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no-coding RNA

Victor F Oliveira, Lauro A G Moares, Ester A Mota, Liana K Jannotti-Passos, Paulo M Z Coelho, Ana C A Mattos, Flávia F B Couto, Brian E Caffrey, Annalisa Marsico, Renata Guerra-Sá
Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni . Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S...
2018: BioMed Research International
J R de Ruiter, L F A Wessels, J Jonkers
Cancer is a complex disease in which cells progressively accumulate mutations disrupting their cellular processes. A fraction of these mutations drive tumourigenesis by affecting oncogenes or tumour suppressor genes, but many mutations are passengers with no clear contribution to tumour development. The advancement of DNA and RNA sequencing technologies has enabled in-depth analysis of thousands of human tumours from various tissues to perform systematic characterization of their (epi)genomes and transcriptomes in order to identify (epi)genetic changes associated with cancer...
August 2018: Open Biology
Jia-Jia Si, Wei-Min Wang, Dan Yu, Si-Lin Gan, Fei-Fei Wu, Ling Sun, Ding-Ming Wan, Xin-Sheng Xie, Yan-Fang Liu, Chong Wang, Hui Sun
OBJECTIVE: To investigate the expression of long non coding RNA RP11-69I8.3 in acute leukemia and its clinical significance. METHODS: lncRNA RP11-69I8.3 expression was detected by RT-PCR in bone marrow samples from 17 healthy controls, 32 newly diagnosed AML patients and 32 newly diagnosed ALL patients, and 25 ALL patients of complete remission after chemotherapy. Meanwhile, the clinical data were collected and the relation of lncRNA RP11-6918.3 expression with the clinical characteristics was analyzed...
August 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
Chao Liang, Yang Yang, Junhong Guan, Tao Lv, Shengtao Qu, Qiang Fu, Hongyu Zhao
Long non-coding RNA urothelial carcinoma associated 1 (lncRNA UCA1) promotes cancer progression and enhances chemoresistance through miR-204-5p in a few cancers. However, no studies have investigated whether UCA1 regulates glioma metastasis through miR-204-5p and its target. In the present study, cell migration, invasion and epithelial-mesenchymal transition (EMT) were evaluated in glioma cells overexpressing UCA1. The relationships among UCA1, miR-204-5p and ZEB1 were examined by real-time PCR, western blotting and dual-luciferase reporter assays...
August 3, 2018: Pathology, Research and Practice
István Szádeczky-Kardoss, Luca Gál, Andor Auber, János Taller, Dániel Silhavy
RNA quality control systems identify and degrade aberrant mRNAs, thereby preventing the accumulation of faulty proteins. Non-stop decay (NSD) and No-go decay (NGD) are closely related RNA quality control systems that act during translation. NSD degrades mRNAs lacking a stop codon, while NGD recognizes and decays mRNAs that contain translation elongation inhibitory structures. NGD has been intensively studied in yeast and animals but it has not been described in plants yet. In yeast, NGD is induced if the elongating ribosome is stalled by a strong inhibitory structure...
October 2018: Plant Science: An International Journal of Experimental Plant Biology
Sebastian Mackedenski, Chuyi Wang, Wai-Ming Li, Chow H Lee
Insulin-like growth factor 2 mRNA-binding protein-1 (IMP1) has high affinity for KRAS mRNA, and it can regulate KRAS expression in cells. We first characterized the molecular interaction between IMP1 and KRAS mRNA. Using IMP1 variants with a point mutation in the GXXG motif at each KH domain, we showed that all KH domains play a critical role for the binding of KRAS RNA. We mapped the IMP1-binding sites on KRAS mRNA and show that IMP1 has the highest affinity for nts 1-185. Although with lower affinity, IMP1 does bind to other coding regions and the 3'UTR of KRAS mRNA...
August 13, 2018: Biochemical Journal
Shuaixi Yang, Zhenqiang Sun, Quanbo Zhou, Weiwei Wang, Guixian Wang, Junmin Song, Zhen Li, Zhiyong Zhang, Yuan Chang, Kunkun Xia, Jinbo Liu, Weitang Yuan
Noncoding RNAs (ncRNAs) can be divided into microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), pRNAs, and tRNAs. Traditionally, miRNAs exert their biological function mainly through the inhibition of translation via the induction of target RNA transcript degradation. lncRNAs and circRNAs were once considered to have no potential to code proteins. Here, we will review the current knowledge on ncRNAs in relation to their origins, characteristics, and functions. We will also review how ncRNAs work as competitive endogenous RNA, gene transcription and expression regulators, and RNA-binding protein sponges in colorectal cancer (CRC)...
