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Circular rna

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https://www.readbyqxmd.com/read/28919414/changes-in-related-circular-rnas-following-er%C3%AE-knockdown-and-the-relationship-to-rbmsc-osteogenesis
#1
Xiaoyun Li, Bojia Peng, Xiaofeng Zhu, Panpan Wang, Yingquan Xiong, Hengrui Liu, Kehuan Sun, Haixia Wang, Ling Ou, Zhidi Wu, Xiaoguang Liu, Haibin He, Shu Mo, Xunqian Peng, Ya Tian, Ronghua Zhang, Li Yang
Recently, several studies have indicated that circular RNAs (circRNAs) play significant roles in various disease; however, Little is known about the chronology of estrogen receptor beta (ERβ) deficiency and altered circRNA expression, or their relationship with osteogenesis. Herein, we show through western-blot and quantitative real-time PCR assays, that when ERβ is silenced, the expression of osteogenesis-related proteins and mRNAs were down-regulated. We then performed RNA-Seq to analyze differential circRNA expression between the control and ERβ knockdown group...
September 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28919308/alternative-splicing-in-cancers-from-aberrant-regulation-to-new-therapeutics
#2
REVIEW
Xiaowei Song, Zhenyu Zeng, Huanhuan Wei, Zefeng Wang
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis...
September 14, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28918159/identification-of-circular-rna-in-the-bombyx-mori-silk-gland
#3
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Bombyx mori is an economically important holometabolous lepidopteran insect. In B. mori endogenous noncoding RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs play crucial biological functions in metamorphosis and sex determination. In addition, circular RNAs (circRNAs) have been recently identified as noncoding RNAs in most common model organisms and show potential as gene regulators. However, to date, there have been few studies on the circRNAs present in the B. mori genome conducted to date. Here, we identified 3916 circRNAs by deep circular transcriptome sequencing using the silk gland of B...
September 13, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28918028/human-dmbt1-derived-cell-penetrating-peptides-for-intracellular-sirna-delivery
#4
Martina Tuttolomondo, Cinzia Casella, Pernille Lund Hansen, Ester Polo, Luciana M Herda, Kenneth A Dawson, Henrik J Ditzel, Jan Mollenhauer
Small interfering RNA (siRNA) is a promising molecule for gene therapy, but its therapeutic administration remains problematic. Among the recently proposed vectors, cell-penetrating peptides show great promise in in vivo trials for siRNA delivery. Human protein DMBT1 (deleted in malignant brain tumor 1) is a pattern recognition molecule that interacts with polyanions and recognizes and aggregates bacteria. Taking advantage of these properties, we investigated whether specific synthetic DMBT1-derived peptides could be used to formulate nanoparticles for siRNA administration...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28913654/discriminating-cirrnas-from-other-lncrnas-using-a-hierarchical-extreme-learning-machine-h-elm-algorithm-with-feature-selection
#5
Lei Chen, Yu-Hang Zhang, Guohua Huang, Xiaoyong Pan, ShaoPeng Wang, Tao Huang, Yu-Dong Cai
As non-coding RNAs, circular RNAs (cirRNAs) and long non-coding RNAs (lncRNAs) have attracted an increasing amount of attention. They have been confirmed to participate in many biological processes, including playing roles in transcriptional regulation, regulating protein-coding genes, and binding to RNA-associated proteins. Until now, the differences between these two types of non-coding RNAs have not been fully uncovered. It is still quite difficult to detect cirRNAs from other lncRNAs using simple techniques...
September 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28910391/different-rates-of-spontaneous-mutation-of-chloroplastic-and-nuclear-viroids-as-determined-by-high-fidelity-ultra-deep-sequencing
#6
Amparo López-Carrasco, Cristina Ballesteros, Vicente Sentandreu, Sonia Delgado, Selma Gago-Zachert, Ricardo Flores, Rafael Sanjuán
Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplast-replicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear potato spindle tuber viroid (PSTVd, Pospiviroidae)...
