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Circular rna

Wenjia Xia, Mantang Qiu, Rui Chen, Siwei Wang, Xuechun Leng, Jie Wang, Youtao Xu, Jingwen Hu, Gaochao Dong, Prof Lin Xu, Rong Yin
Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent and deadly types of cancer worldwide especially in Eastern Asia and the prognosis of ESCC remain poor. Recent evidence suggests that circular RNAs (circRNAs) play important roles in multiple diseases, including cancer. In this study, we characterized a novel circRNA termed hsa_circ_0067934 in ESCC tumor tissues and cell lines. We analyzed a cohort of 51 patients and found that hsa_circ_0067934 was significantly overexpressed in ESCC tissues compared with paired adjacent normal tissues...
October 18, 2016: Scientific Reports
Guoyun Zhang, Aiguo Duan, Jianguo Zhang, Caiyun He
Long non-coding RNAs (lncRNAs), which are >200nt longer transcripts, potentially play important roles in almost all biological processes in plants and mammals. However, the functions and profiles of lncRNAs in fruit is less understood. Therefore, it is urgent and necessary to identify and analyze the functions of lncRNAs in sea buckthorns. Using RNA-sequencing, we synthetically identified lncRNAs in mature fruit from the red and yellow sea buckthorn. We obtained 567,778,938 clean reads from six samples and identified 3428 lncRNAs in mature fruit, including 2498 intergenic lncRNAs, 593 anti-sense lncRNAs, and 337 intronic lncRNAs...
October 14, 2016: Gene
A Bonizzato, E Gaffo, G Te Kronnie, S Bortoluzzi
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program...
October 14, 2016: Blood Cancer Journal
Chu-Yu Ye, Xingchen Zhang, Qinjie Chu, Chen Liu, Yongyi Yu, Weiqin Jiang, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo
Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice...
October 14, 2016: RNA Biology
Linda Szabo, Julia Salzman
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases...
October 14, 2016: Nature Reviews. Genetics
Krystyna Makowska, Slawomir Gonkowski, Lukasz Zielonka, Michal Dabrowski, Jaroslaw Calka
T-2 toxin is a mycotoxin produced by some Fusarium species, which may affect the synthesis of DNA and RNA and causes various pathological processes. Till now, the influence of T-2 toxin on the enteric nervous system (ENS) located in the wall of gastrointestinal tract has not been studied. On the other hand, cocaine- and amphetamine-regulated transcript (CART) is one of enteric neuronal factors, whose exact functions in the intestines still remain not fully explained. The present study describes the influence of low doses of T-2 toxin on CART-positive neuronal structures in porcine stomach, duodenum, and descending colon...
October 13, 2016: Neurotoxicity Research
Winston Koh, Veronica Gonzalez, Sivaraman Natarajan, Robert Carter, Patrick O Brown, Charles Gawad
Circular RNAs comprise a poorly understood new class of noncoding RNA. In this study, we used a combination of targeted deletion, high-resolution splicing detection, and single-cell sequencing to deeply probe ASXL1 circular splicing. We found that efficient circular splicing required the canonical transcriptional start site and inverted AluSx elements. Sequencing-based interrogation of isoforms after ASXL1 overexpression identified promiscuous linear splicing between all exons, with the two most abundant non-canonical linear products skipping the exons that produced the circular isoforms...
2016: PloS One
Sang C Lee, Jack Zhang, Josh Strom, Danzhou Yang, Thai Nho Dinh, Kyle Kappeler, Qin M Chen
Inhibition of protein synthesis serves as a general measure of cellular consequence to chemical stress. A few proteins are translated selectively and influence cell fate. How these proteins can bypass the general control of translation remains unknown. We found that low to mild doses of oxidants induce de novo translation of NRF2 protein. Here we demonstrate the presence of a G-quadruplex structure in 5' Untranslated Region (5' UTR) of NRF2 mRNA, as measured by Circular Dichroism, Nuclear Magnetic Resonance, and Dimethylsulfate Footprinting...
October 10, 2016: Molecular and Cellular Biology
Xiaoping Chen, Ping Han, Tao Zhou, Xuejiang Guo, Xiaofeng Song, Yan Li
It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb...
October 11, 2016: Scientific Reports
Jen-Yu Liao, Irina Anosova, Saikat Bala, Wade D Van Horn, John C Chaput
G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na(+) ) and potassium (K(+) ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-L-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif...
October 7, 2016: Biopolymers
Yi-Zhen Xie, Fenghua Yang, Weijiang Tan, Xiangmin Li, Chunwei Jiao, Ren Huang, Burton B Yang
To examine the role of oral Ganoderma spore oil in cardiovascular disease, we used transverse aortic constriction (TAC) in mice to model pressure overload-induced cardiomyopathy. Our preliminary results demonstrated a potential cardioprotective role for spore oil extracted from Ganoderma. We found that Ganoderma treatment normalized ejection fraction and corrected the fractional shortening generated by TAC. We also found evidence of reduced left ventricular hypertrophy as assessed by left ventricular end diastolic diameter...
