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Circular rna

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https://www.readbyqxmd.com/read/28538214/profiling-and-bioinformatic-analysis-of-circular-rna-expression-regulated-by-c-myc
#1
Qiheng Gou, Ke Wu, Jian-Kang Zhou, Yuxin Xie, Lunxu Liu, Yong Peng
The c-Myc transcription factor is involved in cell proliferation, cell cycle and apoptosis by activating or repressing transcription of multiple genes. Circular RNAs (circRNAs) are widely expressed non-coding RNAs participating in the regulation of gene expression. Using a high-throughput microarray assay, we showed that Myc regulates the expression of certain circRNAs. A total of 309 up- and 252 down-regulated circRNAs were identified. Among them, randomly selected 8 circRNAs were confirmed by real-time PCR...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28534714/profiling-and-bioinformatics-analyses-reveal-differential-circular-rna-expression-in-hypertensive-patients
#2
Na Wu, Ling Jin, Jun Cai
OBJECTIVES: CircRNAs, a novel class of noncoding RNAs, have been reported in many diseases. However, their role in hypertension remains unclear. Here, we aimed to determine the circRNA expression profile in hypertension patients and further construct a circRNA-miRNA-mRNA network for mechanism exploration. METHODS: Plasma circRNA expression profiles were screened by circRNA microarrays and verified by qRT-PCR method. CircRNA-miRNA-mRNA network was established to predict the circRNA targets...
May 23, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28531167/a-role-for-the-host-dna-damage-response-in-hepatitis-b-virus-cccdna-formation-and-beyond
#3
REVIEW
Sabrina Schreiner, Michael Nassal
Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions...
May 22, 2017: Viruses
https://www.readbyqxmd.com/read/28529976/de-novo-generation-and-characterization-of-new-zika-virus-isolate-using-sequence-data-from-a-microcephaly-case
#4
Yin Xiang Setoh, Natalie A Prow, Nias Peng, Leon E Hugo, Gregor Devine, Jessamine E Hazlewood, Andreas Suhrbier, Alexander A Khromykh
Zika virus (ZIKV) has recently emerged and is the etiological agent of congenital Zika syndrome (CZS), a spectrum of congenital abnormalities arising from neural tissue infections in utero. Herein, we describe the de novo generation of a new ZIKV isolate, ZIKVNatal, using a modified circular polymerase extension reaction protocol and sequence data obtained from a ZIKV-infected fetus with microcephaly. ZIKVNatal thus has no laboratory passage history and is unequivocally associated with CZS. ZIKVNatal could be used to establish a fetal brain infection model in IFNAR(-/-) mice (including intrauterine growth restriction) without causing symptomatic infections in dams...
May 2017: MSphere
https://www.readbyqxmd.com/read/28528545/discovery-and-biosynthesis-of-gladiolin-a-burkholderia-gladioli-antibiotic-with-promising-activity-against-mycobacterium-tuberculosis
#5
Lijiang Song, Matthew Jenner, Joleen Masschelein, Cerith Jones, Matthew J Bull, Simon R Harris, Ruben C Hartkoorn, Anthony Vocat, Isolda Romero-Canelón, Paul Coupland, Gordon Webster, Matthew Dunn, Rebecca Weiser, Christopher Paisey, Stewart T Cole, Julian Parkhill, Eshwar Mahenthiralingam, Gregory L Challis
An antimicrobial activity screen of Burkholderia gladioli BCC0238, a clinical isolate from a cystic fibrosis patient, led to the discovery of gladiolin, a novel macrolide antibiotic with potent activity against Mycobacterium tuberculosis H37Rv. Gladiolin is structurally-related to etnangien, a highly unstable antibiotic from Sorangium cellulosum that is also active against Mycobacteria. Like etnangien, gladiolin was found to inhibit RNA polymerase, a validated drug target in M. tuberculosis. However, gladiolin lacks the highly labile hexaene moiety of etnangien and was thus found to possess significantly increased chemical stability...