September 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#7
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28906455/deep-circular-rna-sequencing-provides-insights-into-the-mechanism-underlying-grass-carp-reovirus-infection
#8
Libo He, Aidi Zhang, Lv Xiong, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu, And Yaping Wang
Grass carp hemorrhagic disease, caused by the grass carp reovirus (GCRV), is a major disease that hampers the development of grass carp aquaculture in China. The mechanism underlying GCRV infection is still largely unknown. Circular RNAs (circRNAs) are important regulators involved in various biological processes. In the present study, grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, and 7 days post-infection (dpi). Samples were used to construct and sequence circRNA libraries, and a total of 5052 circRNAs were identified before and after GCRV infection, of which 41 exhibited differential expression compared with controls...
September 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28903484/novel-role-of-fbxw7-circular-rna-in-repressing-glioma-tumorigenesis
#9
Yibing Yang, Xinya Gao, Maolei Zhang, Sheng Yan, Chengjun Sun, Feizhe Xiao, Nunu Huang, Xuesong Yang, Kun Zhao, Huangkai Zhou, Suyun Huang, Bo Xie, Nu Zhang
Background: Circular RNAs (circRNAs) are RNA transcripts that are widespread in the eukaryotic genome. Recent evidence indicates that circRNAs play important roles in tissue development, gene regulation, and carcinogenesis. However, whether circRNAs encode functional proteins remains elusive, although translation of several circRNAs was recently reported. Methods: CircRNA deep sequencing was performed by using 10 pathologically diagnosed glioblastoma samples and their paired adjacent normal brain tissues...
March 1, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28900093/-synthesis-of-circular-dna-templates-with-t4-rna-ligase-for-rolling-circle-amplification
#10
A R Sakhabutdinova, M A Maksimova, R R Garafutdinov
Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28900084/-a-betasatellite-encoded-protein-regulates-key-components-of-gene-silencing-system-in-plants
#11
O Eini
Small circular single-stranded DNA satellites, called betasatellites, have been found in association with some monopartite begomovirus infections. The Cotton leaf curl Multan betasatellite (CLCuMuB) is known to influence symptom induction in cotton leaf curl disease. CLCuMuB contains a single gene, βC1, whose product is a pathogenicity determinant and a suppressor of RNA silencing. Although induction of RNA silencing by RNA and DNA viruses has been well documented in plants, the interactions between betasatellites and the host's silencing machinery remain poorly understood...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28893646/whole-genome-sequence-of-a-carbapenem-resistant-hypermucoviscous-klebsiella-pneumoniae-isolate-swu01-with-capsular-serotype-k47-that-belongs-to-st11-from-a-patient-in-china
#12
Luhua Zhang, Ying Li, Wei Shen, Guangxi Wang, Yingshun Zhou
OBJECTIVES: In recent years, Klebsiella pneumoniae is emerging as a leading cause of nosocomial infection due to the rapid prevalence of multidrug resistant strains, particularly the carbapenem resistant isolates. In this study, we completed the genome sequence of a carbapenem-resistant K. pneumoniae SWU01. METHODS: Antimicrobial susceptibilities and hypermucoviscous phenotype were determined by the disk diffusion method and a positive string test, respectively...
September 8, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28893265/circular-rna_larp4-inhibits-cell-proliferation-and-invasion-of-gastric-cancer-by-sponging-mir-424-5p-and-regulating-lats1-expression
#13
Jing Zhang, Hui Liu, Lidan Hou, Ge Wang, Rui Zhang, Yanxia Huang, Xiaoyu Chen, Jinshui Zhu
BACKGROUND: Non-coding RNAs (ncRNAs) have been shown to regulate gene expression involved in tumor progression of multiple malignancies. Our previous studies indicated that large tumor suppressor kinase 1 (LATS1), a core part of Hippo signaling pathway, functions as a tumor suppressor in gastric cancer (GC). But, the underlying molecular mechanisms by which ncRNAs modulate LATS1 expression in GC remain undetermined. METHODS: The correlation of LATS1 and has-miR-424-5p (miR-424) expression with clinicopathological characteristics and prognosis of GC patients was analyzed by TCGA RNA-sequencing data...
