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LncRNA/dna binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals

BIOINFORMATICS 2017年第10期33卷 1431-1436页

作者： Liu, Haihua Shang, Xiaoxiao Zhu, Hao Southern Med Univ Sch Basic Med Sci Bioinformat Sect Guangzhou 510515 Guangdong Peoples R China

Motivation: Genomic imprinting is regulated by lncRNAs and is important for embryogenesis, physiology and behaviour in mammals. Aberrant imprinting causes diseases and disorders. Experimental studies have examined genomic imprinting primarily in humans and mice, thus leaving some fundamental issues poorly addressed. The cost of experimentally examining imprinted genes in many tissues in diverse species makes computational analysis of lncRNAs' dna binding sites valuable. Results: We performed lncRNA/dna binding analysis in imprinting clusters from multiple mammalian clades and discovered the following: (i) lncRNAs and imprinting sites show significant losses and gains and distinct lineage-specificity;(ii) binding of lncRNAs to promoters of imprinted genes may occur widely throughout the genome;(iii) a considerable number of imprinting sites occur in only evolutionarily more derived species;and (iv) multiple lncRNAs may bind to the same imprinting sites, and some lncRNAs have multiple dna binding motifs. These results suggest that the occurrence of abundant lncRNAs in mammalian genomes makes genomic imprinting a mechanism of adaptive evolution at the epigenome level. Supplementary information: Supplementary data are available at Bioinformatics online.

关键词： GENOMIC imprinting non-coding RNA dna-binding proteins non-coding dna EMBRYOLOGY

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Decoding the evolution of species

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SCIENCE 2017年第6341期356卷 904-905页

作者： Cooper, Kimberly L. Univ Calif San Diego Div Biol Sci La Jolla CA 92093 USA

In the middle of the 20th century, researchers identified dna and proteins and began to understand how they shape organisms. At first, scientists assumed that differences in protein sequence, structure, and function uniquely define any animal, including humans. Yet these building blocks are extraordinarily similar among animals, and human proteins can substitute for their counterparts in far simpler species (1-3). The modern dogma is that differences between species are largely a result of mutations in the noncoding instructions that determine when, where, and how much of a gene is expressed. On page 921 of this issue, Burga et al. (4) show that scientists may have underestimated the contribution of protein-coding mutations to evolution.

关键词： non-coding dna CIS-regulatory elements (Genetics) MUTATION (Biology) BIOSYSTEMATICS EVOLUTION (Biology) GENOMES SPECIATION (Biology)

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Longer Telomere Length and Renal Cell Carcinoma

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EUROPEAN UROLOGY 2017年第5期72卷 755-756页

作者： Casuscelli, Jozefina Hakimi, A. Ari Ludwig Maximilians Univ Munchen Dept Urol Marchioninistr 15 D-81377 Munich Germany Mem Sloan Kettering Canc Ctr Dept Surg Urol Serv New York NY USA

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Decoding non-coding dna: Trash or Treasure?

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RESONANCE-JOURNAL OF SCIENCE EDUCATION 2011年第4期16卷 333-340页

作者： Iyer, Namrata Indian Inst Sci Dept Microbiol & Cell Biol Bangalore 560012 Karnataka India

non-coding dna, once thought of as 'junk', represents a very large portion of an organism's genome. However, recent research has brought to light many functional elements present within non-coding dna sequences and unravelled a fascinating array of functions performed by these elements. These findings have highlighted the nature of the evolutionary forces that led to the accumulation and retention of non-coding dna. In this article, the various elements present within non-coding dna, their functional relevance to the cell and the changing perspective of the scientific community towards this so-called 'junk' dna have been described.

关键词： non-coding dna transposons repeat elements pseudogenes

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Efficient propagation of archetype JC polyomavirus in COS-7 cells: evaluation of rearrangements within the NCCR structural organization after transfection

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ARCHIVES OF VIROLOGY 2017年第12期162卷 3745-3752页

作者： Prezioso, Carla Scribano, Daniela Bellizzi, Anna Anzivino, Elena Rodio, Donatella Maria Trancassini, Maria Palamara, Anna Teresa Pietropaolo, Valeria Sapienza Univ Dept Publ Hlth & Infect Dis Ple Aldo Moro 5 I-00185 Rome Italy Univ G dAnnunzio Dept Expt & Clin Sci Chieti Italy Sapienza Univ Rome Cenci Bolognetti Fdn Inst Pasteur Dept Publ Hlth & Infect Dis Rome Italy San Raffaele Pisana Sci Inst Res Hospitalizat & H Rome Italy

