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Circular rna

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https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#1
A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28636993/polymorphisms-and-expression-pattern-of-circular-rna-circ-itch-contributes-to-the-carcinogenesis-of-hepatocellular-carcinoma
#2
Wenzhi Guo, Jiakai Zhang, Dongyu Zhang, Shengli Cao, Gongquan Li, Shuijun Zhang, Zhihui Wang, Peihao Wen, Han Yang, Xiaoyi Shi, Jie Pan, Hua Ye
Hepatocellular carcinoma (HCC) ranks the sixth most common cancer and the third cause of cancer-related mortality worldwide. Recent studies identified that circ-ITCH Suppresses mutiple cancers proliferation via inhibiting the Wnt/beta-Catenin pathway. In current study, conducted a genetic association study together with epidemiological follow-up study to delineate the role of circ-ITCH in the development and progression of HCC. we found rs10485505 (adjusted OR =1.18; 95% CI=1.06-1.31; P value =3.1×10-3) and rs4911154 (adjusted OR =1...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636394/synthesis-of-rna-5-azides-from-2-o-pivaloyloxymethyl-protected-rnas-and-their-reactivity-in-azide-alkyne-cycloaddition-reactions
#3
Marcin Warminski, Joanna Kowalska, Jacek Jemielity
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m(7)G capped RNAs) were obtained...
June 21, 2017: Organic Letters
https://www.readbyqxmd.com/read/28634583/circular-rnas-biogenesis-function-and-role-in-human-diseases
#4
REVIEW
John Greene, Anne-Marie Baird, Lauren Brady, Marvin Lim, Steven G Gray, Raymond McDermott, Stephen P Finn
Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#5
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629193/telomere-biology-insights-into-an-intriguing-phenomenon
#6
REVIEW
Shriram Venkatesan, Aik Kia Khaw, Manoor Prakash Hande
Bacteria and viruses possess circular DNA, whereas eukaryotes with typically very large DNA molecules have had to evolve into linear chromosomes to circumvent the problem of supercoiling circular DNA of that size. Consequently, such organisms possess telomeres to cap chromosome ends. Telomeres are essentially tandem repeats of any DNA sequence that are present at the ends of chromosomes. Their biology has been an enigmatic one, involving various molecules interacting dynamically in an evolutionarily well-trimmed fashion...
June 19, 2017: Cells
https://www.readbyqxmd.com/read/28625552/coordinated-circrna-biogenesis-and-function-with-nf90-nf110-in-viral-infection
#7
Xiang Li, Chu-Xiao Liu, Wei Xue, Yang Zhang, Shan Jiang, Qing-Fei Yin, Jia Wei, Run-Wen Yao, Li Yang, Ling-Ling Chen
Circular RNAs (circRNAs) generated via back-splicing are enhanced by flanking complementary sequences. Expression levels of circRNAs vary under different conditions, suggesting participation of protein factors in their biogenesis. Using genome-wide siRNA screening that targets all human unique genes and an efficient circRNA expression reporter, we identify double-stranded RNA-binding domain containing immune factors NF90/NF110 as key regulators in circRNA biogenesis. NF90/NF110 promote circRNA production in the nucleus by associating with intronic RNA pairs juxtaposing the circRNA-forming exon(s); they also interact with mature circRNAs in the cytoplasm...
June 12, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28625551/sensing-self-and-foreign-circular-rnas-by-intron-identity
#8
Y Grace Chen, Myoungjoo V Kim, Xingqi Chen, Pedro J Batista, Saeko Aoyama, Jeremy E Wilusz, Akiko Iwasaki, Howard Y Chang
Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail with largely unknown functions. Here we show that transfection of purified in vitro generated circRNA into mammalian cells led to potent induction of innate immunity genes and confers protection against viral infection. The nucleic acid sensor RIG-I is necessary to sense foreign circRNA, and RIG-I and foreign circRNA co-aggregate in cytoplasmic foci. CircRNA activation of innate immunity is independent of a 5' triphosphate, double-stranded RNA structure, or the primary sequence of the foreign circRNA...
