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long noncoding Rnas

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https://www.readbyqxmd.com/read/28548969/transcriptome-profiling-in-preadipocytes-identifies-long-noncoding-rnas-as-sam68-targets
#1
Naomi Li, Steven Hébert, Jingwen Song, Claudia L Kleinman, Stéphane Richard
The KH-type RNA binding protein Sam68 is required for adipogenesis. We have previously shown that Sam68-deficient mice have a lean phenotype and are protected against dietary-induced obesity due to defects in mTOR and S6K1 alternative splicing. Herein we profiled the transcriptome of Sam68 wild type and deficient 3T3-L1 mouse preadipocytes. We identified 652 protein-coding genes and 9 ncRNAs that were significantly altered with the loss of Sam68. As expected, downregulated genes were significantly associated with GO terms linked to cell migration, motility, and fat cell differentiation, while upregulated genes were mostly associated with GO terms linked to neurogenesis...
May 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28546511/the-nanci-nkx2-1-gene-duplex-buffers-nkx2-1-expression-to-maintain-lung-development-and-homeostasis
#2
Michael J Herriges, David J Tischfield, Zheng Cui, Michael P Morley, Yumiao Han, Apoorva Babu, Su Li, MinMin Lu, Isis Cendan, Benjamin A Garcia, Stewart A Anderson, Edward E Morrisey
A subset of long noncoding RNAs (lncRNAs) is spatially correlated with transcription factors (TFs) across the genome, but how these lncRNA-TF gene duplexes regulate tissue development and homeostasis is unclear. We identified a feedback loop within the NANCI (Nkx2.1-associated noncoding intergenic RNA)-Nkx2.1 gene duplex that is essential for buffering Nkx2.1 expression, lung epithelial cell identity, and tissue homeostasis. Within this locus, Nkx2.1 directly inhibits NANCI, while NANCI acts in cis to promote Nkx2...
May 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28546230/tincr-expression-is-associated-with-unfavorable-prognosis-in-patients-with-hepatocellular-carcinoma
#3
Feng Tian, Jian Xu, Fangxi Xue, Encui Guan, Xiaoguang Xu
Emerging evidences are accumulating that long noncoding RNAs (lncRNAs) have recently been identified to participate in various cellular processes. Terminal differentiation-induced ncRNA (TINCR) is a newly identified lncRNA with its functional roles not fully elucidated in human malignancy. The current study aims to identify the clinical significance of TINCR in prognosis and malignant progression of hepatocellular carcinoma (HCC). TINCR expression in HCC specimens with various stages of tumorigenesis were measured by qRT-PCR...
May 25, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28541302/the-long-noncoding-rna-lnc-egfr-stimulates-t-regulatory-cells-differentiation-thus-promoting-hepatocellular-carcinoma-immune-evasion
#4
Runqiu Jiang, Junwei Tang, Yun Chen, Lei Deng, Jie Ji, Yu Xie, Ke Wang, Wei Jia, Wen-Ming Chu, Beicheng Sun
Long noncoding RNAs play a pivotal role in T-helper cell development but little is known about their roles in Treg differentiation and functions during the progression of hepatocellular carcinoma (HCC). Here, we show that lnc-epidermal growth factor receptor (EGFR) upregulation in Tregs correlates positively with the tumour size and expression of EGFR/Foxp3, but negatively with IFN-γ expression in patients and xenografted mouse models. Lnc-EGFR stimulates Treg differentiation, suppresses CTL activity and promotes HCC growth in an EGFR-dependent manner...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28540673/micrornas-long-noncoding-rnas-and-their-functions-in-human-disease
#5
Min Xue, Ying Zhuo, Bin Shan
Majority of the human genome is transcribed into RNAs with absent or limited protein-coding potential. microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two major families of the non-protein-coding transcripts. miRNAs and lncRNAs can regulate fundamental cellular processes via diverse mechanisms. The expression and function of miRNAs and lncRNAs are tightly regulated in development and physiological homeostasis. Dysregulation of miRNAs and lncRNAs is critical to pathogenesis of human disease. Moreover, recent evidence indicates a cross talk between miRNAs and lncRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28538188/identification-and-characterization-of-a-class-of-malat1-like-genomic-loci
#6
Bin Zhang, Yuntao S Mao, Sarah D Diermeier, Irina V Novikova, Eric P Nawrocki, Tom A Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R Eddy, Karissa Y Sanbonmatsu, David L Spector
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28537233/-canonical-and-noncanonical-rna-polyadenylation
#7
I G Ustyantsev, J S Golubchikova, O R Borodulina, D A Kramerov
Polyadenylation is the non-template addition of adenosine nucleotides at the 3'-end of RNA, which occurs after transcription and generates a poly(A) tail up to 250-300 nucleotides long. In the first section of our review, we consider the classical process of mRNA 3'-terminus formation, which involves the cleavage of the transcript synthesized by RNA polymerase II and the associated poly(A) tail synthesis by canonical polyadenylate polymerase. Nucleotide sequences needed for mRNA cleavage and poly(A) tail synthesis, in particular the AAUAAA polyadenylation signal, as well as numerous proteins and their complexes involved in mRNA cleavage and polyadenylation, is described in detail...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28536698/the-critical-role-of-long-noncoding-rna-in-osteogenic-differentiation-of-human-bone-marrow-mesenchymal-stem-cells
#8
Xiaoling Qiu, Bo Jia, Xiang Sun, Weitao Hu, Hongxing Chu, Shuaimei Xu, JianJiang Zhao
Objective. Long noncoding RNAs (lncRNAs) have been demonstrated to regulate many biological processes including differentiation. However, their role in osteogenic differentiation was poorly known. Materials and Methods. In this study, we first globally profiled the differentially expressed lncRNAs and mRNAs during osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMMSCs). Bioinformatics analysis was performed to further analyze these significantly changed molecules. Then the role of lncRNA ENST00000502125...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28535931/the-dimensions-dynamics-and-relevance-of-the-mammalian-noncoding-transcriptome
#9
REVIEW
Ira W Deveson, Simon A Hardwick, Tim R Mercer, John S Mattick
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing...
