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Isolation and Characterization of a Novel noncoding rna from Nickel-Induced Lung Cancer

BIOLOGICAL TRACE ELEMENT RESEARCH 2012年第1-3期150卷 258-263页

作者： Zhang, Jing Zhou, Yang Wu, Youjun Ma, Lin Fan, Yingying Kang, Xuan Shi, Hongjun Zhang, Jun Tongji Univ Sch Med Dept Regenerat Med Shanghai 200092 Peoples R China Tongji Univ Sch Life Sci & Technol Shanghai 200092 Peoples R China Tongji Univ Sch Med Tongji Hosp Shanghai 200065 Peoples R China

noncoding rnas have drawn significant attention in carcinogenesis. In this study, we identified a novel gene named nickel-related gene1 (NRG1) associated with nickel-induced cancer. By using rapid amplification of cDNA end PCR, we obtained the full length of the cDNA. The sequence was analyzed by using related bioinformatics software and comparative genomics methods. The results showed that NRG1 was located on chromosome 2q12, within intron2 of ADAMTS6, a disintegrin and metalloproteinase with thrombospondin motifs. And, NRG1 had a high level of homology (76 %) to rat LINE1 sequence RL1.3 (long interspersed middle repetitive DNA). What's more, there was no continuous open reading frame present in NRG1 sequence. Taken together, these data demonstrate that NRG1 is a novel noncoding rna, and we predicted it may be a transposon-like gene. The identification of NRG1 emphasized the potential role of noncoding rna in nickel carcinogenesis.

关键词： Nickel LINE1 ADAMTS6 noncoding rna

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The association and clinical relevance of phase-separating protein CAPRIN1 with noncoding rna

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CELL STRESS & CHAPERONES 2023年第2期28卷 125-132页

作者： Zhang, Mojian Peng, Shuping Cent South Univ Hunan Canc Hosp Xiangya Sch Med Sch Basic Med Sci Changsha 410013 Hunan Peoples R China Cent South Univ Affiliated Canc Hosp Sch Basic Med Sci Hunan Key Lab Canc MetabXiangya Sch Med Changsha 410013 Hunan Peoples R China Cent South Univ Xiangya Hosp Key Lab Carcinogenesis & Canc Invas Chinese Minist Educ Changsha 410078 Hunan Peoples R China Cent South Univ Xiangya Hosp 3 Dis Genome Res Ctr Hunan Key Lab Nonresolving Inflammat & Canc Changsha 410013 Hunan Peoples R China

CAPRIN1, cell cycle-associated protein 1, is an rna-binding protein in stress granules, P bodies, and messenger rna transport granules and has a high level of expression in cancer. It promotes the proliferation and invasion of cancer cells and enhances their glycolysis and chemoresistance. In addition, it mediates the formation of intracellular SGs in various ways when exposed to endogenous and exogenous stress. As an rna-binding protein, it not only directly binds to several mrnas associated with the cell cycle but also is the target of mirna, lncrna, and circrna. Recently, CAPRIN1 is identified as a phase-separating protein that mediates the liquid-liquid phase separation within tumor cells. Moreover, the formation of CAPRIN1-mediated phase separation is regulated by circrna and lncrna. In addition, CAPRIN1 is associated with ubiquitination, which affects the relevant characteristics of cancer cells. This review discusses the different regulatory mechanisms of CAPRIN1 in various tumors and its association with noncoding rna, suggesting its potential as an oncogenic signal and possibly as a diagnostic indicator in the future. This may provide the multifunctional characteristic insight of CAPRIN1 protein and potential therapeutic target in malignancy with high levels of CAPRIN1.

关键词： CAPRIN1 Cancer SGs noncoding rna Ubiquitination

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Molecular mechanisms of noncoding rna and epigenetic regulation in obesity with consequent diabetes mellitus development

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World Journal of Diabetes 2023年第11期14卷 1621-1631页

作者： Yi-Chen Guo Hao-Di Cao Xiao-Fen Lian Pei-Xian Wu Fan Zhang Hua Zhang Dong-Hui Lu Department of Endocrinology Peking University Shenzhen HospitalShenzhen 518036Guangdong ProvinceChina Department of Endocrinology Zhujiang Hospital of Southern Medical UniversityGuangzhou 510282Guangdong ProvinceChina

Diabetes mellitus(DM)and obesity have become two of the most prevalent and challenging diseases worldwide,with increasing incidence and serious *** studies have shown that noncoding rna(ncrna)and epigenetic regulation play crucial roles in the pathogenesis of DM complicated by *** of the involvement of ncrna and epigenetic regulation in the pathogenesis of diabetes with obesity has opened new avenues of *** these mechanisms with small molecules or rna-based therapies may provide a more precise and effective approach to diabetes treatment than traditional *** this review,we discuss the molecular mechanisms of ncrna and epigenetic regulation and their potential therapeutic targets,and the research prospects for DM complicated with obesity.