June 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28624226/transcriptome-wide-investigation-of-mrna-circrna-in-mir-184-and-its-r-57c-u-mutant-type-treatment-of-human-lens-epithelial-cells
#9
Yueqiu Luo, Siyu Liu, Ke Yao
m-miR-184 (mutant miR-184, r.57c > u) appears in familial hereditary ocular diseases, including keratoconus, cataracts, EDICT (endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning) syndrome, severe keratoconus, and non-ectatic corneal thinning. The biological function of m-miR-184 in these ocular diseases remains unclear. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using two different RNA libraries, we sequenced the complete transcriptome of HLE cells treated with miR-184, m-miR-184, and a negative control...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28624224/optimizing-the-dna-donor-template-for-homology-directed-repair-of-double-strand-breaks
#10
Fei Song, Knut Stieger
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) technology enables rapid and precise genome editing at any desired genomic position in almost all cells and organisms. In this study, we analyzed the impact of different repair templates on the frequency of homology-directed repair (HDR) and non-homologous end joining (NHEJ). We used a stable HEK293 cell line expressing the traffic light reporter (TLR-3) system to quantify HDR and NHEJ events following transfection with Cas9, eight different guide RNAs, and a 1,000 bp donor template generated either as circular plasmid, as linearized plasmid with long 3' or 5' backbone overhang, or as PCR product...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28624198/emerging-roles-of-circrna-related-to-the-mechanical-stress-in-human-cartilage-degradation-of-osteoarthritis
#11
Qiang Liu, Xin Zhang, Xiaoqing Hu, Lan Yuan, Jin Cheng, Yanfang Jiang, Yingfang Ao
Circular RNAs (circRNAs) are involved in the development of various diseases; however, knowledge on circRNAs in osteoarthritis (OA) is limited. This study aims to identify circRNA expression in different regions affected by OA and to explore the function of mechanical stress-related circRNAs (circRNAs-MSR) in cartilage. Bioinformatics was employed to predict the interaction of circRNAs and mRNAs in the cartilage. Loss-of-function experiments for circRNAs-MSR were performed in vitro. A total of 104 circRNAs were differentially expressed in damaged versus intact cartilage...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28622299/a-circular-rna-promotes-tumorigenesis-by-inducing-c-myc-nuclear-translocation
#12
Qi Yang, William W Du, Nan Wu, Weining Yang, Faryal Mehwish Awan, Ling Fang, Jian Ma, Xiangmin Li, Yan Zeng, Zhenguo Yang, Jun Dong, Azam Khorshidi, Burton B Yang
Circular RNAs (circRNAs) are a subclass of noncoding RNAs widely expressed in mammalian cells. We report here the tumorigenic capacity of a circRNA derived from angiomotin-like1 (circ-Amotl1). Circ-Amotl1 is highly expressed in patient tumor samples and cancer cell lines. Single-cell inoculations using circ-Amotl1-transfected tumor cells showed a 30-fold increase in proliferative capacity relative to control. Agarose colony-formation assays similarly revealed a 142-fold increase. Tumor-take rate in nude mouse xenografts using 6-day (219 cells) and 3-day (9 cells) colonies were 100%, suggesting tumor-forming potential of every cell...
June 16, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28621679/circular-rnas-a-novel-type-of-biomarker-and-genetic-tools-in-cancer
#13
REVIEW
Yi-Neng Han, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
Circular RNAs (circRNAs) are a novel type of universal and diverse endogenous noncoding RNAs (ncRNAs) and they form a covalently closed continuous loop without 5' or 3' tails unlike linear RNAs. Most circRNAs are presented with characteristics of abundance, stability, conservatism, and often exhibiting tissue/developmental-stage-specific expression. CircRNAs are generated either from exons or introns by back splicing or lariat introns. CircRNAs play important roles as miRNA sponges, gene transcription and expression regulators, RNA-binding protein (RBP) sponges and protein/peptide translators...
June 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28621670/analyses-of-a-whole-genome-inter-clade-recombination-map-of-hepatitis-delta-virus-suggest-a-host-polymerase-driven-and-viral-rna-structure-promoted-template-switching-mechanism-for-viral-rna-recombination
#14
Mei Chao, Tzu-Chi Wang, Chia-Chi Lin, Robert Yung-Liang Wang, Wen-Bin Lin, Shang-En Lee, Ying-Yu Cheng, Chau-Ting Yeh, Shan-Bei Iang
The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28611215/genome-wide-crispr-screen-identifies-hnrnpl-as-a-prostate-cancer-dependency-regulating-rna-splicing
#15
Teng Fei, Yiwen Chen, Tengfei Xiao, Wei Li, Laura Cato, Peng Zhang, Maura B Cotter, Michaela Bowden, Rosina T Lis, Shuang G Zhao, Qiu Wu, Felix Y Feng, Massimo Loda, Housheng Hansen He, X Shirley Liu, Myles Brown
Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we performed a genome-wide CRISPR/Cas9 knockout screen to identify the genes that are required for prostate cancer growth. Functional annotation defined a set of essential spliceosome and RNA binding protein (RBP) genes, including most notably heterogeneous nuclear ribonucleoprotein L (HNRNPL). We defined the HNRNPL-bound RNA landscape by RNA immunoprecipitation coupled with next-generation sequencing and linked these RBP-RNA interactions to changes in RNA processing...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28610174/the-complete-mitochondrial-genome-of-the-styloperlid-stonefly-species-i-styloperla-i-i-spinicercia-i-wu-insecta-plecoptera-with-family-level-phylogenetic-analyses-of-the-pteronarcyoidea
#16
Ying Wang, Jinjun Cao, Weihai Li
We present the complete mitochondrial (mt) genome sequence of the stonefly, Styloperla spinicercia Wu, 1935 (Plecoptera: Styloperlidae), the type species of the genus Styloperla and the first complete mt genome for the family Styloperlidae. The genome is circular, 16,129 base pairs long, has an A+T content of 70.7%, and contains 37 genes including the large and small ribosomal RNA (rRNA) subunits, 13 protein coding genes (PCGs), 22 tRNA genes and a large non-coding region (CR). All of the PCGs use the standard initiation codon ATN except ND1 and ND5, which start with TTG and GTG...