John Cunningham virus (JCPyV) is an ubiquitous human pathogen that causes disease in immunocompromised patients. The JCPyV genome is composed of an early region and a late region, which are physically separated by the non-coding control region (NCCR). The dna sequence of the NCCR distinguishes two forms of JCPyV, the designated archetype and the prototype, which resulted from a rearrangement of the archetype sequence. To date, the cell culture systems for propagating JCPyV archetype have been very limited in their availability and robustness. Prior to this study, it was demonstrated that JCPyV archetype dna replicates in COS-7 simian kidney cells expressing SV40 TAg and COS-7 cells expressing HIV-1 Tat. Based on these observations, the present study was conducted to reproduce an in vitro model in COS-7 cells transfected with the JCPyV archetype strain in order to study JCPyV dna replication and analyze NCCR rearrangements during the viral life cycle. The efficiency of JCPyV replication was evaluated by quantitative PCR (Q-PCR) and by hemagglutination (HA) assay after transfection. In parallel, sequence analysis of JCPyV NCCR was performed. JCPyV efficiently replicated in kidney-derived COS-7 cells, as demonstrated by a progressive increase in viral load and virion particle production after transfection. The archetypal structure of NCCR was maintained during the viral cycle, but two characteristic point mutations were detected 28 days after transfection. This model is a useful tool for analyzing NCCR rearrangements during in vitro replication in cells that are sites of viral persistence, such as tubular epithelial cells of the kidney.

关键词： JOHN Cunningham virus IMMUNOCOMPROMISED patients non-coding dna VIRAL replication KIDNEY physiology GENE transfection

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Long noncoding RNAs in B-cell development and activation

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BLOOD 2016年第7期128卷 E10-E19页

作者： Brazao, Tiago F. Johnson, Jethro S. Muller, Jennifer Heger, Andreas Ponting, Chris P. Tybulewicz, Victor L. J. Francis Crick Inst London NW7 1AA England Univ Oxford MRC Computat Genom Anal & Training Ctr Funct Genom UnitDept Physiol Anat & Genet Oxford England Imperial Coll London England

Long noncoding RNAs (lncRNAs) are potentially important regulators of cell differentiation and development, but little is known about their roles in Blymphocytes. Using RNAseq and de novo transcript assembly, we identified 4516 lncRNAs expressed in 11 stages of B-cell development and activation. Most of these lncRNAs have not been previously detected, even in the closely related T-cell lineage. Comparison with lncRNAs previously described in human B cells identified 185 mouse lncRNAs that have human orthologs. Using chromatin immunoprecipitation-seq, we classified 20% of the lncRNAs as either enhancer-associated (eRNA) or promoter-associated RNAs. We identified 126 eRNAs whose expression closely correlated with the nearest coding gene, thereby indicating the likely location of numerous enhancers active in the B-cell lineage. Furthermore, using this catalog of newly discovered lncRNAs, we show that PAX5, a transcription factor required to specify the B-cell lineage, bound to and regulated the expression of 109 lncRNAs in pro-B and matureB cells and 184 lncRNAs in acute lymphoblastic leukemia.

关键词： non-coding RNA RNA non-coding dna B cells ANTIGEN presenting cells

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The assessment of noncoding variant of PPOX gene in variegate porphyria reveals post-transcriptional role of the 5′ untranslated exon 1

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BLOOD CELLS MOLECULES AND DISEASES 2016年 61卷 48-53页

作者： Fiorentino, Valeria Brancaleoni, Valentina Granata, Francesca Graziadei, Giovanna Di Pierro, Elena Univ Milan Dipartimento Sci Clin & Comunita Milan Italy Fdn IRCCS Ca Granda Osped Maggiore Policlin UO Med Interna Via F Sforza 35 I-20122 Milan Italy

The PPOX gene encodes for the protoporphyrinogen oxidase, which is involved in heme production. The partial deficiency of protoporphyrinogen oxidase causes variegate porphyria. The tissue-specific regulation of other heme biosynthetic enzymes is extensively studied, but the information concerning transcriptional and post-transcriptional regulation of PPOX gene expression is scarcely available. In this study, we characterized functions of three variants identified in the regulatory regions of the PPOX gene, which show a novel role for the 5' untranslated exon 1. Using luciferase assays and RNA analysis, we demonstrated that only c.1-883G>C promoter variant causes a significant loss in the transcriptional activity of PPOX gene whereas c.1-413G>T 5' UTR variant inhibits translation of PPOX mRNA and c.1-176G>A splicing variant causes 4 bp deletion in 5' UTR of PPOX mRNA variant 2. These observations indicate that the regulation of PPOX gene expression can also occur through a post-transcriptional modulation of the amount of gene product and that this modulation can be mediated by 5' untranslated exon 1. Moreover this study confirms that these regulatory regions represent an important molecular target for the pathogenesis of variegate porphyria. (C) 2016 Elsevier Inc. All rights reserved.

关键词： PORPHYRIA PROTOPORPHYRINOGEN oxidase non-coding dna RNA interference LUCIFERASES TREATMENT

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The Genetics of Transcription Factor dna Binding Variation

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CELL 2016年第3期166卷 538-554页

作者： Deplancke, Bart Alpern, Daniel Gardeux, Vincent Ecole Polytech Fed Lausanne Inst Bioengn Lab Syst Biol & Genet CH-1015 Lausanne Switzerland Swiss Inst Bioinformat CH-1015 Lausanne Switzerland

Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-dna binding motifs. Variable TF-dna interactions are therefore increasingly considered as key drivers of phenotypic variation. However, recent genome-wide studies revealed that the majority of variable TF-dna binding events are not driven by sequence alterations in the motif of the studied TF. This observation implies that the molecular mechanisms underlying TF-dna binding variation and, by extrapolation, inter-individual phenotypic variation are more complex than originally anticipated. Here, we summarize the findings that led to this important paradigm shift and review proposed mechanisms for local, proximal, or distal genetic variation-driven variable TF-dna binding. In addition, we discuss the biomedical implications of these findings for our ability to dissect the molecular role(s) of non-coding genetic variants in complex traits, including disease susceptibility.