September 11, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28892615/quantitative-proteomics-reveals-the-regulatory-networks-of-circular-rna-cdr1as-in-hepatocellular-carcinoma-cells
#14
Yang Xue, Qian Xiong, Ying Wu, Siting Li, Feng Ge
Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here, we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells...
September 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28878270/membrane-association-of-the-bacterial-riboregulator-hfq-and-functional-perspectives
#15
Antoine Malabirade, Javier Morgado-Brajones, Sylvain Trépout, Frank Wien, Ileana Marquez, Jérôme Seguin, Sergio Marco, Marisela Velez, Arluison Véronique
Hfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28877255/characterization-of-the-microdna-through-the-response-to-chemotherapeutics-in-lymphoblastoid-cell-lines
#16
Pamela Mehanna, Vincent Gagné, Mathieu Lajoie, Jean-François Spinella, Pascal St-Onge, Daniel Sinnett, Ivan Brukner, Maja Krajinovic
Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified. They are on average 100 to 400 bp long and are derived from unique non-repetitive genomic regions with high gene density. MicroDNAs are thought to arise from DNA breaks associated with RNA metabolism or replication slippage. Given the paucity of information on this entirely novel phenomenon, we aimed to get an additional insight into microDNA features by performing the microDNA analysis in 20 independent human lymphoblastoid cell lines (LCLs) prior and after treatment with chemotherapeutic drugs...
2017: PloS One
https://www.readbyqxmd.com/read/28870671/relationship-between-serum-hbv-rna-levels-and-intrahepatic-viral-as-well-as-histologic-activity-markers-in-entecavir-treated-patients
#17
Jing Wang, Yiqi Yu, Guojun Li, Chuan Shen, Zhefeng Meng, Jianming Zheng, Yanhong Jia, Shaolong Chen, Xiao Zhang, MengQi Zhu, Jiangjiang Zheng, Zhangzhang Song, Jing Wu, Lingyun Shao, Peiyu Qian, Xiaona Mao, Xuanyi Wang, Yuxian Huang, Caiyan Zhao, Jiming Zhang, Chao Qiu, Wenhong Zhang
BACKGROUND: In diagnostics, serum hepatitis B virus (HBV)-RNA levels are valuable when the HBV-DNA load in circulation is effectively suppressed by nucleos(t)ide analogue (NUC) therapy. This study aimed to determine the intrahepatic viral replication activity reflected in serum HBV-RNA and whether HBV-RNA contributes to liver histological changes in NUC-treated patients. METHODS: A cross-sectional set of serum and liver biopsy samples was obtained from entecavir-treated patients with undetectable levels of serum HBV-DNA...
September 1, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28864418/the-expression-profiles-of-circrnas-in-lung-tissues-from-rats-with-lipopolysaccharide-induced-acute-respiratory-distress-syndrome-a-microarray-study
#18
Qi-Quan Wan, Di Wu, Qi-Fa Ye
The development of circular RNA (circRNA) microarray has facilitated the study of the role of circRNAs in regulating gene expression through a circRNA-miRNA-mRNA network. In our study, microarray was performed to detect the expression profiles of circRNAs during lipopolysaccharide (LPS)-induced acute respiratory distress syndrome (ARDS). Twenty rats were randomly divided into 2 groups, the control group and the LPS group, 10 rats in each group. Three rats each from both groups were randomly selected. Using circRNA microarray data, we compared the circRNA expression profiles in lung tissues between these 6 rats...
August 31, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28860662/analyses-of-mitogenome-sequences-revealed-that-asian-citrus-psyllids-diaphorina-citri-from-california-were-related-to-those-from-florida
#19
Fengnian Wu, Luci Kumagai, Yijing Cen, Jianchi Chen, Christopher M Wallis, MaryLou Polek, Hongyan Jiang, Zheng Zheng, Guangwen Liang, Xiaoling Deng
Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits "Candidatus Liberibacter asiaticus" (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28860313/smooth-muscle-differentiation-control-comes-full-circle-the-circular-noncoding-rna-circacta2-functions-as-a-mirna-sponge-to-fine-tune-%C3%AE-sma-expression
#20
EDITORIAL
Mary C M Weiser-Evans
No abstract text is available yet for this article.
September 1, 2017: Circulation Research
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