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Stable methylation of a non-coding rna gene regulates gene expression in response to abiotic stress in Populus simonii

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JOUrnaL OF EXPERIMENTAL BOTANY 2016年第5期67卷 1477-1492页

作者： Song, Yuepeng Ci, Dong Tian, Min Zhang, Deqiang Beijing Forestry Univ Coll Biol Sci & Technol Natl Engn Lab Tree Breeding 35 Qinghua East Rd Beijing 100083 Peoples R China Beijing Forestry Univ Coll Biol Sci & Technol Key Lab Genet & Breeding Forest Trees & Ornamenta 35 Qinghua East Rd Beijing 100083 Peoples R China

DNA methylation plays important roles in responses to environmental stimuli. However, in perennial plants, the roles of DNA methylation in stress-specific adaptions to different abiotic stresses remain unclear. Here, we present a systematic, comparative analysis of the methylome and gene expression in poplar under cold, osmotic, heat, and salt stress conditions from 3h to 24h. Comparison of the stress responses revealed different patterns of cytosine methylation in response to the four abiotic stresses. We isolated and sequenced 1376 stress-specific differentially methylated regions (SDMRs);annotation revealed that these SDMRs represent 1123 genes encoding proteins, 16 mirna genes, and 17 long non-coding rna (lncrna) genes. The SDMR162 region, consisting of Psi-MIR396e and PsiLNCrna00268512, is regulated by epigenetic pathways and we speculate that PsiLNCrna00268512 regulates miR396e levels by acting as a target mimic. The ratios of methylated cytosine declined to similar to 35.1% after 1 month of recovery from abiotic stress and to similar to 15.3% after 6 months. Among methylated mirna genes, only expression of the methylation-regulated gene MIrna6445a showed long-term stability. Our data provide a strong basis for future work and improve our understanding of the effect of epigenetic regulation of non-coding rna expression, which will enable in-depth functional analysis.

关键词： DNA methylation abiotic stress non-coding rna Populus simonii transcriptome changes

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Targeting long non-coding rna to therapeutically upregulate gene expression

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NATURE REVIEWS DRUG DISCOVERY 2013年第6期12卷 433-446页

作者： Wahlestedt, Claes Univ Miami Sch Med Ctr Therapeut Innovat Miami FL 33136 USA Univ Miami Sch Med Dept Psychiat & Behav Sci Miami FL 33136 USA

The majority of currently available drugs and tool compounds exhibit an inhibitory mechanism of action and there is a relative lack of pharmaceutical agents that are capable of increasing the activity of effectors or pathways for therapeutic benefit. Indeed, the upregulation of many genes, including tumour suppressors, growth factors, transcription factors and genes that are deficient in various genetic diseases, would be desired in specific situations. Recently, key roles for regulatory long non-coding rnas (lncrnas) in the regulation of gene expression have begun to emerge. lncrnas can positively or negatively regulate gene expression and chromatin architecture. Here, we review the current understanding of the mechanisms of action of lncrnas and their roles in disease, focusing on recent work in the design of inhibitors of the natural antisense transcript (NAT) class of lncrnas, known as antagoNAT oligonucleotides, and the issues associated with their potential therapeutic application.

关键词： TUMOR suppressor proteins GROWTH factors TRANSCRIPTION factors GENETIC disorders non-coding rna GENE expression OLIGONUCLEOTIDES

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More than a splicing code: integrating the role of rna, chromatin and non-coding rna in alternative splicing regulation

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CURRENT OPINION IN GENETICS & DEVELOPMENT 2011年第4期21卷 366-372页

作者： Luco, Reini F. Misteli, Tom NCI NIH Bethesda MD 20892 USA

Large portions of the genome undergo alternative pre-mrna splicing in often intricate patterns. Alternative splicing regulation requires extensive control mechanisms since errors can have deleterious consequences and may lead to developmental defects and disease. Recent work has identified a complex network of regulatory rna elements which guide splicing decisions. In addition, the discovery that transcription and splicing are intimately coupled has opened up new directions into alternative splicing regulation. Work at the interface of chromatin and rna biology has revealed unexpected molecular links between histone modifications, the transcription machinery, and non-coding rnas (ncrnas) in the determination of alternative splicing patterns.

