated-and-functions-in-myogenesis
#2
Ivano Legnini, Gaia Di Timoteo, Francesca Rossi, Mariangela Morlando, Francesca Briganti, Olga Sthandier, Alessandro Fatica, Tiziana Santini, Adrian Andronache, Mark Wade, Pietro Laneve, Nikolaus Rajewsky, Irene Bozzoni
Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here we performed expression profiling of circRNAs during in vitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28344080/translation-of-circrnas
#3
Nagarjuna Reddy Pamudurti, Osnat Bartok, Marvin Jens, Reut Ashwal-Fluss, Christin Stottmeister, Larissa Ruhe, Mor Hanan, Emanuel Wyler, Daniel Perez-Hernandez, Evelyn Ramberger, Shlomo Shenzis, Moshe Samson, Gunnar Dittmar, Markus Landthaler, Marina Chekulaeva, Nikolaus Rajewsky, Sebastian Kadener
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry...
March 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28343871/over-expression-of-circrna_100876-in-non-small-cell-lung-cancer-and-its-prognostic-value
#4
Jun-Tao Yao, Shu-Hong Zhao, Qiu-Ping Liu, Mo-Qi Lv, Dang-Xia Zhou, Zi-Jun Liao, Ke-Jun Nan
Circular RNAs (circRNAs) are a novel type of endogenous RNAs featuring stable structure and high tissue-specific expression. Recently, accumulating evidence has revealed that aberrant circRNAs expression plays important roles in carcinogenesis and tumor progression. However, the expression pattern and biological function of circRNAs in non small cell lung cancer (NSCLC) remain largely unknown. Therefore, the purpose of this study was to clarify the possible role of one of typical circRNAs, circRNA_100876 in NSCLC and to define its prognostic value in NSCLC...
February 22, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28342987/circular-rnas-and-cancer
#5
Jun He, Qichao Xie, Hailin Xu, Jiantian Li, Yongsheng Li
Circular RNAs (circRNAs) are a type of non-coding RNA molecules that lack a 5'-terminal cap and 3'-terminal poly A tail. A large number of circRNAs have been identified through biological experiments, computational methods and high-throughput sequencing. CircRNA sequence composition determines if a given circRNA is exonic, intronic or retained-intronic. CircRNAs are more abundant and stable than linear mRNAs, and their expression is both step- and location-specific. CircRNAs mediate transcriptional and post-transcriptional regulation of gene and protein expression...
March 22, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28334396/quantifying-circular-rna-expression-from-rna-seq-data-using-model-based-framework
#6
Musheng Li, Xueying Xie, Jing Zhou, Mengying Sheng, Xiaofeng Yin, Eun-A Ko, Tong Zhou, Wanjun Gu
Motivation: Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type- and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification...
March 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334140/circular-rna-identification-based-on-multiple-seed-matching
#7
Yuan Gao, Jinyang Zhang, Fangqing Zhao
Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage...
February 28, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28288173/microarray-profiling-of-circular-rnas-in-human-papillary-thyroid-carcinoma
#8
Nianchun Peng, Lixin Shi, Qiao Zhang, Ying Hu, Nanpeng Wang, Hui Ye
BACKGROUND: Non-coding circular RNAs (circRNAs) have displayed dysregulated expression in several human cancers. Here, we profiled the circRNA expression of papillary thyroid carcinoma (PTC) tumors to improve our understanding of PTC pathogenesis. METHODS: Microarray profiling was performed on 18 thyroid samples, consisting of six PTC tumors, six matching contralateral normal samples, and six benign thyroid lesions. After low-intensity filtering, hierarchical clustering revealed the circRNA expression patterns...
2017: PloS One
https://www.readbyqxmd.com/read/28287427/the-role-and-molecular-mechanism-of-non-coding-rnas-in-pathological-cardiac-remodeling
#9
REVIEW
Jinning Gao, Wenhua Xu, Jianxun Wang, Kun Wang, Peifeng Li
Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not encode proteins. Studies show that ncRNAs are not only involved in cell proliferation, apoptosis, differentiation, metabolism and other physiological processes, but also involved in the pathogenesis of diseases. Cardiac remodeling is the main pathological basis of a variety of cardiovascular diseases. Many studies have shown that the occurrence and development of cardiac remodeling are closely related with the regulation of ncRNAs. Recent research of ncRNAs in heart disease has achieved rapid development...
March 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28286269/circular-rna-profiling-reveals-that-circcol3a1-859267-regulate-type-i-collagen-expression-in-photoaged-human-dermal-fibroblasts
#10
Yating Peng, Xiaojing Song, Yue Zheng, Xinyi Wang, Wei Lai
Production of type I collagen declines is a main characteristic during photoaging, but the mechanism is still not fully understood. Circular RNAs (circRNAs) are a class of newly identified non-coding RNAs with regulatory potency by sequestering miRNAs like a sponge. It's more stable than linear RNAs, and would be a useful tool for regulation of gene expression. However, the role of circRNAs in collagen expression during photoaging is still unclear. Here we performed deep sequencing of RNA generated from UVA irradiated and no irradiated human dermal fibroblasts (HDFs) and identified 29 significantly differentially expressed circRNAs (fold change ≥ 1...
March 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28282919/characterization-of-hsa_circ_0004277-as-a-new-biomarker-for-acute-myeloid-leukemia-via-circular-rna-profile-and-bioinformatics-analysis
#11
Wei Li, Chaoqin Zhong, Jun Jiao, Peng Li, Baoxia Cui, Chunyan Ji, Daoxin Ma
Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs, which drew little attention in the past. Recently, limited data showed their promising future to act as biomarkers in human cancer, but the characteristics and functions remain largely unknown in hematopoietic malignancies, especially in leukemia. In this study, with the help of circRNA microarray, we demonstrated the expression profile of circRNAs in acute myeloid leukemia (AML) patients, and identified a large number of circRNAs possibly expressed in a leukemia specific manner...
