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https://www.readbyqxmd.com/read/27904771/tumor-suppressive-function-of-long-noncoding-rna-malat1-in-glioma-cells-by-suppressing-mir-155-expression-and-activating-fbxw7-function
#1
Shuanzhu Cao, Yanzhou Wang, Jinquan Li, Mingliang Lv, Haitao Niu, Yong Tian
The human metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA associated with metastasis, and is a favorable prognostic factor for lung cancer. Recent studies have shown that MALAT1 plays an important role in many malignancies. However, little is known about the role of MALAT1 in glioma. In this study, we determined the expression of MALAT1 and explored its prognostic value in glioma. Further, we investigated the regulatory mechanism of MALAT1 in glioma progression. Our results showed that the expression of MALAT1 was significantly decreased in glioma specimens than in noncancerous brain tissues...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27904675/expression-of-long-non-coding-rna-hotair-in-oral-squamous-cell-carcinoma-tca8113-cells-and-its-associated-biological-behavior
#2
Huawei Liu, Zhiyong Li, Chao Wang, Lin Feng, Haitao Huang, Changkui Liu, Fengxia Li
As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27902487/identification-of-laryngeal-cancer-prognostic-biomarkers-using-an-inflammatory-gene-related-competitive-endogenous-rna-network
#3
Qun He, Linli Tian, Hao Jiang, Jiarui Zhang, Qiang Li, Yanan Sun, Jiannan Zhao, Huijun Li, Ming Liu
Competitive endogenous RNAs (ceRNAs) act as molecular sponges for microRNAs (miRNAs), and are associated with tumorigenesis in various cancers, including laryngeal cancer (LC). In this work, we constructed an LC-specific inflammatory gene-related ceRNA network (IceNet). In IceNet, ceRNAs targeting inflammation-related genes tended to be network hubs. Additionally, the betweenness centralities of these hub ceRNAs were higher than those of the inflammation-related genes themselves, indicating that the hub ceRNAs in this study played critical roles in communication between IceNet molecules...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27893425/tag-snps-of-long-non-coding-rna-tincr-affect-the-genetic-susceptibility-to-gastric-cancer-in-a-chinese-population
#4
Xiang Ma, Chi Huang, Dakui Luo, Younan Wang, Ran Tang, Xiangkun Huan, Yi Zhu, Zekuan Xu, Ping Liu, Li Yang
Tissue differentiation-inducing non-protein coding RNA (TINCR) is required for normal epidermal differentiation. TINCR is also strongly overexpressed in human gastric cancer (GC) and contributes to carcinogenesis and tumor progression. However, the association between TINCR polymorphisms and the risk of any diseases, such as GC, remains unknown. In the present study, the tag single nucleotide polymorphisms rs8113645, rs2288947, rs8105637, and rs12610531 were analyzed in 602 patients with GC and 602 age- and sex-matched controls...
November 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27889980/-the-importance-of-free-nucleic-acids-in-the-non-invasive-diagnostics
#5
Bálint Nagy, Zoltán Csanádi, Róbert Póka
There is a great interest to determine the physiological role of "free" nucleic acids, and to use them in the clinical diagnostics. These could be DNA, mRNA, microRNA and long non-coding RNA molecules, they are in the body fluids, like serum, tear, saliva, etc. Their exact role in the normal and pathological physiological processes is still in the focus of the research, while their use in the diagnostics is becoming more and more important. The use of "free" DNA in the non-invasive prenatal diagnosis is the first clinical application of the new generation sequencers, these methods are able to reach 99...
November 2016: Orvosi Hetilap
https://www.readbyqxmd.com/read/27887846/long-non-coding-rna-metastasis-associated-lung-adenocarcinoma-transcript-1-regulates-the-expression-of-gli2-by-mir-202-to-strengthen-gastric-cancer-progression
#6
Yue Zhang, Zhuo Chen, Ming-Jing Li, Huan-Yu Guo, Nian-Cai Jing
BACKGROUND: Gastric cancer (GC) is one of the most common malignancies and ranks the second leading cause of cancer death worldwide. Some studies had reported the tumor-promoting effects of long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) as a competing endogenous RNA (ceRNA) by sponging to microRNAs. However, the molecular mechanism of ceRNA regulatory pathway involving MALAT1 in GC remains unclear. METHODS: MALAT1 and miR -202 expression was detected by quantitative real time PCR (qRT-PCR) in 60 gastric cancer tissues and adjacent normal tissues, CCK8 cell proliferation assays, cell cycle analysis and cell apoptosis assays were performed to detect the GC cell proliferation and apoptosis...
