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Single molecule real-time sequencing and rna-seq unravel the role of long non-coding and circular rna in the regulatory network during Nile tilapia (Oreochromis niloticus) infection with Streptococcus agalactiae

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FISH & SHELLFISH IMMUNOLOGY 2020年 104卷 640-653页

作者： Shen, Yudong Liang, Wanwen Lin, Yong Yang, Huizan Chen, Xiaohan Feng, Pengfei Zhang, Bin Zhu, Jiajie Zhang, Yongde Luo, Honglin Guangxi Acad Fishery Sci Guangxi Key Lab Aquat Genet Breeding & Hlth Aquac Nanning 530021 Guangxi Peoples R China Huazhong Agr Univ Coll Fisheries Key Lab Agr Anim Genet Breeding & Reprod Minist EducKey Lab Freshwater Anim BreedingMini Wuhan 430070 Hubei Peoples R China

Background: The tilapia aquaculture industry is facing heavy economic losses due to Streptococcus agalactiae (S. agalactiae) infections. While progress has been made in past years, the lack of a high-quality tilapia genome and transcript annotations makes systematic and comprehensive exploration for a non-coding rna regulatory network associated with the infection process unfeasible, and it stunts further research focused on disease defense and treatment. Herein, single molecular real time sequencing (SMRT-Seq) and rna-seq data were utilized to generate a high-quality transcript annotation. In addition, Changes in mrna and non-coding rna expression were also analyzed during a S. agalactiae infection in tilapia. Findings: In total, 16.79 Gb of clean data were obtained by sequencing on six SMRT cells, with 712,294 inserts (326,645 full-length non-chimeric reads and 354,188 non-full-length reads). A total of 197,952 consensus transcripts were obtained. Additionally, 55,857 transcript sequences were acquired, with 12,297 previously annotated and 43,560 newly identified transcripts. To further examine the immune response in Oreochromis niloticus following a S. agalactiae infection, a total of 470.62 Gb of clean data was generated by sequencing a library containing 18 S. agalactiae infected tilapia samples. Of the identified genes, 9911 were newly exploited, of which 7102 were functional annotated. Furthermore, 7874 mrnas, 1281 long non-coding rnas (out of 21,860 long non-coding rnas), and 61 circular rnas (out of 1026 circular rnas) were found to be differentially expressed during infection, with the 1026 circrnas not previously identified in tilapia. Moreover, k-means clustering and WGCNA analyses revealed that the immune response of tilapia to a S. agalactiae infection can be divided into three stages: cytokines driven rapid immune response, energy metabolism promotion, and the production of lysosomes and phagosomes. During this response, the head kidney and spleen hav

关键词： Oreochromis niloticus Streptococcus agalactiae Innate immune response non-coding rna Cerna

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A novel CRE recombinase assay for quantification of GAL10-non coding rna suppression on transcriptional leakage

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2016年第4期473卷 1191-1196页

作者： Zacharioudakis, Ioannis Tzamarias, Dimitris Univ Crete Dept Biol POB 1527 Iraklion 71110 Crete Greece

Eukaryotic promoters are tightly regulated and often securely repressed. However, recent reports indicated that transcripts originating from the strictly regulated GAL1-10 promoter can be detected by single-yeast cell imaging under repressive conditions. Such leaky, noisy transcription events were suppressed by a long non-coding rna (GAL10-ncrna) transcribed within the GAL1-10 locus. It was further suggested that GAL10-ncrna repression of GAL1-10 promoter leakage tunes the bimodal expression pattern of the GAL network. Independent evidence has indicated that GAL10-ncrna transcription establishes a repressive chromatin structure through the Set2 histone methyl-transferase and the Rpd3s histone deacetylase complex. In this report we set up a novel, simple genetic Cre recombinase assay in order to readily quantify transcriptional leakage from tightly repressed promoters. By applying this method we demonstrate that GAL10-ncrna, Set2p and Rpd3p all suppress leaky GAL1-10 driven transcription. However, GAL10-ncrna repression is not mediated by Set2p or Rpd3p. Moreover, as opposed to GAL10-ncrna transcription, Set2 and Rpd3 do not influence the bimodal expression of GAL genes, despite their effect on GAL1-10 promoter leakage. We suggest that GAL10-ncrna tunes the expression of GAL genes by additional mechanisms besides suppressing leaky transcription from the GAL1-10 promoter. (C) 2016 Elsevier Inc. All rights reserved.

