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AFAP1-AS1: A novel oncogenic long non-coding rna in human cancers

CELL PROLIFERATION 2018年第1期51卷 1-11页

作者： Zhang, Fuyou Li, Jianfa Xiao, Huizhong Zou, Yifan Liu, Yuchen Huang, Weiren Shenzhen Univ Shenzhen Peoples Hosp 2 Key Lab Med Reprogramming Technol Affiliated Hosp 1 Shenzhen 518039 Guangdong Peoples R China Peking Univ Guangdong & Shenzhen Key Lab Male Reprod Med & Ge Shenzhen PKU HKUST Med Ctr Inst UrolShenzhen Hosp Shenzhen 518036 Peoples R China Univ South China Hengyang 421001 Hunan Peoples R China Shantou Univ Coll Med Shantou 515041 Guangdong Peoples R China

Long non-coding rnas (lncrnas), a group of non-protein-coding rnas with more than 200 nucleotides in length, are involved in multiple biological processes, such as the proliferation, apoptosis, migration and invasion. Moreover, numerous studies have shown that lncrnas play important roles as oncogenes or tumour suppressor genes in human cancers. In this paper, we concentrate on actin filament-associated protein 1-antisense rna 1 (AFAP1-AS1), a well-known long non-coding rna that is overexpressed in various tumour tissues and cell lines, including oesophageal cancer, pancreatic ductal adenocarcinoma, nasopharyngeal carcinoma, lung cancer, hepatocellular carcinoma, ovarian cancer, colorectal cancer, biliary tract cancer and gastric cancer. Moreover, high expression of AFAP1-AS1 was associated with the clinicopathological features and cancer progression. In this review, we sum up the current studies on the characteristics of AFAP1-AS1 in the biological function and mechanism of human cancers.

关键词： non-coding rna NUCLEOTIDES CELL proliferation APOPTOSIS ANTISENSE rna ESOPHAGEAL cancer

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Comprehensive long non-coding rna expression profiling reveals their potential roles in systemic lupus erythematosus

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CELLULAR IMMUNOLOGY 2017年 319卷 17-27页

作者： Li, Lian-Ju Zhao, Wei Tao, Sha-Sha Li, Jun Xu, Shu-Zhen Wang, Jie-Bing Leng, Rui-Xue Fan, Yin-Guang Pan, Hai-Feng Ye, Dong-Qing Anhui Med Univ Sch Publ Hlth Dept Epidemiol & Biostat 81 Meishan Rd Hefei 230032 Anhui Peoples R China Anhui Prov Key Lab Major Autoimmune Dis Hefei Anhui Peoples R China

Long non-coding rnas can regulate gene transcription, modulate protein function, and act as competing endogenous rna. Yet, their roles in systemic lupus erythematosus remain to be elucidated. We determined the expression profiles of lncrnas in T cells of SLE patients and healthy controls using microarrays. Up to 1935 lncrnas and 1977 mrnas were differentially expressed. QRT-PCR showed downregulated uc001ykl. 1 and ENST00000448942 in SLE patients. Expression of uc001ykl.1 correlated with erythrocyte sedimentation rate (ESR) and C-reactive protein, whereas ENST00000448942 level correlated with ESR and anti-Sm antibodies. Short time-series expression miner analysis revealed some lncrnas whose expressions might correlate with disease activity of SLE patients. coding-non-coding gene coexpression analyses showed differential lncrnas might operate via modulating expressions of their correlated, relevant mrnas in SLE. Differential lncrnas might also function through their cernas. Our study established that the aberrant expression profiles of lncrnas may play a role in SLE and thus warrant further investigation.

关键词： Long non-coding rna Systemic lupus erythematosus non-coding rna Microrna cerna

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H19 non-coding rna in urine cells detects urothelial carcinoma: a pilot study

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BIOMARKERS 2017年第7期22卷 661-666页

作者： Gielchinsky, Ilan Gilon, Michal Abu-lail, Rasha Matouk, Imad Hochberg, Avraham Gofrit, Ofer N. Ben-Dov, Iddo Z. Hadassah Hebrew Univ Dept Urol Med Ctr Jerusalem Israel Hebrew Univ Jerusalem Inst Life Sci Dept Biol Chem Jerusalem Israel Hadassah Hebrew Univ Med Ctr Nephrol & Hypertens Serv Jerusalem Israel

Context: Urothelial carcinoma (UC) is common and highly recurrent. Diagnosis and follow-up involve invasive cystoscopies. Objective: To evaluate H19 rna in urine cells as diagnostic tool for UC. Materials and methods: RT-PCR analysis of urine samples from healthy volunteers and UC patients. Results: H19 rna was unequivocally detected in the urine of 90.5% of patients and 25.9% of controls. H19 copies were three orders of magnitude higher in patients. Receiver operating characteristic analysis showed an area under the curve of 0.933. Conclusions: This pilot study shows that urinary cell H19 is a highly sensitive test for UC and pending verification could transform patient management.