2018: Cancer Management and Research
Bufan Xiao, Zhaohao Huang, Ruihao Zhou, Jingtao Zhang, Bentong Yu
BACKGROUND The long non-coding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) is expressed in solid malignant tumors. The aim of this systematic review and meta-analysis was to determine whether expression of the lncRNA SNHG1 was associated with prognosis in patients with malignancy. MATERIAL AND METHODS A literature review from Jan 1970 to July 2018 identified publications in the English language. Databases searched included: PubMed, OVID, Web of Science, the Cochrane Database, Embase, EBSCO, Google Scholar...
August 6, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Lexing Li, Chunxiao Huang, Yulong He, Zhan Sang, Guoquan Liu, Hanchuan Dai
BACKGROUND/AIMS: Autophagy is a process of evolutionarily conservative degradation, which could maintain cellular homeostasis and cope with various types of stress. LncRNAs are considered as competing endogenous RNAs (ceRNAs) contributing to autophagy. GAS5 has been suggested as a new potential factor to mediate autophagy pathway and the underlying mechanism remains to be further confirmed. This study was taken to identify the effect of GAS5/miR-23a/ATG3 axis on autophagy and cell viability...
August 3, 2018: Cellular Physiology and Biochemistry
Renfu Lu, Junjian Chen, Lingwen Kong, Hao Zhu
Background: There is a dispute on the prognostic value of long non-coding RNA regulator of reprogramming (lncRNA ROR) in cancers. The purpose of this study was to evaluate the prognostic significance of lncRNA ROR expression in human cancers. Methods: PubMed, Embase and Cochrane Library were searched to look for relevant studies. The meta-analyses of prognostic and clinicopathological parameters were conducted. Results: A total of 10 studies were finally included into the meta-analysis. High lncRNA ROR expression was significantly associated with shorter overall survival (OS) (HR=2...
August 3, 2018: Bioscience Reports
Victor C Mason, Robert J Schaefer, Molly E McCue, Tosso Leeb, Vinzenz Gerber
BACKGROUND: Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past genome wide association studies (GWAS) have not discovered coding variants associated with RAO, leading to the hypothesis that causative variant(s) underlying the signals are likely non-coding, regulatory variant(s). Regions of the genome containing variants that influence the number of expressed RNA molecules are expression quantitative trait loci (eQTLs)...
August 2, 2018: BMC Genomics
Alejandro M Labella, Esther Garcia-Rosado, Isabel Bandín, Carlos P Dopazo, Dolores Castro, M Carmen Alonso, Juan J Borrego
Betanodaviruses [nervous necrosis virus (NNV)] are the causative agent of the viral encephalopathy and retinopathy, a disease that affects cultured Senegalese sole ( Solea senegalensis ). NNV reassortants, combining genomic segments from redspotted grouper nervous necrosis virus (RGNNV) and striped jack nervous necrosis virus (SJNNV) genotypes, have been previously isolated from several fish species. The wild-type reassortant wSs160.03, isolated from Senegalese sole, has been proven to be more virulent to sole than the parental genotypes (RGNNV and SJNNV), causing 100% mortality...
2018: Frontiers in Immunology
R Klitting, T Riziki, G Moureau, G Piorkowski, E A Gould, X de Lamballerie
Virus attenuation by genome re-encoding is a pioneering approach for generating effective live-attenuated vaccine candidates. Its core principle is to introduce a large number of synonymous substitutions into the viral genome to produce stable attenuation of the targeted virus. Introduction of large numbers of mutations has also been shown to maintain stability of the attenuated phenotype by lowering the risk of reversion and recombination of re-encoded genomes. Identifying mutations with low fitness cost is pivotal as this increases the number that can be introduced and generates more stable and attenuated viruses...