关键词： Leaky transcription non-coding rna GAL10-ncrna Cre

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NDM29, a rna polymerase III-dependent non coding rna, promotes amyloidogenic processing of APP and amyloid β secretion

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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012年第7期1823卷 1170-1177页

作者： Massone, Sara Ciarlo, Eleonora Vella, Serena Nizzari, Mario Florio, Tullio Russo, Claudio Cancedda, Ranieri Pagano, Aldo Univ Genoa Dept Expt Med Genoa Italy IST IRCCS AOU San Martino Genoa Italy Univ Genoa Dept Internal Med Pharmacol Sect I-16126 Genoa Italy Univ Genoa Ctr Excellence Biomed Res Genoa Italy Univ Molise Dept Hlth Sci Campobasso Italy

Neuroblastoma Differentiation Marker 29 (NDM29) is a rna polymerase (pol) III-transcribed non-coding (nc) rna whose synthesis drives neuroblastoma (NB) cell differentiation to a nonmalignant neuron-like phenotype. Since in this process a complex pattern of molecular changes is associated to plasma membrane protein repertoire we hypothesized that the expression of NDM29 might influence also key players of neurodegenerative pathways. In this work we show that the NDM29-dependent cell maturation induces amyloid precursor protein (APP) synthesis, leading to the increase of amyloid beta peptide (A beta) secretion and the concomitant increment of A beta x-42/A beta x-40 ratio. We also demonstrate that the expression of NDM29 rna, and the consequent increase of Ail formation, can be promoted by inflammatory stimuli (and repressed by anti-inflammatory drugs). Moreover, NDM29 expression was detected in normal human brains although an abnormal increased synthesis of this ncrna is induced in patients affected by neurodegenerative diseases. Therefore, the complex of events triggered by NDM29 expression induces a condition that favors the formation of A beta peptides in the extracellular space, as it may occur in Alzheimer's Disease (AD). In addition, these data unexpectedly show that a pol III-dependent small rna can act as key regulator of brain physiology and/or pathology suggesting that a better knowledge of this portion of the human transcriptome might provide hints for neurodegeneration studies. (C) 2012 Elsevier B.V. All rights reserved.

关键词： rna polymerase III Alzheimer's disease Beta amyloid Neuroblastoma non-coding rna

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Mechanistic insights into non-coding Y rna processing

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rna BIOLOGY 2022年第1期19卷 468-480页

作者： Billmeier, Martina Green, Darrell Hall, Adam E. Turnbull, Carly Singh, Archana Xu, Ping Moxon, Simon Dalmay, Tamas Univ East Anglia Sch Biol Sci Norwich Res Pk Norwich NR4 7TJ Norfolk England Univ Regensburg Inst Med Microbiol & Hyg Regensburg Germany Univ East Anglia Norwich Med Sch Norwich Res Pk Norwich Norfolk England Horizon Discovery Cambridge Res Pk Waterbeach England Univ Cambridge Dept Plant Sci Cambridge England Shanghai Normal Univ Coll Life Sci Shanghai Engn Res Ctr Plant Germplasm Resource Shanghai Peoples R China

Y rnas (84-112 nt) are non-coding rnas transcribed by rna polymerase III and are characterized by a distinctive secondary structure. Human Y rnas interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y rnas also perform regulatory roles in DNA and rna replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y rnas are cleaved into 3' and 5' end fragments termed Y rna-derived small rnas (ysrnas). Although some ysrna functions in stress, apoptosis and cancer have been reported, their fundamental biogenesis has not been described. Here we report that 3' end RNY5 cleavage is structure dependent. In high throughput mutagenesis experiments, cleavage occurred between the 2(nd) and 3(rd) nt above a double stranded stem comprising high GC content. We demonstrate that an internal loop above stem S3 is critical for producing 3' end ysrnas (31 nt) with mutants resulting in longer or no ysrnas. We show a UGGGU sequence motif at position 22 of RNY5 is critical for producing 5' end ysrnas (22-25 nt). We show that intact RO60 is critical for ysrna biogenesis. We conclude that ribonuclease L (rnaSEL) contributes to Y rna cleavage in mouse embryonic fibroblasts but is not the only endoribonuclease important in human cells.

关键词： Y rna cancer apoptosis non-coding rna small rna

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MALAT-1, a non protein-coding rna is upregulated in the cerebellum, hippocampus and brain stem of human alcoholics

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ALCOHOL 2012年第7期46卷 629-634页

作者： Kryger, Rosemarie Fan, Li Wilce, Peter A. Jaquet, Vincent Univ Queensland Dept Biochem Sch Chem & Mol Biosci St Lucia Qld 4072 Australia Hop St Justine Dept Pediat Montreal PQ H3T 1C5 Canada Ctr Med Univ Geneva Dept Pathol & Immunol CH-1211 Geneva 4 Switzerland