November 22, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27869204/mrna-changes-in-nucleus-accumbens-related-to-methamphetamine-addiction-in-mice
#7
Li Zhu, Jiaqi Li, Nan Dong, Fanglin Guan, Yufeng Liu, Dongliang Ma, Eyleen L K Goh, Teng Chen
Methamphetamine (METH) is a highly addictive psychostimulant that elicits aberrant changes in the expression of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the nucleus accumbens of mice, indicating a potential role of METH in post-transcriptional regulations. To decipher the potential consequences of these post-transcriptional regulations in response to METH, we performed strand-specific RNA sequencing (ssRNA-Seq) to identify alterations in mRNA expression and their alternative splicing in the nucleus accumbens of mice following exposure to METH...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27862640/long-non-coding-rna-malat1-functions-as-a-mediator-in-cardioprotective-effects-of-fentanyl-in-myocardial-ischemia-reperfusion-injury
#8
Zhi-Hui Zhao, Wei Hao, Qing-Tao Meng, Xiao-Bing Du, Shao-Qing Lei, Zhong-Yuan Xia
Long non-coding (lncRNA) MALAT1 can be increased by hypoxia or ischemic limbs. Also downregulation of MALAT1 contributes to reduction of cardiomyocyte apoptosis. However, the functional involvement of MALAT1 in myocardial ischemia-reperfusion (I/R) injury has not been defined. This study investigated the functional involvement of lncRNA-MALAT1 in cardioprotective effects of fentanyl. HL-1, a cardiac muscle cell line from the AT-1 mouse atrial cardiomyocyte tumor lineage, was pre-treated with fentanyl and generated cell model of hypoxia-reoxygenation (H/R)...
November 9, 2016: Cell Biology International
https://www.readbyqxmd.com/read/27862469/araport11-a-complete-reannotation-of-the-arabidopsis-thaliana-reference-genome
#9
Chia-Yi Cheng, Vivek Krishnakumar, Agnes Chan, Françoise Thibaud-Nissen, Seth Schobel, Christopher D Town
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than five years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress...
November 8, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27835598/snhg8-is-identified-as-a-key-regulator-of-epstein-barr-virus-ebv-associated-gastric-cancer-by-an-integrative-analysis-of-lncrna-and-mrna-expression
#10
Tao Huang, Yan Ji, Dan Hu, Baozheng Chen, Hejun Zhang, Chao Li, Gang Chen, Xingguang Luo, Xiong-Wei Zheng, Xiandong Lin
The Epstein-Barr virus (EBV) is associated with a variety of cancers, including gastric cancer, which has one of the highest mortality rates of all human cancers. Long non-coding RNAs (lncRNAs) have been suggested to have important causal roles in gastric cancer. However, the interaction between lncRNAs and EBV has not yet been studied. To this end, we sequenced 11,311 lncRNAs and 144,826 protein-coding transcripts from four types of tissue: one non-EBV-infected gastric carcinoma (EBVnGC) and its adjacent normal tissue, and one EBV-associated gastric carcinoma (EBVaGC) and its adjacent normal tissue...
November 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27829996/down-regulation-of-long-non-coding-rna-foxd3-antisense-rna-1-foxd3-as1-inhibits-cell-proliferation-migration-and-invasion-in-malignant-glioma-cells
#11
Zhen-Hua Chen, Hong-Kang Hu, Chen-Ran Zhang, Cheng-Yin Lu, Yi Bao, Zheng Cai, Yong-Xiang Zou, Guo-Han Hu, Lei Jiang
Growing evidence indicates that long non-coding RNAs (lncRNAs) play key roles in cancer initiation and progression. However, little is known about the therapeutic significance of lncRNAs in glioma. In this study, we explored the tumorigenic role of a classical lncRNA, FOXD3 antisense RNA 1 (FOXD3-AS1) in glioma. Systemic analysis of the patient specimens and clinical data showed that FOXD3-AS1 was markedly up-regulated in high-grade glioma tissues (WHO grade III-IV) compared with that in low-grade glioma (WHO grade I-II) and normal brain tissues (both P<0...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27826625/integrated-analysis-of-long-non-coding-rna%C3%A2-associated-cerna-network-reveals-potential-lncrna-biomarkers-in-human-lung-adenocarcinoma
#12
Jing Sui, Yun-Hui Li, Yan-Qiu Zhang, Cheng-Yun Li, Xian Shen, Wen-Zhuo Yao, Hui Peng, Wei-Wei Hong, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor biology. However, the roles of cancer specific lncRNAs in lncRNA-related ceRNA network of lung adenocarcinoma (LUAD) are still unclear. In the present study, the 465 RNA sequencing profiles in LUAD patients were obtained from the cancer genome atlas (TCGA) database, which provides large sample RNA sequencing data free of charge, and 41 cancer specific lncRNAs, 25 miRNAs and 1053 mRNAs (fold change >2, p<0...