关键词： GENETIC code CHROMATIN non-coding rna MESSENGER rna GENETIC transcription GENETIC regulation HISTONES rna splicing

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The long non-coding rna NEAT1 is increased in IUGR placentas, leading to potential new hypotheses of IUGR origin/development

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PLACENTA 2014年第1期35卷 44-49页

作者： Gremlich, S. Damnon, F. Reymondin, D. Braissant, O. Schittny, J. C. Baud, D. Gerber, S. Roth-Kleiner, M. Univ Lausanne Hosp Clin Neonatol CH-1011 Lausanne Switzerland Univ Lausanne CH-1011 Lausanne Switzerland Univ Lausanne Hosp Dept Gynecol Obstet & Med Genet CH-1011 Lausanne Switzerland Univ Lausanne Hosp Serv Biomed CH-1011 Lausanne Switzerland Univ Bern Inst Anat CH-3012 Bern Switzerland

Introduction: Intrauterine Growth Restriction (IUGR) is a multifactorial disease defined by an inability of the fetus to reach its growth potential. IUGR not only increases the risk of neonatal mortality/morbidity, but also the risk of metabolic syndrome during adulthood. Certain placental proteins have been shown to be implicated in IUGR development, such as proteins from the GH/IGF axis and angiogenesis/apoptosis processes. Methods: Twelve patients with term IUGR pregnancy (birth weight < 10th percentile) and 12 CTRLs were included. mrna was extracted from the fetal part of the placenta and submitted to a subtraction method (Clontech PCR-Select cDNA Subtraction). Results: One candidate gene identified was the long non-coding rna NEAT1 (nuclear paraspeckle assembly transcript 1). NEAT1 is the core component of a subnuclear structure called paraspeckle. This structure is responsible for the retention of hyperedited mrnas in the nucleus. Overall, NEAT1 mrna expression was 4.14 (+/- 1.16)-fold increased in IUGR vs. CTRL placentas (P = 0.009). NEAT1 was exclusively localized in the nuclei of the villous trophoblasts and was expressed in more nuclei and with greater intensity in IUGR placentas than in CTRLs. PSPC1, one of the three main proteins of the paraspeckle, co-localized with NEAT1 in the villous trophoblasts. The expression of NEAT1_2 mrna, the long isoform of NEAT1, was only modestly increased in IUGR vs. CTRL placentas. Discussion/conclusion: The increase in NEAT1 and its co-localization with PSPC1 suggests an increase in paraspeckles in IUGR villous trophoblasts. This could lead to an increased retention of important mrnas in villous trophoblasts nuclei. Given that the villous trophoblasts are crucial for the barrier function of the placenta, this could in part explain placental dysfunction in idiopathic IUGR fetuses. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： Trophoblast non-coding rna IUGR

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Integrated analysis of non-coding rna and mrna expression profiles of 2 pig breeds differing in muscle traits

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JOUrnaL OF ANIMAL SCIENCE 2017年第3期95卷 1092-1103页

作者： Sun, J. Xie, M. Huang, Z. Li, H. Chen, T. Sun, R. Wang, J. Xi, Qianyun Wu, T. Zhang, Y. South China Agr Univ Natl Engn Res Ctr Breeding Swine Ind Coll Anim Sci Guangdong Prov Key Lab Agroanim Genom & Mol Breed Guangzhou 510642 Guangdong Peoples R China Longyan Univ Coll Life Sci Longyan 364012 Fujian Peoples R China Hainan Acad Agr Sci Inst Anim Sci & Vet Med Haikou 571100 Peoples R China Henan Acad Agr Sci Inst Anim Husb & Vet Med Zhengzhou 450002 Peoples R China