关键词： non-coding rna diagnostic biomarkers urine biomarkers bladder cancer

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Small non-coding rna and cancer

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CARCINOGENESIS 2017年第5期38卷 485-491页

作者： Romano, Giulia Veneziano, Dario Acunzo, Mario Croce, Carlo M. Ohio State Univ Dept Canc Biol & Genet Columbus OH 43210 USA

The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of rna transcribed but not translated into protein can be classified as housekeeping rna (such as rrna, trna) and regulatory rna (such as mirna, pirna, lncrna). Small non-coding rnas, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated. In this review, focusing our attention on recent research results, we provide an overview of the four large classes of small non-coding rnas, namely, mirnas, pirnas, snorna and the new class of trna-derived fragments, highlighting their fundamental role in cancer and their potential as diagnostic and prognostic biomarkers.

关键词： HUMAN genome DNA non-coding rna rna DISEASES

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In Vivo Cleavage Map Illuminates the Central Role of rnase E in coding and non-coding rna Pathways

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MOLECULAR CELL 2017年第1期65卷 39-51页

作者： Chao, Yanjie Li, Lei Girodat, Dylan Foerstner, Konrad U. Said, Nelly Corcoran, Colin Smiga, Michal Papenfort, Kai Reinhardt, Richard Wieden, Hans-Joachim Luisi, Ben F. Vogel, Joerg Univ Wurzburg Inst Mol Infect Biol D-97080 Wurzburg Germany Univ Wurzburg Core Unit Syst Med D-97080 Wurzburg Germany Univ Lethbridge Dept Chem & Biochem Alberta RNA Res & Training Inst Lethbridge AB T1K 3M4 Canada Free Univ Berlin Lab Struct Biochem Berlin Germany Ludwig Maximilians Univ Munchen Microbiol Dept Biol 1 D-82152 Martinsried Germany Max Planck Inst Plant Breeding Res Max Planck Genome Ctr Cologne D-50829 Cologne Germany Univ Cambridge Dept Biochem Cambridge CB2 1GA England Helmholtz Inst RNA Based Infect Res HIRI D-97080 Wurzburg Germany

Understanding rna processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by rna-seq) to profile cleavage products of the essential endoribonuclease rnase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor rnase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small rnas whereby rnase E acts together with the rna chaperone Hfq to liberate stable 30 fragments from various precursor rnas. Recapitulating this process in vitro, Hfq guides rnase E cleavage of a representative small-rna precursor for interaction with a mrna target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators.

关键词： rnase E rna degradome non-coding rna Hfq 3′ UTR ArcZ RprA srna maturation uridine ruler TIER-seq

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MALAT1: a druggable long non-coding rna for targeted anti-cancer approaches

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JOUrnaL OF HEMATOLOGY & ONCOLOGY 2018年第1期11卷 63-63页

作者： Amodio, Nicola Raimondi, Lavinia Juli, Giada Stamato, Maria Angelica Caracciolo, Daniele Tagliaferri, Pierosandro Tassone, Pierfrancesco Magna Graecia Univ Catanzaro Dept Expt & Clin Med Viale Europa I-88100 Catanzaro Italy IRCSS Rizzoli Orthoped Inst Bologna Italy Rizzoli Orthoped Inst Innovat Technol Platforms Tissue Engn Theranost & Palermo Italy

The deeper understanding of non-coding rnas has recently changed the dogma of molecular biology assuming protein-coding genes as unique functional biological effectors, while non-coding genes as junk material of doubtful significance. In the last decade, an exciting boom of experimental research has brought to light the pivotal biological functions of long non-coding rnas (lncrnas), representing more than the half of the whole non-coding transcriptome, along with their dysregulation in many diseases, including cancer. In this review, we summarize the emerging insights on lncrna expression and functional role in cancer, focusing on the evolutionary conserved and abundantly expressed metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) that currently represents the best characterized lncrna. Altogether, literature data indicate aberrant expression and dysregulated activity of MALAT1 in human malignancies and envision MALAT1 targeting as a novel treatment strategy against cancer.