Chronic alcohol intake induces neurochemical adaptative changes in the brain characterised by altered gene expression. A role for non-coding rnas in alcoholism is beginning to emerge. PCR-differential display using total rna extracted from brain material of human alcoholics and control cases identified a cDNA fragment corresponding to a section of a known non protein-coding rna (ncrna), MALAT-1, (also known as NEAT2). Comparison of mrna levels of MALAT-1 was performed by northern and dot blot experiments using different regions of brain from human alcoholics and rats chronically treated with ethanol vapours and following withdrawal. A massive increase of MALAT-1 transcripts was detected in cerebellum of human alcoholics and increases were also noted in hippocampus and brain stem, while no significant increase of MALAT-1 expression was noted in frontal or motor cortices. In the rat no significant difference of MALAT-1 ortholog mrna could be detected in cerebellum. In addition, similarly to humans, no significant increase of MALAT-1 expression was detected in cortex of alcohol-treated rats, however, after 24 h alcohol withdrawal, a significant upregulation of MALAT-1 expression was observed in rat cortex. MALAT-1 is upregulated in specific regions of the human alcoholic brain and following alcohol withdrawal in the rat. As MALAT-1 regulates rna processing, this suggests that alcohol-induced upregulation of MALAT-1 represents an important novel mechanism for alcohol actions in the CNS. (c) 2012 Elsevier Inc. All rights reserved.

关键词： Alcohol Brain non-coding rna MALAT-1 Gene expression

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The emerging role of non-coding circulating rna as a biomarker in renal cell carcinoma

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EXPERT REVIEW OF MOLECULAR DIAGNOSTICS 2016年第10期16卷 1059-1065页

作者： Ellinger, Joerg Gevensleben, Heidrun Mueller, Stefan C. Dietrich, Dimo Univ Hosp Bonn Dept Urol Bonn Germany Univ Hosp Bonn Inst Pathol Bonn Germany Univ Hosp Bonn Dept Otolaryngol Head & Neck Surg Bonn Germany

Introduction: Bodily fluids like serum and plasma contain significant amounts of tumor-derived circulating cell-free rna, which holds the potential to serve as diagnostic biomarker. Consequently, liquid biopsies comprising circulating cell-free rna might help to facilitate personalized treatment strategies for patients with renal cell carcinoma (RCC).Areas covered: The present review provides a summary of the literature obtained by a PubMed search and covers the current knowledge on circulating non-coding cell-free rna in patients with *** commentary: Altered circulating microrna and long non-coding rnas signatures allow for the discrimination of patients with RCC and healthy individuals. On the other hand, little is known about non-coding rna expression in benign tumors. Cell-free microrna expression levels may help to identify patients at risk for disease recurrence. However, accurate determination of cell-free rnas is methodologically challenging and currently no biomarker candidate has reached a sufficient level of clinical validation. Thus, short-term implementation of cell-free circulating microrna into clinical routine seems unlikely.

关键词： Renal cell carcinoma biomarker rna circulating cell-free rna microrna mirna non-coding rna ncrna long non-coding rna lncrna serum plasma bodily fluids

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piR-823, a novel non-coding small rna, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells

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CANCER LETTERS 2012年第1期315卷 12-17页

作者： Cheng, Jia Deng, Hongxia Xiao, Bingxiu Zhou, Hui Zhou, Fei Shen, Zhisen Guo, Junming Ningbo Univ Sch Med Ningbo 315211 Zhejiang Peoples R China Ningbo Univ Sch Med Affiliated Lihuili Hosp Ningbo 315040 Zhejiang Peoples R China

Piwi-interacting rnas (pirnas), new non-coding small rnas, are association with chromatin organization, messenger rna stability and genome structure. However, the roles of pirna in carcinogenesis are not clearly defined. By using real-time reverse transcription-polymerase chain reaction technology, we found that the expression level of piR-823 in gastric cancer tissues was significant lower than that in non-cancerous tissues. After increase the level of piR-823 in gastric cancer cells, cell growth was inhibited. The results of xenograft nude mice model confirmed its tumor suppressive properties. All of the evidences indicated that piR-823 play a crucial role in the occult of gastric cancer. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

关键词： Pirna non-coding rna Carcinogenesis Gastric cancer

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Identification of a potential non-coding rna biomarker signature for amyotrophic lateral sclerosis

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BRAIN COMMUNICATIONS 2020年第1期2卷 fcaa053页

作者： Joilin, Greig Gray, Elizabeth Thompson, Alexander G. Bobeva, Yoana Talbot, Kevin Weishaupt, Jochen Ludolph, Albert Malaspina, Andrea Leigh, P. Nigel Newbury, Sarah F. Turner, Martin R. Hafezparast, Majid Univ Sussex Sch Life Sci Brighton BN1 9QG E Sussex England Univ Oxford Nuffield Dept Clin Neurosci Oxford England Queen Mary Univ London Ctr Neurosci & Trauma Blizard Inst London England Univ Ulm Dept Neurol Ulm Germany Univ Sussex Brighton & Sussex Med Sch Dept Neurosci Brighton E Sussex England Univ Sussex Brighton & Sussex Med Sch Dept Clin & Expt Med Brighton E Sussex England