November 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27816055/genome-wide-profiling-of-chicken-dendritic-cell-response-to-infectious-bursal-disease
#13
Jian Lin, Jing Xia, Keyun Zhang, Qian Yang
BACKGROUND: Avian infectious bursal disease virus (IBDV) is a highly contagious, immunosuppressive disease of young chickens, which causes high mortality rates and large economic losses in the poultry industry. Dendritic cells (DCs), which are antigen-presenting cells, have the unique ability to induce both innate and acquired immune responses and may significantly influence virus pathogenicity. To understand the interaction between IBDV and DCs, a microarray was used to analyse the response of DCs infected by IBDV...
November 5, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27802301/the-conserved-dcw-gene-cluster-of-r-sphaeroides-is-preceded-by-an-uncommonly-extended-5-leader-featuring-the-srna-upsm
#14
Lennart Weber, Clemens Thoelken, Marcel Volk, Bernhard Remes, Marcus Lechner, Gabriele Klug
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5' UTR followed by the first gene mraZ...
2016: PloS One
https://www.readbyqxmd.com/read/27801428/retroposition-as-a-source-of-antisense-long-non-coding-rnas-with-possible-regulatory-functions
#15
Oleksii Bryzghalov, Michał Wojciech Szcześniak, Izabela Makałowska
Long non-coding RNAs (lncRNAs) are a class of intensely studied, yet enigmatic molecules that make up a substantial portion of the human transcriptome. In this work, we link the origins and functions of some lncRNAs to retroposition, a process resulting in the creation of intronless copies (retrocopies) of the so-called parental genes. We found 35 human retrocopies transcribed in antisense and giving rise to 58 lncRNA transcripts. These lncRNAs share sequence similarity with the corresponding parental genes but in the sense/antisense orientation, meaning they have the potential to interact with each other and to form RNA:RNA duplexes...
November 2, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27801298/dysregulation-of-mitotic-machinery-genes-precedes-genome-instability-during-spontaneous-pre-malignant-transformation-of-mouse-ovarian-surface-epithelial-cells
#16
Ulises Urzúa, Sandra Ampuero, Katherine F Roby, Garrison A Owens, David J Munroe
BACKGROUND: Based in epidemiological evidence, repetitive ovulation has been proposed to play a role in the origin of ovarian cancer by inducing an aberrant wound rupture-repair process of the ovarian surface epithelium (OSE). Accordingly, long term cultures of isolated OSE cells undergo in vitro spontaneous transformation thus developing tumorigenic capacity upon extensive subcultivation. In this work, C57BL/6 mouse OSE (MOSE) cells were cultured up to passage 28 and their RNA and DNA copy number profiles obtained at passages 2, 5, 7, 10, 14, 18, 23, 25 and 28 by means of DNA microarrays...
October 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27797329/-apoptotic-endonuclease-endog-regulates-alternative-splicing-of-human-telomerase-catalytic-subunit-htert
#17
D D Zhdanov, D A Vasina, E V Orlova, V S Orlova, M V Pokrovskaya, S S Aleksandrova, N N Sokolov
Human telomerase catalytic subunit hTERT is subjected to alternative splicing results in loss of its function and leads to decrease of telomerase activity. However, very little is known about the mechanism of hTERT pre-mRNA alternative splicing. Apoptotic endonuclease EndoG is known to participate this process. The aim of this study was to determine the role of EndoG in regulation of hTERT alternative splicing. Increased expression of b-deletion splice variant was determined during EndoG over-expression in CaCo-2 cell line, after EndoG treatment of cell cytoplasm and nuclei and after nuclei incubation with EndoG digested cell RNA...
July 2016: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/27784795/the-potential-roles-of-long-noncoding-rnas-lncrna-in-glioblastoma-development
#18
Shuang Liu, Ramkrishna Mitra, Ming-Ming Zhao, Wenhong Fan, Christine M Eischen, Feng Yin, Zhongming Zhao
Long noncoding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between glioblastoma and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly upregulated in glioblastoma, as well as 198 lncRNA and 285 mRNA significantly downregulated in glioblastoma. We identified 138 coexpressed lncRNA-mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB-EPHB, p75-mediated signaling, TNFα/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in glioblastoma...
December 2016: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/27782844/transcriptome-wide-effects-of-inverted-sines-on-gene-expression-and-their-impact-on-rna-polymerase-ii-activity
#19
Mansoureh Tajaddod, Andrea Tanzer, Konstantin Licht, Michael T Wolfinger, Stefan Badelt, Florian Huber, Oliver Pusch, Sandy Schopoff, Michael Janisiw, Ivo Hofacker, Michael F Jantsch
BACKGROUND: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels...
October 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27782208/differential-expression-of-lncrnas-during-the-hiv-replication-cycle-an-underestimated-layer-in-the-hiv-host-interplay
#20
Wim Trypsteen, Pejman Mohammadi, Clarissa Van Hecke, Pieter Mestdagh, Steve Lefever, Yvan Saeys, Pieter De Bleser, Jo Vandesompele, Angela Ciuffi, Linos Vandekerckhove, Ward De Spiegelaere
Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell's molecular network. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay...
October 26, 2016: Scientific Reports
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