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Circular rna

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https://www.readbyqxmd.com/read/29166612/impediment-of-replication-forks-by-long-non-coding-rna-provokes-chromosomal-rearrangements-by-error-prone-restart
#1
Takaaki Watanabe, Michael Marotta, Ryusuke Suzuki, Scott J Diede, Stephen J Tapscott, Atsushi Niida, Xiongfong Chen, Lila Mouakkad, Anna Kondratova, Armando E Giuliano, Sandra Orsulic, Hisashi Tanaka
Naturally stalled replication forks are considered to cause structurally abnormal chromosomes in tumor cells. However, underlying mechanisms remain speculative, as capturing naturally stalled forks has been a challenge. Here, we captured naturally stalled forks in tumor cells and delineated molecular processes underlying the structural evolution of circular mini-chromosomes (double-minute chromosomes; DMs). Replication forks stalled on the DM by the co-directional collision with the transcription machinery for long non-coding RNA...
November 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/29165116/circular-rna-profiles-in-mouse-lung-tissue-induced-by-radon
#2
Weiwei Pei, Lijing Tao, Leshuai W Zhang, Shuyu Zhang, Jianping Cao, Yang Jiao, Jian Tong, Jihua Nie
BACKGROUND: Radon is a known human lung carcinogen, whose underlying carcinogenic mechanism remains unclear. Recently, circular RNA (circRNA), a class of endogenous non-protein coding RNAs that contain a circular loop, was found to exhibit multiple biological effects. In this study, circRNA profiles in mouse lung tissues between control and radon exposure were analyzed. METHODS: Six mice were exposed to radon at concentration of 100,000 Bq/m(3), 12 h/d, for up to cumulative doses of 60 working level months (WLM)...
April 7, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29159270/the-circular-rna-micra-for-risk-stratification-after-myocardial-infarction
#3
Antonio Salgado-Somoza, Lu Zhang, Melanie Vausort, Yvan Devaux
Background: A significant proportion of patients develop heart failure (HF) after acute myocardial infarction (MI). Predicting this development with novel biomarkers would allow tailoring healthcare to each individual. We recently identified a circular RNA called MICRA which was associated with HF development after MI. Here, we tested whether MICRA was able to risk stratify MI patients. Methods: MICRA was assessed in whole blood samples collected at reperfusion in 472 patients with acute MI...
December 2017: IJC Heart & Vasculature
https://www.readbyqxmd.com/read/29158818/identifying-and-characterizing-circrna-protein-interaction
#4
REVIEW
William W Du, Chao Zhang, Weining Yang, Tianqiao Yong, Faryal Mehwish Awan, Burton B Yang
Circular RNAs have been identified as naturally occurring RNAs that are highly represented in the eukaryotic transcriptome. Although a large number of circRNAs have been reported, circRNA functions remain largely unknown. CircRNAs can function as miRNA sponges, thereby reducing their ability to target mRNAs. We hypothesize that circRNAs may bind, store, sort, and sequester proteins to particular subcellular locations, and act as dynamic scaffolding molecules that modulate protein-protein interactions. Here, we review the biological implication and function of circRNA-protein interaction, and reveal a dynamic model of the interaction in various tissues, development stages and physiological conditions...
2017: Theranostics
https://www.readbyqxmd.com/read/29156822/circular-rna-expression-profiles-reveal-that-hsa_circ_0018289-is-up-regulated-in-cervical-cancer-and-promotes-the-tumorigenesis
#5
Ya-Li Gao, Ming-Yun Zhang, Bo Xu, Li-Jie Han, Shou-Feng Lan, Ju Chen, Yu-Jin Dong, Li-Li Cao
Circular RNAs (circRNAs) are a type of non-coding RNAs that have been identified as critical regulators in various diseases, especially in cancers. However, the expression profiles and functions of circRNAs in cervical cancer are still unclear. In present study, human circRNAs microarray were performed to screen the circRNAs expression in cervical cancer tissue. Microarray analysis revealed 45 significantly expressed circRNAs with 4 fold change. Among these up-regulated circRNAs, hsa_circ_0018289 was validated to be significantly up-regulated in 35 pairs of cervical cancer tissue compared with adjacent normal tissue and cell lines...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156814/screening-circular-rna-expression-patterns-following-focal-cerebral-ischemia-in-mice
#6
Cuiying Liu, Chencheng Zhang, Jian Yang, Xiaokun Geng, Huishan Du, Xunming Ji, Heng Zhao
Circular RNAs (circRNAs) have been demonstrated to act as microRNA (miRNA) sponges and they play important roles in regulating gene expression through a circRNA-miRNA-gene pathway. The specific roles of circRNAs in the pathogenesis of cerebral ischemia, however, are still unclear. Thus, the aim of this study is to determine circRNA expression profiles in the ischemic brain after stroke, which was induced by 45 min of transient middle cerebral artery occlusion (MCAO). The results from the circRNA microarrays revealed that 1027 circRNAs were significantly altered 48 hours after reperfusion in the ischemic brain compared with the sham group...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155438/circular-rnas-mediated-by-transposons-are-associated-with-transcriptomic-and-phenotypic-variation-in-maize
#7
Lu Chen, Pei Zhang, Yuan Fan, Qiong Lu, Qing Li, Jianbing Yan, Gary J Muehlbauer, Patrick S Schnable, Mingqiu Dai, Lin Li
Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies have shown that circRNAs can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNA-Seq on B73 seedling leaves and uncovered 2804 high-confidence maize circRNAs, which show distinct genomic features...