关键词： Diabetes mellitus Obesity noncoding rna Epigenetic regulation Insulin resistance

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Lost in translation The 3′-UTR of IGF1R as an ancient long noncoding rna

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EVOLUTION MEDICINE AND PUBLIC HEALTH 2018年第1期2018卷 82-91页

作者： Mainieri, Avantika Haig, David Harvard Univ Dept Organism & Evolutionary Biol 26 Oxford St Cambridge MA 02138 USA

Background and objectives: The insulin-like growth factor (IGF) signaling system is a major arena of intragenomic conflict over embryonic growth between imprinted genes of maternal and paternal origin and the IGF type 1 receptor (IGF1R) promotes proliferation of many human cancers. The 3'-untranslated region (3'-UTR) of the mouse Igf1r mrna is targeted by miR-675-3p derived from the imprinted H19 long noncoding rna. We undertook a comparative sequence analysis of vertebrate IGF1R 3'-UTRs to determine the evolutionary history of miR-675 target sequences and to identify conserved features that are likely to be involved in post-transcriptional regulation of IGF1R translation. Methodology: Sequences of IGF1R 3'-UTRs were obtained from public databases and analyzed using publicly available algorithms. Results: A very long 3'-UTR is a conserved feature of vertebrate IGF1R mrnas. We found that some ancient micrornas, such as let-7 and mir-182, have predicted binding sites that are conserved between cartilaginous fish and mammals. One very conserved region is targeted by multiple, maternally expressed imprinted micrornas that appear to have evolved more recently than the targeted sequences. Conclusions and implications: The conserved structures we identify in the IGF1R 3'-UTR are strong candidates for regulating cell proliferation during development and carcinogenesis. These conserved structures are now targeted by multiple imprinted micrornas. These observations emphasize the central importance of IGF signaling pathways in the mediation of intragenomic conflicts over embryonic growth and identify possible targets for therapeutic interventions in cancer.

关键词： H19 IGF1R evolution genomic imprinting microrna noncoding rna

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mirna regulates noncoding rna: a noncanonical function model

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TRENDS IN BIOCHEMICAL SCIENCES 2012年第11期37卷 457-459页

作者： Chen, Xi Liang, Hongwei Zhang, Chen-Yu Zen, Ke Nanjing Univ Sch Life Sci State Key Lab Pharmaceut Biotechnol Jiangsu Engn Res Ctr MicroRNA Biol & Biotechnol Nanjing 210093 Jiangsu Peoples R China

It has long been assumed that mirnas can only target protein-coding mrnas in the cytoplasm. Recent studies, however, reveal mirnas are also transported from the cytoplasm to the nucleus, where they function in a nonca... 详细信息

关键词： mirna noncoding rna nucleus Argonaute exportin importin

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FPQrna: Hardware-accelerated qrna package for noncoding rna gene detecting on FPGA

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Journal of Bioinformatics and Computational Biology 2010年第4期8卷 743-761页

作者： Xia, Fei Dou, Yong Lei, Guo-Qing National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

noncoding rnas (ncrnas) have important functional roles in biological processes and have become a central research interest in modern molecular biology. However, how to find ncrna attracts much more attention since ncrna gene sequences do not have strong statistical signals, unlike protein coding genes. Qrna is a powerful program and has been widely used as an efficient analysis tool to detect ncrna gene at present. Unfortunately, the O(L ³) computing requirements and complicated data dependency greatly limit the usefulness of Qrna package with the explosion in gene database. In this paper, we present a fine-grained parallel Qrna prototype system, FPQrna, for accelerating ncrna gene detection application on FPGA chip. We propose a systolic-like array architecture with multiple PEs (Processing Elements). We partition the tasks by columns and assign tasks to PEs for load balance. We exploit data reuse schemes to reduce the need to load matrices from external memory. The experimental results show a speedup factor of more than 18× over the Qrna - 2.0.3c software running on a PC platform with AMD Phenom 9650 Quad CPU for pairwise sequence alignment with 996 residues, however the power consumption of our FPGA accelerator is only about 30% of that of the general-purpose microprocessors. © 2010 Imperial College Press.

关键词： Bioinformatics fine-grained parallelism FPGA hardware accelerator noncoding rna

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rnaZ 2.0: IMPROVED noncoding rna DETECTION

RNAZ 2.0: IMPROVED NONCODING RNA DETECTION

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15th Pacific Symposium on Biocomputing (PSB)

作者： Gruber, Andreas R. Findeiss, Sven Washietl, Stefan Hofacker, Ivo L. Stadler, Peter F. Univ Leipzig Dept Comp Sci Bioinformat Grp Hartelstr 16-18 D-04107 Leipzig Germany Univ Leipzig Interdisciplinary Ctr Bioinformat D-04107 Leipzig Germany Univ Vienna Inst Theoret Chem A-1090 Vienna Austria European Bioinformat Inst European Mol Biol Lab Hinxton CB10 1SD Cambs England

