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Marco Ragusa, Cristina Barbagallo, Duilia Brex, Angela Caponnetto, Matilde Cirnigliaro, Rosalia Battaglia, Davide Barbagallo, Cinzia Di Pietro, Michele Purrello
Over the past few years, noncoding RNAs (ncRNAs) have been extensively studied because of the significant biological roles that they play in regulation of cellular mechanisms. ncRNAs are associated to higher eukaryotes complexity; accordingly, their dysfunction results in pathological phenotypes, including cancer. To date, most research efforts have been mainly focused on how ncRNAs could modulate the expression of protein-coding genes in pathological phenotypes. However, recent evidence has shown the existence of an unexpected interplay among ncRNAs that strongly influences cancer development and progression...
2017: International Journal of Genomics
Liang Shi, Peijian Yan, Yuelong Liang, Yin Sun, Jiliang Shen, Senjun Zhou, Hui Lin, Xiao Liang, Xiujun Cai
Hepatocellular carcinoma (HCC) is a heterogeneous malignancy as a result of complex genetic and epigenetic alterations. HCC is characterized by a clear gender disparity for which there is lack of a clear mechanistic understanding. Androgen receptor (AR) is thought to be critical for such bias. Meanwhile, the potential function of circular RNA (circRNA), regulated by RNA editing enzyme, remained largely unknown in malignancy till now. By utilizing circRNA microarray survey coupled with in vitro analysis, we analyzed the influence of AR on circRNA expression in HCC...
November 16, 2017: Cell Death & Disease
Meisheng Zou, Chixiong Huang, Xinzhong Li, Xiang He, Yanmei Chen, Wangjun Liao, Yulin Liao, Jie Sun, Ze Liu, Lintao Zhong, Jianping Bin
Objective: To assess the circular RNAs (circRNAs) expression profile and explore the potential functions in human thoracic aortic dissection (TAD). Methods: The differentially expressed circRNAs profiles of the aortic segments between human type A TAD patients (n=3) and age-matched normal donors (NA; n=3) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was used to validate the expression pattern of circRNAs, parental genes, and hsa-miR-320a; Western blotting confirmed MMP9 expression with additional samples...
October 10, 2017: Oncotarget
Lin Liu, Lifei Li, Xiaoling Ma, Feng Yue, Yiqing Wang, Liyan Wang, Panpan Jin, Xuehong Zhang
BACKGROUND/AIMS: CircRNAs play an important role in regulating gene expression and the specific role of circRNAs in the pathogenesis of repeated implantation failure remains unclear. The aim of this study is to assess the differentially expressed circRNAs in patients with repeated implantation failure. METHODS: We screened circRNA expression profiles in endometrial biopsies taken from six women with repeated implantation failure and control group using circRNA microarray...
November 13, 2017: Cellular Physiology and Biochemistry
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRX2577343 and SRX2577342)...
December 2017: Data in Brief
Fan Zhuo, Huashan Lin, Zhixin Chen, Zhijun Huang, Jiaping Hu
Colorectal cancer (CRC) remains a major health problem worldwide and the detailed mechanisms of CRC still need further understanding. Circular RNAs (circRNAs), a special class of endogenous RNAs, have emerged recently as a new potential player in governing fundamental biological process and cancer progression. In this study, we chose circRNA0003906 as a targeted circRNA to evaluate its expression pattern and clinical value in CRC patients. circRNA0003906 expression level in 6 CRC cell lines and 122 paired CRC tissues was measured by quantitative real-time polymerase chain reaction...
2017: OncoTargets and Therapy
Nian Deng, Longyang Li, Jinghao Gao, Jun Zhou, Yan Wang, Chao Wang, Yong Liu
Circular RNAs (circRNAs) have recently shown capabilities as gene regulators in mammals. Some of them interact with microRNAs (miRNAs) and function as sponges to affect related miRNAs' activities. In this study, the molecular function of circRNA_0009910 and its potential downstream miRNA targets were explored. The expression levels of hsa_circ_0009910 were found to be overexpressed in osteosarcoma (OS) cells. Knockdown of circ_0009910 induced cell proliferation inhibition, cell cycle arrest, and apoptosis in OS cells...