Objective biomarkers for the clinically heterogeneous adult-onset neurodegenerative disorder amyotrophic lateral sclerosis are crucial to facilitate assessing emerging therapeutics and improve the diagnostic pathway in what is a clinically heterogeneous syndrome. With non-coding rna transcripts including microrna, piwi-rna and transfer rna present in human biofluids, we sought to identify whether non-coding rna in serum could be biomarkers for amyotrophic lateral sclerosis. Serum samples from our Oxford Study for Biomarkers in motor neurone disease/amyotrophic lateral sclerosis discovery cohort of amyotrophic lateral sclerosis patients (n = 48), disease mimics (n = 16) and age- and sex-matched healthy controls (n = 24) were profiled for non-coding rna expression using rna-sequencing, which showed a wide range of non-coding rna to be dysregulated. We confirmed significant alterations with reverse transcription-quantitative PCR in the expression of hsa-miR-16-5p, hsa-miR-21-5p, hsa-miR-92a-3p, hsa-piR-33151, TRV-AAC4-1.1 and TRA-AGC6-1.1. Furthermore, hsa-miR-206, a previously identified amyotrophic lateral sclerosis biomarker, showed a binary-like pattern of expression in our samples. Using the expression of these non-coding rna, we were able to discriminate amyotrophic lateral sclerosis samples from healthy controls in our discovery cohort using a random forest analysis with 93.7% accuracy with promise in predicting progression rate of patients. Importantly, cross-validation of this novel signature using a new geographically distinct cohort of samples from the United Kingdom and Germany with both amyotrophic lateral sclerosis and control samples (n = 156) yielded an accuracy of 73.9%. The high prediction accuracy of this non-coding rna-based biomarker signature, even across heterogeneous cohorts, demonstrates the strength of our approach as a novel platform to identify and stratify amyotrophic lateral sclerosis patients.

关键词： amyotrophic lateral sclerosis ALS biomarker non-coding rna rna-seq

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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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Tetraarsenic oxide affects non-coding rna transcriptome through deregulating polycomb complexes in MCF7 cells

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Advances in Biological Regulation 2021年 80卷 100809-100809页

作者： Jeong, Jaehyeon Hamza, Muhammed Taofiq Kang, Keunsoo Jo, Doo Sin Bae, Ill Ju Kim, Deukyeong Cho, Dong-Hyung Bunch, Heeyoun Department of Applied Biosciences College of Agriculture and Life Sciences Kyungpook National University Daegu 41566 South Korea Department of Microbiology College of Natural Sciences Dankook University Cheonan 31116 South Korea School of Life Sciences BK21 Four KNU Creative Bioresearch Group Kyungpook National University Daegu 41566 South Korea Department of Drug Development Chemas Pharmaceuticals Seoul 06163 South Korea School of Applied Biosciences College of Agriculture and Life Sciences Kyungpook National University Daegu 41566 South Korea

non-coding rnas (ncrnas) play important and diverse roles in mammalian cell biology and pathology. Although the functions of an increasing number of ncrnas have been identified, the mechanisms underlying ncrna gene expression remain elusive and are incompletely understood. Here, we investigated ncrna gene expression in Michigan cancer foundation 7 (MCF7), a malignant breast cancer cell line, on treatment of tetraarsenic oxide (TAO), a potential anti-cancer drug. Our genomic analyses found that TAO up- or down-regulated ncrna genes genome-wide. A subset of identified ncrnas with critical biological and clinical functions were validated by real-time quantitative polymerase chain reaction. Intriguingly, these TAO-regulated genes included CDKN2B-AS, HOXA11-AS, SHH, and DUSP5 that are known to interact with or be targeted by polycomb repressive complexes (PRCs). In addition, the PRC subunits were enriched in these TAO-regulated ncrna genes and TAO treatment deregulated the expression of PRC subunits. Strikingly, TAO decreased the cellular and gene-specific levels of EZH2 expression and H3K27me3. In particular, TAO reduced EZH2 and H3K27me3 and increased transcription at MALAT1 gene. Inhibiting the catalytic activity of EZH2 using GSK343 increased representative TAO-inducible ncrna genes. Together, our findings suggest that the expression of a subset of ncrna genes is regulated by PRC2 and that TAO could be a potent epigenetic regulator through PRCs to modulate the ncrna gene expression in MCF7 cells. © 2021 Elsevier Ltd

关键词： Gene expression H3K27me3 non-coding rna Polycomb complexes Tetraarsenic oxide

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