Production of high-quality meat is important to satisfy the consumer and allow the pork industry to be competitive. It is evident that different muscle fiber types in different breeds greatly influence the pork quality, but the underlying molecular mechanism remains unclear. We used Ribo-Zero rna-Seq and mirna-Seq to examine global expressions of protein-coding transcripts and non-coding rnas including mirna, lncrna, and circrna in the longissimus dorsi of Landrace and Lantang pigs. Of the 22,469 identified coding transcripts, only 547 candidates were differentially expressed, including 461 upregulated and 86 downregulated transcripts in the Lantang pigs compared with Landrace. Gene ontology analysis of these differentially-expressed transcripts further revealed 17 genes involved in myogenesis. In addition, 5,566 lncrna and 4,360 circrna candidates were found to be differentially expressed. Of these, 3,976 lncrnas and 1,401 circrnas were upregulated in the Lantang library, while 1,590 lncrnas and 2,959 circrnas were downregulated. Of the differentially expressed circrnas, 236 candidates were edited from 93 functional hosting-genes related to myogenesis. We found 96 showed upregulation and 140 showed downregulation. By analyzing Ribo-Zero rna-Seq data in combination with matched mirna profiles, we identified 68 sponge modulators participating in 26 mirna-mediated cerna interactions, including 19 lncrnas, 40 circrnas, and 9 mrnas. Our study uncovered a novel post-transcriptional regulation layer which could help in the understanding of the mechanisms that underlie porcine myofiber development in different breeds.

关键词： cerna myofiber non-coding rna pig

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Deep sequencing of coding and non-coding rna in the CNS

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BRAIN RESEARCH 2010年 1338卷 146-154页

作者： van der Brug, Marcel Nalls, Michael A. Cookson, Mark R. NIA Cell Biol & Gene Express Unit Neurogenet Lab Bethesda MD 20892 USA Scripps Res Inst Dept Neurosci Jupiter FL 33458 USA

Several methods now exist for identifying and quantifying many biological events in parallel and in a relatively unbiased fashion. For gene expression experiments, cloning approaches have been supplemented with microarray platforms over the past few years. The focus of this review is on deep sequencing, a new set of techniques that can be used to both identify rna species and quantify them in a massively parallel fashion. Deep sequencing has some advantages over other methods, driven largely by the high depth of coverage for any library of nucleic acids. This allows, for example, estimates of alternative splicing and untranslated region utilization. We will discuss how deep sequencing methods are being applied to characterization of gene expression in the brain and how these technologies might develop over the next few years. Published by Elsevier B.V.

关键词： Alternative splicing Deep sequencing Gene expression Massively parallel signature sequencing Next generation sequencing non-coding rna Small rna

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Long non-coding rna modifies chromatin Epigenetic silencing by long non-coding rnas

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BIOESSAYS 2011年第11期33卷 830-839页

作者： Saxena, Alka Carninci, Piero RIKEN Yokohama Inst Om Sci Ctr Tsurumi Ku Yokohama Kanagawa 2300045 Japan

Common themes are emerging in the molecular mechanisms of long non-coding rna-mediated gene repression. Long non-coding rnas (lncrnas) participate in targeted gene silencing through chromatin remodelling, nuclear reorganisation, formation of a silencing domain and precise control over the entry of genes into silent compartments. The similarities suggest that these are fundamental processes of transcription regulation governed by lncrnas. These findings have paved the way for analogous investigations on other lncrnas and chromatin remodelling enzymes. Here we discuss these common mechanisms and provide our view on other molecules that warrant similar investigations. We also present our concepts on the possible mechanisms that may facilitate the exit of genes from the silencing domains and their potential therapeutic applications. Finally, we point to future areas of research and put forward our recommendations for improvements in resources and applications of existing technologies towards targeted outcomes in this active area of research.

关键词： airn/Kcnq1ot1 enhancers epigenetic modifications non-coding rna Xist/HOTAIR imprinting

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Evidence for further non-coding rna genes in the fungal rDNA region

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MYCOKEYS 2022年第90期90卷 203-213页

作者： Rosenblad, Magnus Alm Larsson, Ellen Walker, Arttapon Thongklang, Naritsada Wurzbacher, Christian Nilsson, R. Henrik Univ Gothenburg Dept Chem & Mol Biol Lundberg Lab Natl Infrastructure Bioinformat NBIS Gothenburg Sweden Univ Gothenburg Gothenburg Global Biodivers Ctr Dept Biol & Environm Sci Box 461 S-40530 Gothenburg Sweden Mae Fah Luang Univ Ctr Excellence Fungal Res Chiang Rai 57100 Thailand Mae Fah Luang Univ Sch Sci Chiang Rai 57100 Thailand Tech Univ Munich Chair Urban Water Syst Engn Coulombwall 3 D-85748 Garching Germany