November 5, 2017: Biochemical and Biophysical Research Communications
Lesca M Holdt, Alexander Kohlmaier, Daniel Teupser
Protein-coding and noncoding genes in eukaryotes are typically expressed as linear messenger RNAs, with exons arranged colinearly to their genomic order. Recent advances in sequencing and in mapping RNA reads to reference genomes have revealed that thousands of genes express also covalently closed circular RNAs. Many of these circRNAs are stable and contain exons, but are not translated into proteins. Here, we review the emerging understanding that both, circRNAs produced by co- and posttranscriptional head-to-tail "backsplicing" of a downstream splice donor to a more upstream splice acceptor, as well as circRNAs generated from intronic lariats during colinear splicing, may exhibit physiologically relevant regulatory functions in eukaryotes...
November 7, 2017: Cellular and Molecular Life Sciences: CMLS
Ying Bai, Yuan Zhang, Bing Han, Li Yang, Xufeng Chen, Rongrong Huang, Fangfang Wu, Jie Chao, Pei Liu, Gang Hu, John H Zhang, Honghong Yao
Circular RNAs (circRNAs) are highly expressed in the central nervous system and regulate physiological and pathophysiological processes. However, the potential role of circRNAs in stroke remains largely unknown. Here, we show that the circular RNA DLGAP4 (circDLGAP4) functions as an endogenous microRNA-143 (miR-143) sponge to inhibit miR-143 activity, resulting in the inhibition of HECT domain E3 ubiquitin protein ligase 1 (HECTD1) expression. CircDLGAP4 levels were significantly decreased in the plasma of acute ischemic stroke patients (13 females and 13 males) and in a mouse stroke model...
November 7, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
October 3, 2017: Oncotarget
Hu Tao, Qi Xiong, Feng Zhang, Nian Zhang, Yang Liu, Xiaojun Suo, Xiaofeng Li, Qianping Yang, Mingxin Chen
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...
October 26, 2017: Genomics
Jing Feng, Yu Xiang, Siyu Xia, Huan Liu, Jun Wang, Fatma Muge Ozguc, Lijun Lei, Ruoshan Kong, Lixia Diao, Chunjiang He, Leng Han
Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. However, there is no existing tool to visualize and explore circRNAs. Therefore, we introduce CircView, a user-friendly visualization tool for circRNAs detected from existing tools...
June 30, 2017: Briefings in Bioinformatics
Handong Sun, Weiwei Tang, Dawei Rong, Hui Jin, Kai Fu, Wenling Zhang, Zhaojing Liu, Hongyong Cao, Xiufeng Cao
BACKGROUND: Circular RNAs (circRNAs) have been found playing important roles in regulating cancer progression. Human circRNA microarray was performed to screen for abnormally expressed circRNA in gastric cancer tissues. In this study, we are aimed to investigate the relationship between a new circular RNA named hsa_circ_0000520 and gastric cancer development. METHODS: The hsa_circ_0000520 levels were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in gastric tissue, cell and plasma levels, respectively...
October 18, 2017: Cancer Biomarkers: Section A of Disease Markers
Tianwen Li, Yongfu Shao, Liyun Fu, Yi Xie, Linwen Zhu, Weiliang Sun, Rui Yu, Bingxiu Xiao, Junming Guo
To observe the diagnostic values of circular RNAs (circRNAs), their expression profiles between gastric cancer patients' plasma and healthy controls were first assessed by circRNA microarray. Then, circRNA levels were measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR), respectively. A total of 343 differentially expressed circRNAs were found. The top 10 elevated circRNAs in patients were hsa_circ_0088300, hsa_circ_0075825, hsa_circ_0019172, hsa_circ_0000220, hsa_circ_0035277, hsa_circ_0000301, hsa_circ_0000189, hsa_circ_0090080, hsa_circ_0001888, and hsa_circ_0001874...