May 20, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28535506/long-noncoding-rna-afap1-as1-promoted-tumor-growth-and-invasion-in-cholangiocarcinoma
#10
Xu Lu, Chuang Zhou, Renfeng Li, Yilei Deng, Longshuan Zhao, Wenlong Zhai
BACKGROUND: Long non-coding RNAs (lncRNAs) have been shown to play important roles in a wide range of pathophysiological processes, including cancer progression. Our previous study has shown that AFAP1-AS1 was upregulated and acted as an oncogene in hepatocellular carcinoma. However, the expression and biological functions of lncRNA AFAP1-AS1 in intrahepatic cholangiocarcinoma (CCA) remains largely unknown. METHODS: The expression level of AFAP1-AS1 was measured in 56 pairs of human cholangiocarcinoma tumor tissues and corresponding adjacent normal bile duct tissues...
May 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28533023/the-rna-modification-n-6-methyladenosine-and-its-implications-in-human-disease
#11
REVIEW
Pedro J Batista
Impaired gene regulation lies at the heart of many disorders, including developmental diseases and cancer. Furthermore, the molecular pathways that control gene expression are often the target of cellular parasites, such as viruses. Gene expression is controlled through multiple mechanisms that are coordinated to ensure the proper and timely expression of each gene. Many of these mechanisms target the life cycle of the RNA molecule, from transcription to translation. Recently, another layer of regulation at the RNA level involving RNA modifications has gained renewed interest of the scientific community...
May 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28529365/long-noncoding-rnas-new-evidence-for-overlapped-pathogenesis-between-major-depressive-disorder-and-generalized-anxiety-disorder
#12
Xuelian Cui, Wei Niu, Lingming Kong, Mingjun He, Kunhong Jiang, Shengdong Chen, Aifang Zhong, Wanshuai Li, Jim Lu, Liyi Zhang
BACKGROUND: About half of patients with major depressive disorder (MDD) have clinically meaningful levels of anxiety. Greater severity of depressive illness and functional impairment has been reported in patients with high levels of anxiety accompanying depression. The pathogenesis for the comorbidity was still unsure. AIM: This study aimed to determine whether there would be molecular link for overlapped pathogenesis between MDD and anxiety disorder. MATERIALS AND METHODS: Using long noncoding RNA (lncRNA) microarray profiling and reverse transcription polymerase chain reaction, six downregulated lncRNAs and three upregulated lncRNAs had been identified to be the potential biomarkers for MDD and generalized anxiety disorder (GAD), respectively...
January 2017: Indian Journal of Psychiatry
https://www.readbyqxmd.com/read/28528706/long-noncoding-rnas-in-the-pathogenesis-of-barrett-s-esophagus-and-esophageal-carcinoma
#13
REVIEW
John M Abraham, Stephen J Meltzer
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development...
May 18, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28528181/overexpression-of-long-noncoding-rna-h19-indicates-a-poor-prognosis-for-cholangiocarcinoma-and-promotes-cell-migration-and-invasion-by-affecting-epithelial-mesenchymal-transition
#14
Yi Xu, Zhidong Wang, Xingming Jiang, Yunfu Cui
Cholangiocarcinoma (CCA) is a deadly disease that poorly responds to chemotherapy and radiotherapy and whose incidence has increased worldwide. Furthermore, long noncoding RNAs (lncRNAs) play important roles in multiple biological processes, including tumorigenesis. Specifically, H19, the first discovered lncRNA, has been reported to be overexpressed in diverse human carcinomas, but the overall biological role and clinical significance of H19 in CCA remains unknown. In the present study, expression levels of H19 were investigated in CCA tissues and cell lines and were correlated with clinicopathological features...
