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https://www.readbyqxmd.com/read/27892769/circrnas-in-the-brain
#1
Mor Hanan, Hermona Soreq, Sebastian Kadener
Circular RNAs (circRNAs) are highly abundant and evolutionarily conserved non-coding RNAs produced by circularization of specific exons. Since their re-discovery as potential regulators of gene expression, thousands of circRNAs were detected in different tissues and cell types across most organisms. Accumulating data suggest key roles for them in the central nervous system. Neuronal-expressed RNAs are diverted to yield highly enriched CircRNAs in human, mouse, pig and flies, with many of them enriched in neuronal tissues...
November 28, 2016: RNA Biology
https://www.readbyqxmd.com/read/27892494/circular-rnas-are-down-regulated-in-kras-mutant-colon-cancer-cells-and-can-be-transferred-to-exosomes
#2
Yongchao Dou, Diana J Cha, Jeffrey L Franklin, James N Higginbotham, Dennis K Jeppesen, Alissa M Weaver, Nripesh Prasad, Shawn Levy, Robert J Coffey, James G Patton, Bing Zhang
Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27878945/regulatory-non-coding-rnas-in-acute-myocardial-infarction
#3
REVIEW
Yuan Guo, Fei Luo, Qiong Liu, Danyan Xu
Acute myocardial infarction (AMI) is one of the most common cardiovascular diseases that leads to high mortality and morbidity globally. Various therapeutic targets for AMI have been investigated in recent years, including the non-coding RNAs (ncRNAs). NcRNAs, a class of RNA molecules that typically do not code proteins, are divided into several subgroups. Among them, microRNAs (miRNAs) are widely studied for their modulation of several pathological aspects of AMI, including cardiomyocyte apoptosis, inflammation, angiogenesis and fibrosis...
November 23, 2016: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/27878383/hsa_circ_0054633-in-peripheral-blood-can-be-used-as-a-diagnostic-biomarker-of-pre-diabetes-and-type-2-diabetes-mellitus
#4
Zhenzhou Zhao, Xuejie Li, Dongdong Jian, Peiyuan Hao, Lixin Rao, Muwei Li
AIMS: The purpose of the current study was to investigate the characteristic expression of circular RNAs (circRNAs) in the peripheral blood of type 2 diabetes mellitus (T2DM) patients and their potential as diagnostic biomarkers for pre-diabetes and T2DM. METHODS: CircRNAs in the peripheral blood from six healthy individuals and six T2DM patients were collected for microarray analysis, and an independent cohort study consisting of 20 normal cases, 20 pre-diabetes patients and 20 T2DM patients was conducted to verify the five chosen circRNAs...
November 23, 2016: Acta Diabetologica
https://www.readbyqxmd.com/read/27829232/circular-rnas-and-their-associations-with-breast-cancer-subtypes
#5
Asha A Nair, Nifang Niu, Xiaojia Tang, Kevin J Thompson, Liewei Wang, Jean-Pierre Kocher, Subbaya Subramanian, Krishna R Kalari
Circular RNAs (circRNAs) are highly stable forms of non-coding RNAs with diverse biological functions. They are implicated in modulation of gene expression thus affecting various cellular and disease processes. Based on existing bioinformatics approaches, we developed a comprehensive workflow called Circ-Seq to identify and report expressed circRNAs. Circ-Seq also provides informative genomic annotation along circRNA fused junctions thus allowing prioritization of circRNA candidates. We applied Circ-Seq first to RNA-sequence data from breast cancer cell lines and validated one of the large circRNAs identified...
November 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27812869/rt-qpcr-detection-of-senescence-associated-circular-rnas
#6
Amaresh C Panda, Kotb Abdelmohsen, Myriam Gorospe
Primary cells that reach the end of their replicative potential, encounter sublethal stress, or experience the activation of certain oncogenes cease proliferation and enter a state of long-term growth arrest named senescence. The senescent process has been implicated in a variety of age-related diseases and also in the pathogenesis of cancer. Senescence is characterized by distinct changes in the types and levels of coding RNAs (mRNAs) as well as in the vast collective of regulatory noncoding (nc)RNAs, which includes microRNAs, long noncoding RNAs (lncRNAs), and circular (circRNAs)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27796758/circular-rnas-the-emerging-class-of-non-coding-rnas-and-their-potential-role-in-human-neurodegenerative-diseases
#7
REVIEW
Lalit Kumar, Shamsuzzama, Rizwanul Haque, Tanvi Baghel, Aamir Nazir
The exciting world of research with RNAs has to its credit some breakthrough findings that led to newer insights on multiple problems including that of human diseases. After the advent of siRNA, microRNA, and lncRNA, exciting novel molecules called circular RNAs (circRNAs) have been recently described. circRNAs are a class of non-coding RNAs, which are produced by scrambling of exons at the time of splicing. They are primarily produced in the brain region and are naturally present inside the cell. The best known ones so far include a particular type of circRNA namely "circular RNA sponge for miR-7" (ciRS-7 and CDR1as) which is the inhibitor of miR-7 microRNA-known to regulate various diseases like, cancer, neurodegenerative diseases, diabetes, and atherosclerosis...