November 2, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
Yu Zhang, Wei Liang, Peng Zhang, Jingyan Chen, Hui Qian, Xu Zhang, Wenrong Xu
CircRNAs are a class of RNA molecules that structurally form closed loops. CircRNAs are abundant in eukaryotic transcripts and show certain levels of tissue and cell specificity. CircRNAs have been suggested to regulate gene expression at transcriptional, post-transcriptional, and translational levels. An increasing number of studies have shown that circRNAs play important roles in the development and progression of diseases including cancer. In particular, circRNAs have shown great potential in cancer diagnosis, prognosis, and therapy...
November 2, 2017: Journal of Experimental & Clinical Cancer Research: CR
Cong Fu, Renrong Lv, Guangqi Xu, Linfeng Zhang, Jianhai Bi, Li Lin, Xiaowen Liu, Ran Huo
BACKGROUND: Circular RNAs (circRNAs) are a recently identified class of noncoding RNAs that participate in several physiological processes. However, the expression of circRNAs in infantile hemangioma (IH) remains unknown. METHODS: The profile of circRNAs was assessed by microarray in four pairs of IH and adjacent skin tissues. The expression of circRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, circRNA-microRNAs (miRNA)-mRNA networks were constructed using bioinformatics tools...
2017: PloS One
Chaofang Zhong, Shaojun Yu, Maozhen Han, Jiahuan Chen, Kang Ning
The single-cell analysis is becoming a powerful method for early detection of the abnormal variant in tissues, especially for profiling a small number of heterogeneous cells. With the advancement of sequencing technologies, many types of non-coding elements including miRNAs and lncRNAs which shed light on their heterogeneous patterns and functions among cells, have been profiled at the single-cell level. However, the complete picture of circRNA profile at single-cell level is still lacking. In this study, RNA-Seq data obtained from single HEK293T cells have been used to analyze expressions and functions of heterogeneous circRNA profiles...
October 31, 2017: Scientific Reports
Chun-Ying Yu, Tung-Cheng Li, Yi-Ying Wu, Chan-Hsien Yeh, Wei Chiang, Ching-Yu Chuang, Hung-Chih Kuo
Accumulating evidence indicates that circular RNAs (circRNAs) are abundant in the human transcriptome. However, their involvement in biological processes, including pluripotency, remains mostly undescribed. We identified a subset of circRNAs that are enriched in undifferentiated human embryonic stem cells (hESCs) and demonstrated that two, circBIRC6 and circCORO1C, are functionally associated with the pluripotent state. Mechanistically, we found that circBIRC6 is enriched in the AGO2 complex and directly interacts with microRNAs, miR-34a, and miR-145, which are known to modulate target genes that maintain pluripotency...
October 27, 2017: Nature Communications
Xuefeng Wei, Hui Li, Jiameng Yang, Dan Hao, Dong Dong, Yongzhen Huang, Xianyong Lan, Martin Plath, Chuzhao Lei, Fengpeng Lin, Yueyu Bai, Hong Chen
Circular RNAs (circRNAs) have been identified from various tissues and species, but their regulatory functions during developmental processes are not well understood. We examined circRNA expression profiles of two developmental stages of bovine skeletal muscle (embryonic and adult musculus longissimus) to provide first insights into their potential involvement in bovine myogenesis. We identified 12 981 circRNAs and annotated them to the Bos taurus reference genome, including 530 circular intronic RNAs (ciRNAs)...
October 26, 2017: Cell Death & Disease
Dawei Rong, Handong Sun, Zhouxiao Li, Shuheng Liu, Chaoxi Dong, Kai Fu, Weiwei Tang, Hongyong Cao
Circular RNAs (circRNAs), a novel class of long noncoding RNAs, are characterized by a covalently closed continuous loop without 5' or 3' polarities structure and have been widely found in thousands of lives including plants, animals and human beings. Utilizing the high-throughput RNA sequencing (RNA-seq) technology, recent findings have indicated thata great deal of circRNAs, which are endogenous, stable, widely expressed in mammalian cells, often exhibit cell type-specific, tissue-specific or developmental-stage-specific expression...
September 22, 2017: Oncotarget
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