July 2018: Virus Evolution
Zarin Sharifnia, Mojgan Bandehpour, Bahram Kazemi, Nosratollah Zarghami
Background: Hepatitis C virus (HCV) is a ‎blood-borne pathogen, resulting in liver cirrhosis and liver cancer. Despite of many efforts in development of treatments for HCV, no vaccine has been licensed yet. The purpose of this study was ‎to design and prepare a specific mRNA, without 5' cap and poly (A) tail transcribed in vitro capable of coding core protein and also to determine its functionality. Methods: Candidate mRNA was prepared by in vitro transcription of the designed construct consisting of ‎‎5ʹ and 3ʹ untranslated regions of heat shock proteins 70 (hsp70) mRNA, T7 promoter, internal ribosome entry site (IRES) sequences of eIF4G related to human dendritic cells (DCs), and the ‎Core gene of HCV...
July 30, 2018: Iranian Biomedical Journal
Jiao Jiao, Bei Shi, Tianren Wang, Yuanyuan Fang, Tiefeng Cao, Yiming Zhou, Xiuxia Wang, Da Li
STUDY QUESTION: Do long non-coding RNA (lncRNA) and messenger RNA (mRNA) profiles in follicular fluid from mature and immature ovarian follicles differ between healthy women and women with polycystic ovary syndrome (PCOS)? SUMMARY ANSWER: lncRNA and mRNA profiles in follicular fluid from both mature and immature ovarian follicles differed significantly between healthy women and PCOS patients. WHAT IS KNOWN ALREADY: Unlike microRNAs, which have been extensively studied, lncRNAs present in follicular fluid have never been sequenced and the biological associations of lncRNAs in healthy follicles and follicles in women who develop PCOS remain largely unknown...
July 25, 2018: Human Reproduction
Romika Kumari, Audrey Mannion Michel, Pavel V Baranov
The process of translation is characterized by irregularities in the local decoding rates of specific mRNA codons. This includes the occurrences of long pauses that can take place when ribosomes decode certain peptide sequences, encounter strong RNA secondary structures or decode "hungry" codons. Examples are known where such pausing or stalling is used for regulating protein synthesis. This can be achieved at the level of translation via direct alteration of ribosome progression through mRNA or by altering mRNA stability via NoGo decay...
July 26, 2018: RNA
Claire L Riggs, Amanda Summers, Daniel E Warren, Göran E Nilsson, Sjannie Lefevre, W W Dowd, Sarah Milton, Jason E Podrabsky
Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus , the most anoxia-tolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance...
2018: Frontiers in Genetics
Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
BACKGROUND: Long non-coding RNAs (lncRNAs) are typically expressed at low levels and are inherently highly variable. This is a fundamental challenge for differential expression (DE) analysis. In this study, the performance of 25 pipelines for testing DE in RNA-seq data is comprehensively evaluated, with a particular focus on lncRNAs and low-abundance mRNAs. Fifteen performance metrics are used to evaluate DE tools and normalization methods using simulations and analyses of six diverse RNA-seq datasets...
July 24, 2018: Genome Biology
Ying Ni, Jian Fang, Linqi Zhu, Hui Jiang, Yun Liu, Renjie Miao, Chen Shao, Shihe Shao
Zinc finger E-box binding homeobox 1 antisense 1 (ZEB1-AS1) is a long non-coding RNA, which has found to unregulated in various kinds of cancer. This meta-analysis was conducted to demonstrate the association between ZEB1-AS1 expression levels and clinical outcome or prognosis of cancer patients.10 studies with 783 cancer patients were included in this meta-analysis by retrieving 5 databases (PubMed Central, EMBASE, Cochrane Library, Wiley Online Library and Medline).The result showed that overexpression of ZEB1-AS1 is significantly correlated with poor OS (Hazard ratio, HR=2...
2018: Journal of Cancer
Xiulan Zhao, Baocun Sun, Tieju Liu, Bing Shao, Ran Sun, Dongwang Zhu, Yanhui Zhang, Qiang Gu, Xueyi Dong, Fang Liu, Nan Zhao, Danfang Zhang, Yanlei Li, Jie Meng, Wenchen Gong, Yanjun Zheng, Xu Zheng
Vasculogenic mimicry (VM) refers to the unique capability of aggressive tumor cells to mimic the pattern of embryonic vasculogenic networks. Cancer stem cells (CSCs) represent a subpopulation of tumor cells endowed with the capacity for self-renewal and multi-lineage differentiation. Previous studies have indicated that CSCs may participate in the formation of VM. With the advance of high-resolution microarrays and massively parallel sequencing technology, long non-coding RNAs (lncRNAs) are suggested to play a critical role in the tumorigenesis and, in particular, the development of human hepatocellular carcinoma (HCC)...
July 19, 2018: Cancer Science
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