2016: Oncoscience
Helena Guiset Miserachs, Daniela Donghi, Richard Börner, Silke Johannsen, Roland K O Sigel
RNA G-quadruplexes, as their well-studied DNA analogs, require the presence of cations to fold and remain stable. This is the first comprehensive study on the interaction of RNA quadruplexes with metal ions. We investigated the formation and stability of two highly conserved and biologically relevant RNA quadruplex-forming sequences (24nt-TERRA and 18nt-NRAS) in the presence of several monovalent and divalent metal ions, namely Li(+), Na(+), K(+), Rb(+), Cs(+), NH4(+), Mg(2+), Ca(2+), Sr(2+), and Ba(2+). Circular dichroism was used to probe the influence of these metal ions on the folded fraction of the parallel G-quadruplexes, and UV thermal melting experiments allowed to assess the relative stability of the structures in each cationic condition...
October 4, 2016: Journal of Biological Inorganic Chemistry: JBIC
Peng-Cheng Fu, Yan-Zhao Zhang, Hui-Min Geng, Shi-Long Chen
BACKGROUND: The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). METHODS: Using high throughput sequencing technology, we got the complete nucleotide sequence of the G...
2016: PeerJ
Thanh Hoa Le, Nga Thi Bich Nguyen, Khue Thi Nguyen, Huong Thi Thanh Doan, Do Trung Dung, David Blair
The complete mitochondrial (mt) genome of the trematode Echinochasmus japonicus Tanabe, 1926 was fully determined and annotated. The circular mt molecule of this species is 15,865bp in length, containing 12 protein-coding genes (arranged in the following order: cox3-cob-nad4L-nad4-atp6-nad2-nad1-nad3-cox1-cox2-nad6-nad5), two ribosomal RNA genes (rrnL and rrnS) and 22 transfer RNA genes (trnH; trnQ; trnF; trnM; trnV; trnA; trnD; trnN; trnP; trnI; trnK; trnS1(AGN); trnW; trnT; trnC; trnL1(CUN); trnS2(UCN); trnL2(UUN); trnG; and trnE)...
October 1, 2016: Infection, Genetics and Evolution
Bhumika Ray, Shweta Agarwal, Heena Kadian, Kaweri Gambhir, Parag Sharma, Ranjana Mehrotra
Mitoxantrone (1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]ethyl]amino]-9,10-anthracenedione) is a synthetically designed antineoplastic agent and structurally similar to classical anthracyclines. It is widely used as a potent chemotherapeutic component against various kinds of cancer and possesses lesser cardio-toxic effects with respect to naturally occurring anthracyclines. In the present study, we have investigated the binding features of mitoxantrone-tRNA complexation at physiological pH using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and UV-visible absorption spectroscopic techniques...
August 9, 2016: Journal of Biomolecular Structure & Dynamics
Davide S Sardina, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Posttranscriptional cross talk and communication between genes mediated by microRNA response element (MREs) yield large regulatory competing endogenous RNA (ceRNA) networks. Their inference may improve the understanding of pathologies and shed new light on biological mechanisms. A variety of RNA: messenger RNA, transcribed pseudogenes, noncoding RNA, circular RNA and proteins related to RNA-induced silencing complex complex interacting with RNA transfer and ribosomal RNA have been experimentally proved to be ceRNAs...
September 26, 2016: Briefings in Bioinformatics
C Xie, X Jin, H Su
No abstract text is available yet for this article.
October 1, 2016: International Journal of Radiation Oncology, Biology, Physics
Franceli Rodrigues Kulcheski, Ana Paula Christoff, Rogerio Margis
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. The development of deep sequencing of ribosomal RNA (rRNA)-depleted RNA libraries, associated with improved computational tools, has provided the identification of several new circRNAs in all sorts of organisms, from protists, plants and fungi to animals. Recently, it was discovered that endogenous circRNAs can work as microRNA (miRNA) sponges. This means that the circRNAs bind to miRNAs and consequently repress their function, providing a new model of action for this class of ncRNA, as well as indicating another mechanism that regulates miRNA activity...
November 20, 2016: Journal of Biotechnology
Sabine Müller, Bettina Appel
Over the past two decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 years ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics...
September 26, 2016: RNA Biology
Kazuhiro Umezawa, Tomohiro Watanabe, Aya Miura, Hisaya Kojima, Manabu Fukui
Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria belonging to the family Acidiferrobacteraceae in the order Acidiferrobacterales. The type strains of these species, strain skN76(T) and strain HA5(T), were isolated from lakes in Japan. Here we describe the complete genome sequences of Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). The genome of Sulfurifustis variabilis skN76(T) consists of one circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences...
2016: Standards in Genomic Sciences
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