October 29, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27754374/endogenous-multiple-exon-skipping-and-back-splicing-at-the-dmd-mutation-hotspot
#8
Hitoshi Suzuki, Yoshitsugu Aoki, Toshiki Kameyama, Takashi Saito, Satoru Masuda, Jun Tanihata, Tetsuya Nagata, Akila Mayeda, Shin'ichi Takeda, Toshifumi Tsukahara
Duchenne muscular dystrophy (DMD) is a severe muscular disorder. It was reported that multiple exon skipping (MES), targeting exon 45-55 of the DMD gene, might improve patients' symptoms because patients who have a genomic deletion of all these exons showed very mild symptoms. Thus, exon 45-55 skipping treatments for DMD have been proposed as a potential clinical cure. Herein, we detected the expression of endogenous exons 44-56 connected mRNA transcript of the DMD using total RNAs derived from human normal skeletal muscle by reverse transcription polymerase chain reaction (RT-PCR), and identified a total of eight types of MES products around the hotspot...
October 13, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27752108/circular-rna-has_circ_0067934-is-upregulated-in-esophageal-squamous-cell-carcinoma-and-promoted-proliferation
#9
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
https://www.readbyqxmd.com/read/27740630/circrnas-in-hematopoiesis-and-hematological-malignancies
#10
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
https://www.readbyqxmd.com/read/27739910/full-length-sequence-assembly-reveals-circular-rnas-with-diverse-non-gt-ag-splicing-signals-in-rice
#11
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
https://www.readbyqxmd.com/read/27739534/detecting-circular-rnas-bioinformatic-and-experimental-challenges
#12
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
https://www.readbyqxmd.com/read/27736885/dynamic-asxl1-exon-skipping-and-alternative-circular-splicing-in-single-human-cells
#13
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
https://www.readbyqxmd.com/read/27725737/circrnadb-a-comprehensive-database-for-human-circular-rnas-with-protein-coding-annotations
#14
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
https://www.readbyqxmd.com/read/27698349/retraction-are-circrnas-involved-in-cancer-pathogenesis
#15
Carlo M Croce
No abstract text is available yet for this article.
October 4, 2016: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/27677588/circrna-expression-pattern-and-circrna-mirna-mrna-network-in-the-pathogenesis-of-nonalcoholic-steatohepatitis
#16
Xi Jin, Chun-Yan Feng, Zun Xiang, Yi-Peng Chen, You-Ming Li
The pathogenesis of nonalcoholic steatohepatitis (NASH) is still unclear, where involvement of circRNA is considered for its active role as "miRNA sponge". Therefore, we aimed to investigate the circRNA expression pattern in NASH and further construct the circRNA-miRNA-mRNA network for in-depth mechanism exploration. Briefly, NASH mice model was established by Methionine and choline deficiency (MCD) diet feeding. Liver circRNA and mRNA profile was initially screened by microarray and ensuing qRT-PCR verification was carried out...
September 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27671698/circular-rnas-are-mirna-sponges-and-can-be-used-as-a-new-class-of-biomarker
#17
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
https://www.readbyqxmd.com/read/27668458/in-vitro-circularization-of-rna
#18
Sabine Müller, Bettina Appel
Over the past 2 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 y 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
https://www.readbyqxmd.com/read/27642589/circular-rna-itch-suppresses-lung-cancer-proliferation-via-inhibiting-the-wnt-%C3%AE-catenin-pathway
#19
Li Wan, Lin Zhang, Kai Fan, Zai-Xing Cheng, Quan-Chao Sun, Jian-Jun Wang
As a special form of noncoding RNAs, circular RNAs (circRNAs) played important roles in regulating cancer progression mainly by functioning as miRNA sponge. While the function of circular RNA-ITCH (cir-ITCH) in lung cancer is still less reported, in this study, we firstly detected the expression of cir-ITCH in tumor tissues and paired adjacent noncancer tissues of 78 patients with lung cancer using a TaqMan-based quantitative real-time PCR (qRT-PCR). The results showed that the expression of cir-ITCH was significantly decreased in lung cancer tissues...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27642518/disease-onset-and-aging-in-the-world-of-circular-rnas
#20
Kenneth Maiese
Circular ribonucleic acids (circRNAs) are non-coding RNAs of approximately 100 nucleotides in length with thousands of members in mammalian cells. The presence of circRNAs is believed to be even greater than that of messenger RNAs. Identification of circRNAs occurred approximately 37 years ago with the subsequent demonstration that covalent bonds are necessary for the unique circular structure of these ribonucleic acids. However, present understanding of the complex biological role of circRNAs remains limited and requires further elucidation...
2016: Journal of Translational Science
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