ISBN: (纸本)9789814295291

rnaz is a widely used software package for de novo detection of structured noncoding rnas in comparative genomics data. Four years of experience have not only demonstrated the applicability of the approach, but also helped us to identify limitations of the current implementation. rnaz 2.0 provides significant improvements in two respects: (1) The accuracy is increased by the systematic use of dinucleotide models. (2) Technical limitations of the previous version, such as the inability to handle alignments with more than six sequences, are overcome by increased training data and the usage of an entropy measure to represent sequence similarities. rnaz 2.0 shows a significantly lower false discovery rate on a dinucleotide background model than the previous version. Separate models for structural alignments provide an additional way to increase the predictive power. rnaz is open source software and can be obtained free of charge at: http://***-wash/rnaz/

关键词： rna structure noncoding rna structure conservation comparative genomics gene prediction

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Involvement of noncoding rna in blood-brain barrier integrity in central nervous system disease

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NON-CODING rna RESEARCH 2021年第3期6卷 130-138页

作者： Liu, Xi Shen, Ling Han, Bing Yao, Honghong Southeast Univ Sch Med Nanjing 210009 Jiangsu Peoples R China

Given the important role of the blood-brain barrier (BBB) in the central nervous system (CNS), increasing studies have been carried out to determine how the structural and functional integrity of the BBB impacts the pathogenesis of CNS diseases such as stroke, traumatic brain injuries (TBIs), and gliomas. Emerging studies have revealed that noncoding rnas (ncrnas) help to maintain the integrity and permeability of the BBB, thereby mediating CNS homeostasis. This review summarizes recent studies that focus on the effects of ncrnas on the BBB in CNS diseases, including regulating the biological processes of inflammation, necrosis, and apoptosis of cells, affecting the translational dysfunction of proteins and regulating tight junctions (TJs). A comprehensive and detailed understanding of the interaction between ncrnas and the BBB will lay a solid foundation for the development of early diagnostic methods and effective treatments for CNS diseases.

关键词： noncoding rna Blood-brain barrier Central nervous system disease

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T-Helper Polarization: Regulation by noncoding rna and Super-Enhancers

T-Helper Polarization: Regulation by Noncoding RNA and Super...

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作者： Gibbons, Hunter R. Vanderbilt University

学位级别：Ph.D.

Naïve CD4+ T cells polarize into many varied CD4+ T-helper (TH) cell subsets depending on the cytokine milieu present during T cell receptor stimulation. Each T cell subset produces a unique cytokine profile to defend against varied pathogens. The polarization of each T cell subset is regulated by unique transcription factors and noncoding elements to induce cytokine expression. The research detailed identifies a noncoding rna, GATA3-AS1, which is necessary for the expression of GATA3 and TH2 cell polarization. Furthermore, we describe the repression of IFN-γ by super-enhancer disruption via bromodomain inhibitor JQ1. Our results lend novel insight into the regulation of hallmark genes by noncoding elements in T-helper cell polarization.

关键词： T-Helper noncoding rna Super-enhancer cytokine transcription Immunoprecipitation

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Regulatory Roles of noncoding rna in Development and Disease

Regulatory Roles of Noncoding RNA in Development and Disease

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作者： GAURAV KUMAR PANDEY Uppsala University

学位级别：博士

Long noncoding rnas (lncrnas) are being realized as important players in gene regulation and their misregulation has been considered as one of the underlying causes for tumor initiation and progression in many human pathologies. In the current thesis, I have addressed the functional role of lncrnas in development and disease model systems. Genomic imprinting is an epigenetic phenomenon by which subset of genes are expressed in a parent of origin-specific manner. The Kcnq1 imprinted locus is epigenetically regulated by Kcnq1ot1 lncrna. Deletion of an 890bp region at the 5' end of Kcnq1ot1 in mouse resulted in the loss of silencing of neighboring ubiqui-tously imprinted genes (UIGs). In addition, we observed loss of DNA methylation at the UIG promoters. We have shown that Kcnq1ot1 rna establishes CpG methylation by interacting with DNMT1. To explore the stability of lncrna mediated silencing pathways, we have conditionally deleted Kcnq1ot1 in the mouse in a stage and tissue-specific manner. We have shown that Kcnq1ot1 is continuously required for maintaining the silencing of UIGs, whereas the silencing of the placental im-printed genes is maintained in an rna independent manner. To identify chromatin-associated lncrna (CARs) on a genome-wide scale, we purified rna from the sucrose gradient fractionated chromatin and subjected it to rna sequencing. Our study has identified 141 intronic and 74 long intergenic CARs. Characterization of one of the CARs revealed that it regulates the expression of neighboring genes in cis by modulating the chromatin structure. We have explored the functional role of lncrna in tumor progression and initiation by using pediatric neuroblastoma. By transcriptional profiling of low- and high-risk tumors, we have identified several lncrnas differentially expressed between these subtypes. We report an uncharacterized rna NBAT-1, expressed at lower levels in high-risk tumors relative to low- risk tumors. Using neuroblastoma cell culture system, we

关键词： noncoding rna Genomic Imprinting Epigenetics Neuroblastoma

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