May 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28523907/unexpected-position-dependent-effects-of-ribose-g-quartets-in-g-quadruplexes
#6
Jun Zhou, Samir Amrane, Frédéric Rosu, Gilmar F Salgado, Yunqiang Bian, Hisae Tateishi-Karimata, Eric Largy, Dursun Nizam Korkut, Anne Bourdoncle, Daisuke Miyoshi, Jian Zhang, Huangxian Ju, Wei Wang, Naoki Sugimoto, Valérie Gabelica, Jean-Louis Mergny
To understand the role of ribose G-quartets and how they affect the properties of G-quadruplex structures, we studied three systems in which one, two, three, or four deoxyribose G-quartets were substituted with ribose G-quartets. These systems were a parallel DNA intramolecular G-quadruplex d(TTGGGTGGGTTGGGTGGGTT) and two tetramolecular G-quadruplexes d(TGGGT) and d(TGGGGT). Thermal denaturation experiments revealed that ribose G-quartets have position-dependent and cumulative effects on G-quadruplex stability...
May 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28523555/alzheimer-s-disease-and-ncrnas
#7
Rotem Maoz, Benjamin P Garfinkel, Hermona Soreq
Alzheimer's disease is a devastating neurodegenerative disorder affecting a significant portion of the world's rapidly growing aging population. In spite of its prevalence, the etiology of the disease is still poorly understood, and effective therapy is all but unavailable. Over the past decade, noncoding RNA, including microRNA (miRNA), has emerged as a major class of regulatory molecules involved in virtually all physiological and disease states. The specificity provided by miRNA sequence complementarity, together with the ability of these molecules to regulate complex networks of genes, has made them exciting novel targets for therapeutic agents...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28520103/circular-rna-mto1-acts-as-the-sponge-of-mir-9-to-suppress-hepatocellular-carcinoma-progression
#8
Dan Han, Jiangxue Li, Huamin Wang, Xiaoping Su, Jin Hou, Yan Gu, Cheng Qian, Yun Lin, Xiang Liu, Mingyan Huang, Nan Li, Weiping Zhou, Yizhi Yu, Xuetao Cao
Non-coding RNAs play important roles in cancer biology, providing potential targets for cancer intervention. As a new class of endogenous non-coding RNAs, circular RNAs (circRNAs) have been recently identified in the development, cell function and certain types of pathological responses, generally acting as microRNA (miRNA) sponge to regulate gene expression. Identifying the deregulated circRNAs and their roles in cancer has attracted much attention. However, the expression profile and function of circRNAs in human hepatocellular carcinoma (HCC) remain to be investigated...
May 18, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28514762/novel-circular-rna-expression-profiles-reflect-progression-of-patients-with-hypopharyngeal-squamous-cell-carcinoma
#9
Shengda Cao, Dongmin Wei, Xu Li, Jieyu Zhou, Wenming Li, Ye Qian, Zhanwang Wang, Guojun Li, Xinliang Pan, Dapeng Lei
Circular RNAs (circRNAs), a novel class of endogenous noncoding RNAs, have been shown to have important roles in a number of diseases, including several types of cancers. We hypothesized that circRNAs are involved in the pathogenesis of hypopharyngeal squamous cell carcinoma (HSCC). To test our hypothesis, we initially compared the expression profiles of circRNAs in 4 paired HSCC and adjacent normal tissue samples by using a circRNA microarray. The microarray data showed that 2392 circRNAs, including 1304 upregulated and 1088 downregulated circRNA transcripts, were significantly dysregulated in the HSCC tissues...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28511668/structural-similarities-and-functional-differences-clarify-evolutionary-relationships-between-trna-healing-enzymes-and-the-myelin-enzyme-cnpase
#10
Gopinath Muruganandam, Arne Raasakka, Matti Myllykoski, Inari Kursula, Petri Kursula
BACKGROUND: Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase)...