关键词： MALAT1 Long non-coding rna lncrna non-coding rna Epigenetics Experimental therapeutics

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HSV1 latent transcription and non-coding rna: A critical retrospective

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JOUrnaL OF NEUROIMMUNOLOGY 2017年 308卷 65-101页

作者： Phelan, Dane Barrozo, Enrico R. Bloom, David C. Univ Florida Dept Mol Genet & Microbiol Coll Med Gainesville FL 32611 USA

Virologists have invested great effort into understanding how the herpes simplex viruses and their relatives are maintained dormant over the lifespan of their host while maintaining the poise to remobilize on sporadic occasions. Piece by piece, our field has defined the tissues in play (the sensory ganglia), the transcriptional units (the latency-associated transcripts), and the responsive genomic region (the long repeats of the viral genomes). With time, the observed complexity of these features has compounded, and the totality of viral factors regulating latency are less obvious. In this review, we compose a comprehensive picture of the viral genetic elements suspected to be relevant to herpes simplex virus 1 (HSV1) latent transcription by conducting a critical analysis of about three decades of research. We describe these studies, which largely involved mutational analysis of the notable latency-associated transcripts (LATs), and more recently a series of viral mirnas. We also intend to draw attention to the many other less characterized non-coding rnas, and perhaps coding rnas, that may be important for consideration when trying to disentangle the multitude of phenotypes of the many genetic modifications introduced into recombinant HSV1 strains. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Herpes simplex virus HSV1 Latency Transcription mirna non-coding rna ncrna

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Linking deregulation of non-coding rna to the core pathophysiology of Alzheimer's disease: An integrative review

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PROGRESS IN NEUROBIOLOGY 2017年第0期156卷 1-68页

作者： Millan, Mark J. Inst Rech Servier Ctr Therapeut Innovat Neuropsychiat 125 Chemin Ronde F-78290 Croissy Sur Seine France

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 beta-amyloid-42 (A beta 42);anomalies in the production, cleavage and post-translational marking of Tau;impaired clearance of A beta 42 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. Intriguingly, some classes of mirna provoke these cellular anomalies, whereas others act in a counter-regulatory, protective mode. Moreover, changes in levels of certain species of mirna are a consequence of the above-mentioned anomalies. In addition to mirnas, circular rnas, pirnas, long non-coding rnas and other types of ncrna are being increasingly implicated in AD. Overall, a complex mesh of deregulated and multi-tasking ncrnas reciprocally interacts with core pathophysiological mechanisms underlying AD. Alterations in ncrnas can be detected in CSF and the circulation as well as the brain and are showing promise as biomarkers, with the ultimate goal clinical exploitation as targets for novel modes of symptomatic and course-altering therapy. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： Microrna miR non-coding rna ncrna lncrna Long non-coding rna pirna Circular rna beta-amyloid Tau Endoplasmic reticulum Unfolded protein response Oxidative stress Secretase Cell cycle re-entry Apoptosis Autophagy Neuroinflammation Neurodegenerative Epigenetic

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Expanding the plant non-coding rna world

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JOUrnaL OF PLANT RESEARCH 2017年第1期130卷 3-5页

作者： Ohtani, Misato Nara Inst Sci & Technol Grad Sch Biol Sci Ikoma 6300192 Japan RIKEN Ctr Sustainable Resource Sci Yokohama Kanagawa 2300045 Japan

Ribonucleic acid (rna) is one of the biopolymers essential for organisms. In the classical view of molecular biology, functional rna species have been categorized into three major groups, such as messenger rnas (mrnas), template molecules to biosynthesize proteins, ribosomal rnas (rrnas), components of huge molecular machinery ribo-some for protein biosynthesis, and transfer rnas (trnas), molecular couriers of amino acids to the ribosome. Function of these rnas brought the perspective of so-called central dogma, in which rna molecules are considered as the mediators of genomic information written within DNA molecules for protein biosynthesis to achieve required cell activity.

关键词： non-coding rna PLANT genetics MOLECULAR biology MESSENGER rna PROTEIN synthesis

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LncSLdb: A resource for long non-coding rna subcellular localization

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Database 2018年第2018期2018卷 1-N.PAG页

作者： Wen, Xiao Gao, Lin Guo, Xingli Li, Xing Huang, Xiaotai Wang, Ying Xu, Haifu He, Ruijie Jia, Chenglong Liang, Feixiang School of Computer Science and Technology Xidian University Xi'an Shaanxi 710071 China

While long non-coding rnas (lncrnas) may play important roles in cellular function and biological process, we still know little about them. Growing evidences indicate that subcellular localization of lncrnas may provide clues to their functionality. To facilitate researchers functionally characterize thousands of lncrnas, we developed a database-driven application, lncSLdb, which stores and manages user-collected qualitative and quantitative subcellular localization information of lncrnas from literature mining. The current release contains >11 000 transcripts from three species. Based on the accumulated region of lncrnas, we classify transcripts into three basic localization types (nucleus, cytoplasm and nucleus/cytoplasm). In some conditions, the nucleus and cytoplasm types can be divided into three more accurate subtypes (chromosome, nucleoplasm and ribosome). Besides browsing and downloading data in lncSLdb, our system provides a set of comprehensive tools to search by gene symbols, genome coordinates or sequence similarity. We hope that lncSLdb will provide a convenient platform for researchers to investigate the functions and the molecular mechanisms of lncrnas in the view of subcellular localization. © The Author(s) 2018. Published by Oxford University Press.

关键词： non-coding rna NUCLEOTIDE sequence

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