March 13, 2017: Zootaxa
https://www.readbyqxmd.com/read/28608528/overexpression-of-circular-rna-cirs-7-abrogates-the-tumor-suppressive-effect-of-mir-7-on-gastric-cancer-via-pten-pi3k-akt-signaling-pathway
#17
Haiyan Pan, Tao Li, Yugang Jiang, Congcong Pan, Yuanlin Ding, Zhigang Huang, Haibing Yu, Danli Kong
OBJECTIVE: Gastric cancer (GC) has one of the highest mortality rates of malignancies globally. Currently, ciRS-7, a novel circular RNA, has emerged as a potential sponge for miR-7. However, few studies on ciRS-7 in GC have been performed. In this study, we investigated the clinical significance and function of ciRS-7 in GC. MATERIALS AND METHODS: Firstly, the expression levels of ciRS-7 in 102 primary GC tissues and the matched para-carcinoma tissues were evaluated and the clinical relevance was confirmed in an independent validation cohort (n = 154)...
June 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28598992/ribosome-reinitiation-can-explain-length-dependent-translation-of-messenger-rna
#18
David W Rogers, Marvin A Böttcher, Arne Traulsen, Duncan Greig
Models of mRNA translation usually presume that transcripts are linear; upon reaching the end of a transcript each terminating ribosome returns to the cytoplasmic pool before initiating anew on a different transcript. A consequence of linear models is that faster translation of a given mRNA is unlikely to generate more of the encoded protein, particularly at low ribosome availability. Recent evidence indicates that eukaryotic mRNAs are circularized, potentially allowing terminating ribosomes to preferentially reinitiate on the same transcript...
June 9, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28598284/the-circular-rna-landscape-of-periodontal-ligament-stem-cells-during-osteogenesis
#19
Yunfei Zheng, Xiaobei Li, Yiping Huang, Lingfei Jia, Weiran Li
BACKGROUND: The aim of the present study was to investigate the distinct expression pattern of circular RNAs (circRNAs) in periodontal ligament stem cells (PDLSCs) during osteogenesis. METHODS: PDLSCs were isolated and cultured in osteogenic medium. Total RNA from cells at Day 0 (D0), Day 3 (D3), Day 7 (D7), and Day 14 (D14) were extracted, and submitted to RNA-sequencing to detect the expression profiles of circRNAs, mRNAs, and microRNAs (miRNAs). Real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to validate the expression of circRNAs and miRNAs...
June 9, 2017: Journal of Periodontology
https://www.readbyqxmd.com/read/28595834/the-completely-annotated-genome-and-comparative-genomics-of-the-peptoniphilaceae-bacterium-str-ing2-d1g-a-novel-acidogenic-bacterium-isolated-from-a-mesophilic-biogas-reactor
#20
Geizecler Tomazetto, Sarah Hahnke, Thomas Langer, Daniel Wibberg, Jochen Blom, Irena Maus, Alfred Pühler, Michael Klocke, Andreas Schlüter
The strictly anaerobic Peptoniphilaceae bacterium str. ING2-D1G (=DSM 28672=LMG 28300) was isolated from a mesophilic laboratory-scale completely stirred tank biogas reactor (CSTR) continuously co-digesting maize silage, pig and cattle manure. Based on 16S rRNA gene sequence comparison, the closest described relative to this strain is Peptoniphilus obesi ph1 showing 91.2% gene sequence identity, the most closely related species with a validly published name is Peptoniphilus indolicus DSM 20464(T) whose 16S rRNA gene sequence is 90...
June 5, 2017: Journal of Biotechnology
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