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Circular rna

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https://www.readbyqxmd.com/read/28334744/stabilization-of-rna-hairpins-using-non-nucleotide-linkers-and-circularization
#1
Agnieszka Kiliszek, Leszek Blaszczyk, Ryszard Kierzek, Wojciech Rypniewski
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334396/quantifying-circular-rna-expression-from-rna-seq-data-using-model-based-framework
#2
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
#3
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/28323040/-machine-learning-based-identification-of-endogenous-cellular-microrna-sponges-against-viral-micrornas
#4
Soowon Kang, Seunghyun Park, Sungroh Yoon, Hyeyoung Min
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions...
March 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28322921/linking-deregulation-of-non-coding-rna-to-the-core-pathophysiology-of-alzheimer-s-disease-an-integrative-review
#5
REVIEW
Mark J Millan
The human genome encodes a vast repertoire of protein non-coding RNAs (ncRNA), some specific to the brain. MicroRNAs, which interfere with the translation of target mRNAs, are of particular interest since their deregulation has been implicated in neurodegenerative disorders like Alzheimer's disease (AD). However, it remains challenging to link the complex body of observations on miRNAs and AD into a coherent framework. Using extensive graphical support, this article discusses how a diverse panoply of miRNAs convergently and divergently impact (and are impacted by) core pathophysiological processes underlying AD: neuroinflammation and oxidative stress; aberrant generation of β-amyloid-42 (Aβ42); anomalies in the production, cleavage and post-translational marking of Tau; impaired clearance of Aβ42 and Tau; perturbation of axonal organisation; disruption of synaptic plasticity; endoplasmic reticulum stress and the unfolded protein response; mitochondrial dysfunction; aberrant induction of cell cycle re-entry; and apoptotic loss of neurons...
March 17, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28297795/-the-potential-use-of-serum-hbv-rna-to-guide-the-functional-cure-of-chronic-hepatitis-b
#6
F M Lu, J Wang, X M Chen, J N Jiang, W H Zhang, J M Zhao, H Ren, J L Hou, N S Xia
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in infected hepatocytes is the main cause of off-therapy viral rebound. The half-life of cccDNA is only 33-50 days, so the conversion of newly synthesized rcDNA to cccDNA in the nucleus is essential for the maintenance of cccDNA pool in infected hepatocytes. Though not directly targeting the existing cccDNA, current nucleos(t)ide analogues (NAs) may exhaust the cccDNA reservoir by blocking the rcDNA formation. Indeed, a prolonged consolidation therapy post loss of serum HBV DNA can achieve sustained remission and thus safe drug discontinuation in a small proportion of chronic hepatitis B (CHB) patients...
February 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
https://www.readbyqxmd.com/read/28296235/the-circular-rna-cirs-7-promotes-app-and-bace1-degradation-in-an-nf-%C3%AE%C2%BAb-dependent-manner
#7
Zhemin Shi, Ting Chen, Qingbin Yao, Lina Zheng, Zhen Zhang, Jingzhao Wang, Zhimei Hu, Hongmei Cui, Yawei Han, Xiaohui Han, Kun Zhang, Wei Hong
The aberrant accumulation of β-amyloid peptide (Aβ) in the brain is a key feature of Alzheimer's disease (AD), and enhanced cleavage of β-amyloid precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) has a major causative role in AD. Despite their prominence in AD pathogenesis, the regulation of BACE1 and APP is incompletely understood. In this study, we report that the circular RNA circular RNA sponge for miR-7 (ciRS-7) has an important role in regulating BACE1 and APP protein levels. Previous studies have shown that ciRS-7, which is highly expressed in the human brain, is down-regulated in the brain of people with AD but the relevance of this finding was not clear...
March 13, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28287427/the-role-and-molecular-mechanism-of-non-coding-rnas-in-pathological-cardiac-remodeling
#8
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/28287172/killing-of-staphylococcus-aureus-and-salmonella-enteritidis-and-neutralization-of-lipopolysaccharide-by-17-residue-bovine-lactoferricins-improved-activity-of-trp-ala-containing-molecules
#9
Ya Hao, Na Yang, Xiumin Wang, Da Teng, Ruoyu Mao, Xiao Wang, Zhanzhan Li, Jianhua Wang
Bovine lactoferricin (LfcinB) has potent antibacterial, antifungal and antiparasitic activities but is also hemolytic. Our objective was to identify LfcinB17-31 derivatives with reduced hemolysis and improved antimicrobial activity via substituting Cys3, Arg4, Gln7, Met10, and Gly14 with more hydrophobic residues. Two peptides, Lfcin4 and Lfcin5, showed higher activity against Staphylococcus aureus and Salmonella enteritidis and lower hemolytic activity than the parent peptide LfcinB17-31. These peptides permeabilized the outer and inner membranes of S...
March 13, 2017: Scientific Reports
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/28283070/circular-concatemers-of-ultra-short-dna-segments-produce-regulatory-rnas
#11
Sarah E Allen, Iris Hug, Sylwia Pabian, Iwona Rzeszutek, Cristina Hoehener, Mariusz Nowacki
In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production...
March 9, 2017: Cell
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
#12
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
#13
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/28280365/downregulation-of-long-noncoding-rna-hotairm1-promotes-monocyte-dendritic-cell-differentiation-through-competitively-binding-to-endogenous-mir-3960
#14
Jiaxuan Xin, Jing Li, Yue Feng, Liyang Wang, Yuan Zhang, Rongcun Yang
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28279183/circles-reshaping-the-rna-world-from-waste-to-treasure
#15
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/28278047/roles-of-the-circular-rna-circ-foxo3-in-breast-cancer-progression
#16
Wei-Yang Lu
No abstract text is available yet for this article.
February 25, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28277897/high-throughput-sequencing-reveals-circular-substrates-for-an-archaeal-rna-ligase
#17
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
#18
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/28272342/the-characterization-of-gsdmb-splicing-and-backsplicing-profiles-identifies-novel-isoforms-and-a-circular-rna-that-are-dysregulated-in-multiple-sclerosis
#19
Giulia Cardamone, Elvezia Maria Paraboschi, Valeria Rimoldi, Stefano Duga, Giulia Soldà, Rosanna Asselta
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune diseases (AIDs). In particular, a growing body of evidence suggests the existence of a pathogenic association between a generalized defect in splicing regulatory genes and multiple sclerosis (MS). Moreover, several studies have documented an unbalance in alternatively-spliced isoforms in MS patients possibly contributing to the disease etiology. In this work, using a combination of PCR-based techniques (reverse-transcription (RT)-PCR, fluorescent-competitive, real-time, and digital RT-PCR assays), we investigated the alternatively-spliced gene encoding Gasdermin B, GSDMB, which was repeatedly associated with susceptibility to asthma and AIDs...
March 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28265491/fuchs-towards-full-circular-rna-characterization-using-rnaseq
#20
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
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