non-coding rna (ncrna) genes play important, but incompletely understood, roles in various cellular processes, notably translation and gene regulation. A recent report on the detection of the ncrna Signal Recognition Particle gene in the nuclear ribosomal internal transcribed spacer region of several species of three genera of ectomycorrhizal basidiomycetes prompted a more thorough bioinformatics search for additional ncrna genes in the full fungal ribosomal operon. This study reports on the detection of three ncrna genes hitherto not known from the fungal ribosomal region: nuclear rnase P rna, rnase MRP rna, and a possible snorna U14 in a total of five species ofAuricularia and Inocybe. We verified their presence through resequencing of independent specimens. Two completedAuricularia genomes were found to lack these ncrnas elsewhere than in the ribosomal operon, suggesting that these are functional genes. It seems clear that ncrna genes play a larger role in fungal ribosomal genetics than hitherto thought.

关键词： Basidiomycetes IGS ITS MRP non-coding rna rnase MRP rnase P SRP

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The long intergenic non-coding rna CCR492 functions as a let-7 competitive endogenous rna to regulate c-Myc expression

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BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016年第10期1859卷 1322-1332页

作者： Maldotti, Mara Incarnato, Danny Neri, Francesco Krepelova, Anna Rapelli, Stefania Anselmi, Francesca Parlato, Caterina Basile, Giulia Dettori, Daniela Calogero, Raffaele Oliviero, Salvatore Univ Torino Dipartimento Sci Vita & Biol Sistemi Via Accademia Albertina 13 I-10123 Turin Italy Human Genet Fdn HuGeF Via Nizza 52 I-10126 Turin Italy Univ Torino Dipartimento Biotecnol Mol & Sci Salute Via Nizza 52 Turin Italy

In mammals the cell-cycle progression through the G1 phase is a tightly regulated process mediated by the transcriptional activation of early genes in response to mitogenic stimuli, whose dysregulation often leads to tumorigenesis. We here report the discovery by rna-seq of cell-cycle regulated (CCR) long intergenic non-coding rna5 (lincrnas), potentially involved in the control of the cell-cycle progression. We identified 10 novel lincrnas expressed in response to serum treatment in mouse embryonic fibroblasts (MEF5) and in BALB/c fibroblasts, comparably to early genes. By loss-of-function experiments we found that lincrna CCR492 is required for G1/S progression, localizes in the cell cytoplasm and contains 4 let-7 microrna recognition elements (MREs). Mechanistically, CCR492 functions as a competing endogenous rna (cerna) to antagonize the function of let-7 micrornas, leading to the de-repression of c-Myc. Moreover, we show that ectopic expression of CCR492 along with a constitutively active H-Ras promotes cell transformation. Thus, we identified a new lincrna expressed as an early gene in mammalian cells to regulate the cell-cycle progression by upregulating c-Myc expression. (C) 2016 Elsevier B.V. All rights reserved.

关键词： non-coding rna c-Myc Let-7 cerna Cell cycle

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A New rna-Seq Method to Detect the Transcription and non-coding rna in Prostate Cancer

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PATHOLOGY & ONCOLOGY RESEARCH 2014年第1期20卷 43-50页

作者： Zhang, Xiao-Ming Ma, Zhong-Wei Wang, Qiang Wang, Jian-Ning Yang, Ji-Wei Li, Xian-Duo Li, Hao Men, Tong-Yi Shandong Univ Dept Urol Qianfoshan Hosp Jinan 250014 Shandong Peoples R China Hosp Shandong Aluminum Corp Dept Urol Zibo 255069 Peoples R China Chinese Peoples Liberat Army Dept Urol Hosp 309 Beijing 100091 Peoples R China

Prostate cancer is a big killer in many regions especially American men, and this year, the diagnosed rate rises rapidly. We aimed to find the biomarker or any changing in prostate cancer patients. With the development of next generation sequencing, much genomic alteration has been found. Here, basing on the rna-seq result of human prostate cancer tissue, we tried to find the transcription or non-coding rna expressed differentially between normal tissue and prostate cancer tissue. 10 T sample data is the rna-seq data for prostate cancer tissue in this study, we found the differential gene is TFF3-Trefoil factor 3, which was more than seven fold change from prostate cancer tissue to normal tissue, and the most outstanding transcript is C15orf21. Additionally, 9 lncrnas were found according our method. Finally, we found the many important non-coding rna related to prostate cancer, some of them were long non-coding rna (lncrna).

关键词： Prostate cancer rna-seq Transcription non-coding rna lncrna

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