November 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/29152037/complete-genome-sequence-of-pseudomonas-corrugata-strain-rm1-1-4-a-stress-protecting-agent-from-the-rhizosphere-of-an-oilseed-rape-bait-plant
#8
Christin Zachow, Henry Müller, Christina M Laireiter, Ralf Tilcher, Gabriele Berg
10.1601/nm.2592 strain RM1-1-4 is a rhizosphere colonizer of oilseed rape. A previous study has shown that this motile, Gram-negative, non-sporulating bacterium is an effective stress protecting and biocontrol agent, which protects their hosts against abiotic and biotic stresses. Here, we announce and describe the complete genome sequence of P. corrugata RM1-1-4 consisting of a single 6.1 Mb circular chromosome that encodes 5189 protein coding genes and 85 RNA-only encoding genes. Genome analysis revealed genes predicting functions such as detoxifying mechanisms, stress inhibitors, exoproteases, lipoproteins or volatile components as well as rhizobactin siderophores and spermidine...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29151929/identification-of-circular-rna-signature-in-bladder-cancer
#9
Xiao Yang, Wenbo Yuan, Jun Tao, Peng Li, Chengdi Yang, Xiaheng Deng, Xiaolei Zhang, Jingyuan Tang, Jie Han, Jingzi Wang, Pengchao Li, Qiang Lu, Min Gu
Circular RNA (circRNA) comprises a class of endogenous species of RNA consisting of a circular loop that is crucial for genetic and epigenetic regulation. The significance of circRNA in bladder cancer (BCa) remains to be investigated. Here we performed genome‑wide circRNA analysis of 5 paired tumour and adjacent normal tissue samples from BCa patients via next generation sequencing (NGS) technology. Next we confirmed NGS data in a separate set of 32 paired BCa samples using quantitative real-time reverse transcription polymerase chain reaction...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#10
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29144509/circular-rna-expression-is-suppressed-by-androgen-receptor-ar-regulated-adenosine-deaminase-that-acts-on-rna-adar1-in-human-hepatocellular-carcinoma
#11
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
https://www.readbyqxmd.com/read/29137225/circular-rna-expression-profile-and-potential-function-of-hsa_circrna_101238-in-human-thoracic-aortic-dissection
#12
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
https://www.readbyqxmd.com/read/29137151/the-complete-mitogenome-of-the-wood-feeding-cockroach-cryptocercus-meridianus-blattodea-cryptocercidae-and-its-phylogenetic-relationship-among-cockroach-families
#13
Weijun Li, Zongqing Wang, Yanli Che
In this study, the complete mitochondrial genome of Cryptocercus meridianus was sequenced. The circular mitochondrial genome is 15,322 bp in size and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes, and one D-loop region. We compare the mitogenome of C. meridianus with that of C. relictus and C. kyebangensis. The base composition of the whole genome was 45.20%, 9.74%, 16.06%, and 29.00% for A, G, C, and T, respectively; it shows a high AT content (74...
November 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29133306/quaking-inhibits-doxorubicin-mediated-cardiotoxicity-through-regulation-of-cardiac-circular-rna-expression
#14
Shashi K Gupta, Ankita Garg, Christian Bär, Shambhabi Chatterjee, Ariana Foinquinos, Hendrik Milting, Katrin Streckfuss-Bömeke, Jan Fiedler, Thomas Thum
Rationale: RNA-binding proteins (RBPs) have been described to be expressed and regulated in various organs including the heart. Little is known about the role of RBPs in heart failure induced by the chemotherapy drug doxorubicin and their interaction with circular RNAs. Objective: We aimed to identify key RBPs involved in doxorubicin-mediated heart failure and to elucidate their function. Methods and Results: Global transcriptome profiling from murine myocardium exposed to doxorubicin identified five differentially expressed RBPs...
November 13, 2017: Circulation Research
https://www.readbyqxmd.com/read/29132310/rapid-evolutionary-divergence-of-diploid-and-allotetraploid-gossypium-mitochondrial-genomes
#15
Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
BACKGROUND: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29132137/altered-circular-rna-expression-in-patients-with-repeated-implantation-failure
#16
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
https://www.readbyqxmd.com/read/29125888/circular-rna-hsa_circ_0003221-circptk2-promotes-the-proliferation-and-migration-of-bladder-cancer-cells
#17
Zhen-Qiang Xu, Ming-Gen Yang, Hong-Jie Liu, Chen-Qiang Su
Emerging studies have shown that circular RNAs could be ideal biomarkers and even potential therapeutic targets for some tumors, including bladder cancer. However, only a few studies have investigated the circular RNAs in human bladder cancer. The key circular RNA molecules are closely related to bladder cancer and their roles remain largely unknown. Here, we investigated a novel circular RNA molecule, hsa-circ-0003221(circPTK2), which is differentially expressed in bladder carcinoma. Significant differential expression levels of circPTK2 were confirmed with quantitative PCR in 40 pairs of tissue and blood samples from patients with bladder carcinoma...
November 10, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29124095/circular-transcriptome-sequencing-of-the-middle-silk-gland-and-posterior-silk-gland-in-the-bombyx-mori
#18
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
https://www.readbyqxmd.com/read/29122970/a-novel-form-of-rna-double-helix-based-on-g%C3%A2-u-and-c%C3%A2-a-wobble-base-pairing
#19
Ankur Garg, Udo Heinemann
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A(+) wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds...
November 9, 2017: RNA
https://www.readbyqxmd.com/read/29117562/primer-independent-dna-synthesis-by-a-family-b-dna-polymerase-from-self-replicating-mobile-genetic-elements
#20
Modesto Redrejo-Rodríguez, Carlos D Ordóñez, Mónica Berjón-Otero, Juan Moreno-González, Cristian Aparicio-Maldonado, Patrick Forterre, Margarita Salas, Mart Krupovic
Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities...
November 7, 2017: Cell Reports
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