关键词： TRANSCRIPTION factors dna-binding proteins HUMAN genetics variation GENETICS of disease susceptibility non-coding dna NUCLEOTIDE sequence EXTRAPOLATION PHENOTYPE

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Predicting regulatory variants with composite statistic

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BIOINFORMATICS 2016年第18期32卷 2729-2736页

作者： Li, Mulin Jun Pan, Zhicheng Liu, Zipeng Wu, Jiexing Wang, Panwen Zhu, Yun Xu, Feng Xia, Zhengyuan Sham, Pak Chung Kocher, Jean-Pierre A. Li, Miaoxin Liu, Jun S. Wang, Junwen Harvard Univ Dept Stat Boston MA 02138 USA Univ Hong Kong Ctr Genom Sci Hong Kong Hong Kong Peoples R China Univ Hong Kong Sch Biomed Sci Hong Kong Hong Kong Peoples R China Univ Hong Kong Dept Anaesthesiol Hong Kong Hong Kong Peoples R China Univ Hong Kong Dept Psychiat Hong Kong Hong Kong Peoples R China Univ Hong Kong Ctr Reprod Dev & Growth LKS Fac Med Hong Kong Hong Kong Peoples R China Tsinghua Univ Ctr Stat Sci Beijing 100084 Peoples R China Mayo Clin Ctr Individualized Med Dept Hlth Sci Res Scottsdale AZ 85259 USA Arizona State Univ Dept Biomed Informat Scottsdale AZ 85259 USA

Motivation: Prediction and prioritization of human non-coding regulatory variants is critical for understanding the regulatory mechanisms of disease pathogenesis and promoting personalized medicine. Existing tools utilize functional genomics data and evolutionary information to evaluate the pathogenicity or regulatory functions of non-coding variants. However, different algorithms lead to inconsistent and even conflicting predictions. Combining multiple methods may increase accuracy in regulatory variant prediction. Results: Here, we compiled an integrative resource for predictions from eight different tools on functional annotation of non-coding variants. We further developed a composite strategy to integrate multiple predictions and computed the composite likelihood of a given variant being regulatory variant. Benchmarked by multiple independent causal variants datasets, we demonstrated that our composite model significantly improves the prediction performance. Availability and Implementation: We implemented our model and scoring procedure as a tool, named PRVCS, which is freely available to academic and non-profit usage at http://***/PRVCS. Contact: ***@***, jliu@***, or limx54@*** Supplementary information: Supplementary data are available at Bioinformatics online.

关键词： PREDICTION (Logic) GENOMICS non-coding dna VIRULENCE (Microbiology) MEDICINE

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C9orf72 is required for proper macrophage and microglial function in mice

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SCIENCE 2016年第6279期351卷 1324-1329页

作者： O'Rourke, J. G. Bogdanik, L. Yanez, A. Lall, D. Wolf, A. J. Muhammad, A. K. M. G. Ho, R. Carmona, S. Vit, J. P. Zarrow, J. Kim, K. J. Bell, S. Harms, M. B. Miller, T. M. Dangler, C. A. Underhill, D. M. Goodridge, H. S. Lutz, C. M. Baloh, R. H. Cedars Sinai Med Ctr Board Governors Regenerat Med Inst 8700 Beverly Blvd Los Angeles CA 90048 USA Jackson Lab 600 Main St Bar Harbor ME 04609 USA Cedars Sinai Med Ctr Div Biomed Sci 8700 Beverly Blvd Los Angeles CA 90048 USA Cedars Sinai Med Ctr Dept Neurol 8700 Beverly Blvd Los Angeles CA 90048 USA Washington Univ Sch Med Dept Neurol 660 South Euclid Ave St Louis MO 63110 USA

Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Decreased expression of C9orf72 is seen in expansion carriers, suggesting that loss of function may play a role in disease. We found that two independent mouse lines lacking the C9orf72 ortholog (3110043021Rik) in all tissues developed normally and aged without motor neuron disease. Instead, C9orf72 null mice developed progressive splenomegaly and lymphadenopathy with accumulation of engorged macrophage-like cells. C9orf72 expression was highest in myeloid cells, and the loss of C9orf72 led to lysosomal accumulation and altered immune responses in macrophages and microglia, with age-related neuroinflammation similar to C9orf72 ALS but not sporadic ALS human patient tissue. Thus, C9orf72 is required for the normal function of myeloid cells, and altered microglial function may contribute to neurodegeneration in C9orf72 expansion carriers.

关键词： Macrophages Neuroglia Mice as laboratory animals Microsatellites (Genetics) non-coding dna Amyotrophic lateral sclerosis -- Genetic aspects Frontotemporal dementia Neurodegeneration

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