May 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28526319/lncrna-gas5-controls-cardiac-fibroblast-activation-and-fibrosis-by-targeting-mir-21-via-pten-mmp-2-signaling-pathway
#15
Hui Tao, Jia-Gui Zhang, Run-He Qin, Chen Dai, Peng Shi, Jing-Jing Yang, Zi-Yu Deng, Kai-Hu Shi
Long noncoding RNAs (LncRNAs) are aberrantly expressed in many diseases including cardiac fibrosis. LncRNA growth arrest-specific 5 (GAS5) is reported as a significant mediator in the control of cell proliferation and growth; however, the role and function in cardiac fibrosis remain unknown. In this study, we confirmed that GAS5 was lowly expressed in cardiac fibrosis tissues as well as activated cardiac fibroblast. Overexpression of GAS5 inhibited the proliferation of cardiac fibroblast. Moreover, microRNA-21 (miR-21) has been reported to be overexpressed in cardiac fibrosis tissues as well as activated cardiac fibroblast, which is responsible for the progression of cardiac fibrosis...
May 17, 2017: Toxicology
https://www.readbyqxmd.com/read/28525899/the-prognostic-value-of-long-noncoding-rnas-in-prostate-cancer-a-systematic-review-and-meta-analysis
#16
Weijie Ma, Xi Chen, Lu Ding, Jianhong Ma, Wei Jing, Tian Lan, Haseeb Sattar, Yongchang Wei, Fuling Zhou, Yufeng Yuan
The abnormally expressed LncRNAs played irreplaceable roles in the prognosis of prostate cancer (PCa). Therefore, we conducted this systematic review and meta-analysis to summarize the association between the expression of LncRNAs, prognosis and clinicopathology of PCa. 18 eligible studies were recruited into our analysis, including 18 on prognosis and 9 on clinicopathological features. Results indicated that aberrant expression of LncRNAs was significantly associated with biochemical recurrence-free survival (BCR-FS) (HR = 1...
May 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28523555/alzheimer-s-disease-and-ncrnas
#17
Rotem Maoz, Benjamin P Garfinkel, Hermona Soreq
Alzheimer's disease is a devastating neurodegenerative disorder affecting a significant portion of the world's rapidly growing aging population. In spite of its prevalence, the etiology of the disease is still poorly understood, and effective therapy is all but unavailable. Over the past decade, noncoding RNA, including microRNA (miRNA), has emerged as a major class of regulatory molecules involved in virtually all physiological and disease states. The specificity provided by miRNA sequence complementarity, together with the ability of these molecules to regulate complex networks of genes, has made them exciting novel targets for therapeutic agents...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522613/dehydration-stress-extends-mrna-3-untranslated-regions-with-noncoding-rna-functions-in-arabidopsis
#18
Hai-Xi Sun, Yan Li, Qi-Wen Niu, Nam-Hai Chua
The 3' untranslated regions (3' UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3' UTRs, but the involvement of this process in stress response has not yet been clarified. Here, we report that a subset of stress-related genes exhibits 3' UTR extensions of their mRNAs during dehydration stress. These extended 3' UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28520497/lncrna-pvt1-regulates-chondrocyte-apoptosis-in-osteoarthritis-by-acting-as-a-sponge-for-mir-488-3p
#19
Yufei Li, Shuhua Li, Yatong Luo, Yong Liu, Nanhui Yu
Long noncoding RNAs (lncRNAs) have been known to be involved in multiple diverse diseases, including osteoarthritis (OA). The present study aims at exploring the biological role of lncRNA plasmacytoma variant translocation 1 (PVT1) in OA and the underlying mechanism. Results showed that the expression of PVT1 was upregulated in OA chondrocytes compared with normal chondrocytes, silencing PVT1 inhibited the apoptosis of OA chondrocytes, and overexpression of PVT1 promoted the apoptosis of normal chondrocytes...
May 18, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28519068/long-noncoding-rna-gas5-suppresses-cell-growth-and-epithelial-mesenchymal-transition-in-osteosarcoma-by-regulating-the-mir-221-arhi-pathway
#20
Kaishan Ye, Shuanke Wang, Haihong Zhang, Hua Han, Bing Ma, Wei Nan
Dysregulated long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play key roles in the development of human cancers. The lncRNA growth arrest-specific 5 (GAS5) is reported to be a tumor suppressor in multiple cancers. However, the roles of GAS5 and its related miRNAs in osteosarcoma are poorly understood. This study explored the potential functions and mechanisms of GAS5 in the tumorigenesis of osteosarcoma. Here, the expression of GAS5, miR-221 and aplasia Ras homologue member I (ARHI) was determined in osteosarcoma tissues and cells by Real-time PCR (RT-qPCR)...
May 18, 2017: Journal of Cellular Biochemistry
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