March 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28281539/extensive-translation-of-circular-rnas-driven-by-n-6-methyladenosine
#12
Yun Yang, Xiaojuan Fan, Miaowei Mao, Xiaowei Song, Ping Wu, Yang Zhang, Yongfeng Jin, Yi Yang, Lingling Chen, Yang Wang, Catherine Cl Wong, Xinshu Xiao, Zefeng Wang
Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N(6)-methyladenosine (m(6)A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells. We discover that consensus m(6)A motifs are enriched in circRNAs and a single m(6)A site is sufficient to drive translation initiation. This m(6)A-driven translation requires initiation factor eIF4G2 and m(6)A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock...
March 10, 2017: Cell Research
https://www.readbyqxmd.com/read/28279183/circles-reshaping-the-rna-world-from-waste-to-treasure
#13
REVIEW
Jing Liu, Tian Liu, Xiaman Wang, Aili He
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions...
March 9, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28277897/high-throughput-sequencing-reveals-circular-substrates-for-an-archaeal-rna-ligase
#14
Hubert F Becker, Alice Heliou, Kamel Djaout, Roxane Lestini, Mireille Regnier, Hannu Myllykallio
It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiological significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates...
March 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/28276108/circrna-hsa_circ_0005105-up-regulates-nampt-expression-and-promotes-chondrocyte-extracellular-matrix-degradation-by-sponging-mir-26a
#15
You Wu, Ying Zhang, Yu Zhang, Jia-Jia Wang
Osteoarthritis (OA) is a chronic disease pathologically characterized by articular cartilage degeneration and damage. Currently, studies have found that circular RNA (circRNA) is involved in intracellular RNA regulating network and is closely related to the occurrence and development of diseases, therefore it may become a new biological marker and therapeutic target. After stimulating chondrocytes with interleukin-1 beta (IL-1β), hsa_circ_0005105 expression was significantly upregulated, while miR-26a expression was significantly inhibited...
March 8, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28265491/fuchs-towards-full-circular-rna-characterization-using-rnaseq
#16
Franziska Metge, Lisa F Czaja-Hasse, Richard Reinhardt, Chistoph Dieterich
Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5' splice site is linked to an upstream 3' splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing...
2017: PeerJ
https://www.readbyqxmd.com/read/28255427/circular-rnas-in-colorectal-cancer-possible-roles-in-regulation-of-cancer-cells
#17
REVIEW
María Isabel Taborda, Sebastián Ramírez, Giuliano Bernal
Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the world and the fourth principal cause of cancer deaths worldwide. Currently, there is a lack of low cost and noninvasive screening tests for CRC, becoming a serious health problem. In this context, a potential biomarker for the early detection of CRC has recently gained attention. Circular RNAs (circRNA), a re-discovered, abundant RNA specie, is a type of noncoding covalent closed RNAs formed from both exonic and intronic sequences. These circular molecules are widely expressed in cells, exceeding the abundance of the traditional linear mRNA transcript...
February 15, 2017: World Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28253710/detection-and-characterization-of-cirs-7-a-potential-promoter-of-the-development-of-cancer
#18
X B Zheng, M Zhang, M Q X
Circular RNAs (circRNAs) are a class of newly-identified non-coding RNA molecules. CircRNAs are conserved across different species and display specific organization, sequence, and expression in disease. Moreover, circRNAs' closed ring structure, insensitivity to RNase, and stability are advantages over linear RNAs in terms of development and application as a new kind of clinical marker. In addition, according to recent studies, circular RNA-7 (ciRS-7) acts as a sponge of miR-7 and thus inhibits its activity...
March 3, 2017: Neoplasma
https://www.readbyqxmd.com/read/28249903/non-coding-effects-of-circular-rna-ccdc66-promote-colon-cancer-growth-and-metastasis
#19
Kuei-Yang Hsiao, Ya-Chi Lin, Sachin Kumar Gupta, Ning Chang, Laising Yen, H Sunny Sun, Shaw-Jenq Tsai
Circular RNA (circRNA) is a class of non-coding RNA whose functions remain mostly unknown. Recent studies indicate circRNA may be involved in disease pathogenesis, but direct evidence is scarce. Here we characterize the functional role of a novel circRNA, circCCDC66, in colorectal cancer (CRC). RNA-Seq data from matched normal and tumor colon tissue samples identified numerous circRNAs specifically elevated in cancer cells, several of which were verified by quantitative RT-PCR. CircCCDC66 expression was elevated in polyps and colon cancer and was associated with poor prognosis...
March 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/28236760/differential-expression-of-circular-rnas-in-glioblastoma-multiforme-and-its-correlation-with-prognosis
#20
Junle Zhu, Jingliang Ye, Lei Zhang, Lili Xia, Hongkang Hu, Heng Jiang, Zhiping Wan, Fei Sheng, Yan Ma, Wen Li, Jun Qian, Chun Luo
OBJECTIVE: The present study aimed to explore the expression profiles of circular RNAs (circRNAs) in glioblastoma multiforme (GBM) in an attempt to identify potential core genes in the pathogenesis of this tumor. METHODS: Differentially expressed circRNAs were screened between tumor tissues from five GBM patients and five normal brain samples using Illumina Hiseq. Bioinformatics analysis was used to analyze their potential function. CircBRAF was further detected in different WHO grades glioma tissues and normal brain tissues...
April 2017: Translational Oncology
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