May 16, 2017: BMC Biochemistry
https://www.readbyqxmd.com/read/28502821/sasp-regulation-by-noncoding-rna
#11
REVIEW
Amaresh C Panda, Kotb Abdelmohsen, Myriam Gorospe
Noncoding RNAs (ncRNAs), including micro (mi)RNAs, long noncoding (lnc)RNAs, and circular (circ)RNAs, control specific gene expression programs by regulating transcriptional, post-transcriptional, and post-translational processes. Through their broad influence on protein expression and function, ncRNAs have been implicated in virtually all cellular processes such as proliferation, senescence, quiescence, differentiation, apoptosis, and the stress and immune responses. Senescence is a cellular phenotype associated with the physiologic decline of aging and with age-related pathologies...
May 11, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28501625/circular-rnas-roll-into-the-regulatory-network-of-plants
#12
Quan-Feng Li, Yu-Chan Zhang, Yue-Qin Chen, Yang Yu
As a novel class of endogenous non-coding RNAs, circular RNAs (circRNAs) have become a new research hotspot in recent years. The wide distribution of circRNAs in different plant species has been proven. Furthermore, circRNAs show significant tissue-specific expression patterns in plant development and are responsive to a variety of biotic and abiotic stresses, indicating that circRNAs might have important biological functions in plant development. Here, we summarize the current knowledge of plant circRNAs in recent years and discuss views and perspectives on the possible regulatory roles of plant circRNAs, including the function of miRNA sponges, regulating the expression of their parental genes or linear mRNAs, translating into peptides or proteins and responses to different stresses...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28500746/higher-viral-load-and-genetic-diversity-of-hiv-1-in-the-seminal-compartments-than-in-the-blood-of-seven-chinese-homosexual-men-with-early-hiv-1-infection
#13
Yan-Mei Jiao, Guang-Lei Chen, Wei-Jun Zhu, Hui-Huang Huang, Jun-Liang Fu, Wei-Wei Chen, Ming Shi, Tong Zhang, Hao Wu, Fu-Sheng Wang
To date, there have been no reports characterizing the Human Immunodeficiency Virus-1 (HIV-1) in the semen of Chinese men having sex with men (MSM) with early infection of HIV-1.We examined genetic diversity and viral load of HIV-1 in the seminal compartments and blood of Chinese MSM with early HIV-1 infection in this study. Viral load and genetic diversity of HIV-1 in paired samples of semen and blood were analyzed in seven homosexual patients who were with early HIV-1 infection. Levels of HIV-1 RNA and DNA were tested by real-time PCR assays...
May 13, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28499864/role-of-hepatitis-b-core-protein-in-hbv-transcription-and-recruitment-of-histone-acetyltransferases-to-cccdna-minichromosome
#14
Chun Kong Chong, Ching Yan Serene Cheng, Sin Yi Jasmine Tsoi, Fung-Yu Huang, Fen Liu, Wai-Kay Seto, Ching-Lung Lai, Man-Fung Yuen, Danny Ka-Ho Wong
The hepatitis B core protein (HBc) has been suggested to interact with covalently closed circular DNA (cccDNA) and regulate hepatitis B virus (HBV) transcription. However, direct evidence is lacking. We aimed to identify the specific HBc region(s) responsible for transcription regulation and its interaction with cccDNA. Seventeen mutants with mutations at the four arginine-rich clusters of the HBc carboxyl-terminal domain (CTD) were created. The effect of HBc mutations on the levels of HBV DNA, RNA, and hepatitis B surface antigen (HBsAg) were measured...
May 10, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28498369/circular-rna-mediates-cardiomyocyte-death-via-mirna-dependent-upregulation-of-mtp18-expression
#15
Kun Wang, Tian-Yi Gan, Na Li, Cui-Yun Liu, Lu-Yu Zhou, Jin-Ning Gao, Chao Chen, Kao-Wen Yan, Murugavel Ponnusamy, Yu-Hui Zhang, Pei-Feng Li
Circular RNAs (circRNAs) have important roles in several cellular processes. No study has established the pathophysiological role for circRNAs in the heart. Here, we show that a circRNA (mitochondrial fission and apoptosis-related circRNA (MFACR)) regulates mitochondrial fission and apoptosis in the heart by directly targeting and downregulating miR-652-3p; this in turn blocks mitochondrial fission and cardiomyocyte cell death by suppressing MTP18 translation. MTP18 deficiency reduces mitochondrial fission and suppresses cardiomyocyte apoptosis and MI...
June 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28485684/circular-rna-new-member-of-noncoding-rna-with-novel-functions
#16
Kuei-Yang Hsiao, H Sunny Sun, Shaw-Jenq Tsai
A growing body of evidence indicates that circular RNAs are not simply a side product of splicing but a new class of noncoding RNAs in higher eukaryotes. The progression for the studies of circular RNAs is accelerated by combination of several advanced technologies such as next generation sequencing, gene silencing (small interfering RNAs) and editing (CRISPR/Cas9). More and more studies showed that dysregulated expression of circular RNAs plays critical roles during the development of several human diseases...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28461498/cell-geometry-dictates-tnf%C3%AE-induced-genome-response
#17
Aninda Mitra, Saradha Venkatachalapathy, Prasuna Ratna, Yejun Wang, Doorgesh Sharma Jokhun, G V Shivashankar
Cells in physiology integrate local soluble and mechanical signals to regulate genomic programs. Whereas the individual roles of these signals are well studied, the cellular responses to the combined chemical and physical signals are less explored. Here, we investigated the cross-talk between cellular geometry and TNFα signaling. We stabilized NIH 3T3 fibroblasts into rectangular anisotropic or circular isotropic geometries and stimulated them with TNFα and analyzed nuclear translocation of transcription regulators -NFκB (p65) and MKL and downstream gene-expression patterns...
May 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28460063/wopper-web-server-for-position-related-data-analysis-of-gene-expression-in-prokaryotes
#18
Simone Puccio, Giorgio Grillo, Flavio Licciulli, Marco Severgnini, Sabino Liuni, Silvio Bicciato, Gianluca De Bellis, Francesco Ferrari, Clelia Peano
The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28458561/novel-insights-into-circular-rnas-in-clinical-application-of-carcinomas
#19
REVIEW
Dawei Rong, Weiwei Tang, Zhouxiao Li, Jian Zhou, Junfeng Shi, Hanjin Wang, Hongyong Cao
Circular RNAs (circRNAs), formed by nonsequential back-splicing of pre-messenger RNA (pre-mRNA) transcripts, have been widely concerned in recent years. With advances in high-throughput RNA sequencing (RNA-seq) technology, previous work has revealed that a large number of circRNAs, which are endogenous, abundant and stable in mammalian cells, may be involved in atherosclerotic vascular disease risk, neurological disorders, prion diseases and carcinomas. Remarkably, interaction between circRNAs and microRNA has already been observed to perform a significant role in a variety of cancers, including gastric cancer and colorectal cancer...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28457014/unusual-dimerization-of-a-bccsp-mutant-leads-to-reduced-conformational-dynamics
#20
Alonso I Carvajal, Gabriel Vallejos, Elizabeth A Komives, Victor Castro-Fernández, Diego A Leonardo, Richard C Garratt, César A Ramírez-Sarmiento, Jorge Babul
Cold shock proteins (Csp) constitute a family of ubiquitous small proteins that act as RNA-chaperones to avoid cold-induced termination of translation. All members contain two subdomains composed of 2 and 3 β-strands respectively, which are connected by a hinge loop and fold into a β-barrel. Bacillus caldolyticus Csp (BcCsp) is one of the most studied members of the family in terms of its folding, function and structure. This protein has been described as a monomer in solution, although a recent crystal structure showed dimerization via domain swapping (DS)...
April 29, 2017: FEBS Journal
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