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long noncoding Rnas

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https://www.readbyqxmd.com/read/28640079/a-genome-wide-association-scan-of-biological-processes-involved-in-oral-lichen-planus-and-oral-squamous-cell-carcinoma
#1
Qiaozhen Yang, Beiyun Xu, Hongying Sun, Xiaxia Wang, Jie Zhang, Xuedi Yu, Xiaojuan Ma
BACKGROUND: In this study, the molecular mechanisms underlying malignant transformation from oral lichen planus (OLP) to oral squamous cell carcinoma (OSCC) were examined. METHODS: High-throughput sequencing of long noncoding RNAs (lncRNAs) and mRNAs of normal subjects and patients with OLP and OSCC was conducted. RNA-seq reads were mapped, lncRNA and mRNA transcripts were assembled, and expression levels were estimated. The targets of lncRNAs were predicted. Finally, Gene Ontology (GO) and pathway enrichment analyses of differentially expressed genes (DEGs) and lncRNA targets were performed...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28639619/long-noncoding-rna-lnchifcar-mir31hg-is-a-hif-1%C3%AE-co-activator-driving-oral-cancer-progression
#2
Jing-Wen Shih, Wei-Fan Chiang, Alexander T H Wu, Ming-Heng Wu, Ling-Yu Wang, Yen-Ling Yu, Yu-Wen Hung, Wen-Chang Wang, Cheng-Ying Chu, Chiu-Lien Hung, Chun A Changou, Yun Yen, Hsing-Jien Kung
Long noncoding RNAs (lncRNAs) have been implicated in hypoxia/HIF-1-associated cancer progression through largely unknown mechanisms. Here we identify MIR31HG as a hypoxia-inducible lncRNA and therefore we name it LncHIFCAR (long noncoding HIF-1α co-activating RNA); we describe its oncogenic role as a HIF-1α co-activator that regulates the HIF-1 transcriptional network, crucial for cancer development. Extensive analyses of clinical data indicate LncHIFCAR level is substantially upregulated in oral carcinoma, significantly associated with poor clinical outcomes and representing an independent prognostic predictor...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28638716/long-noncoding-rna-expression-in-peripheral-blood-mononuclear-cells-and-suicide-risk-in-chinese-patients-with-major-depressive-disorder
#3
Xuelian Cui, Wei Niu, Lingming Kong, Mingjun He, Kunhong Jiang, Shengdong Chen, Aifang Zhong, Wanshuai Li, Jim Lu, Liyi Zhang
BACKGROUND: WHO stated that nearly one million people commit suicide every year worldly, and 40% of the suicide completer suffered from depression. The primary aim of this study was to explore the association between long noncoding RNAs (lncRNAs) expression in peripheral blood mononuclear cells (PBMCs) and suicide risk of patients with major depressive disorder (MDD). METHODS: Using Human LncRNA 3.0 microarray profiling which includes 30,586 human lncRNAs and RT-PCR, six down-regulated lncRNAs were identified differentially expressed in MDD patients...
June 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28637928/the-long-noncoding-rna-wisper-controls-cardiac-fibrosis-and-remodeling
#4
Rudi Micheletti, Isabelle Plaisance, Brian J Abraham, Alexandre Sarre, Ching-Chia Ting, Michael Alexanian, Daniel Maric, Damien Maison, Mohamed Nemir, Richard A Young, Blanche Schroen, Arantxa González, Samir Ounzain, Thierry Pedrazzini
Long noncoding RNAs (lncRNAs) are emerging as powerful regulators of cardiac development and disease. However, our understanding of the importance of these molecules in cardiac fibrosis is limited. Using an integrated genomic screen, we identified Wisper (Wisp2 super-enhancer-associated RNA) as a cardiac fibroblast-enriched lncRNA that regulates cardiac fibrosis after injury. Wisper expression was correlated with cardiac fibrosis both in a murine model of myocardial infarction (MI) and in heart tissue from human patients suffering from aortic stenosis...
June 21, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28637507/dysregulated-expression-of-long-noncoding-rnas-in-gynecologic-cancers
#5
REVIEW
Elahe Seyed Hosseini, Matthieu Meryet-Figuiere, Hamed Sabzalipoor, Hamed Haddad Kashani, Hossein Nikzad, Zatollah Asemi
Cancers of the female reproductive system include ovarian, uterine, vaginal, cervical and vulvar cancers, which are termed gynecologic cancer. The emergence of long noncoding RNAs (lncRNAs), which are believed to play a crucial role in several different biological processes, has made the regulation of gene expression more complex. Although the function of lncRNAs is still rather elusive, their broad involvement in the initiation and progression of various cancers is clear. They are also involved in the pathogenesis of cancers of the female reproductive system...
June 21, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#6
A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28635400/the-long-noncoding-rna-foxcut-promotes-proliferation-and-migration-by-targeting-foxc1-in-nasopharyngeal-carcinoma
#7
Yu-Zhong Xu, Fang-Fang Chen, Yu Zhang, Qin-Fei Zhao, Xiao-Long Guan, Hai-Yong Wang, Ang Li, Xin Lv, Shu-Sheng Song, Ying Zhou, Xiao-Jun Li
Long noncoding RNAs play an important role in various biological processes, including tumorigenesis. FOXC1 (Forkhead box C1) is a member of the Forkhead box family of transcription factors and plays a crucial role in nasopharyngeal carcinoma. In this study, a novel long noncoding RNA (FOXCUT) located upstream of FOXC1 was investigated in 42 nasopharyngeal carcinoma patients. Our analysis revealed that the expression levels of FOXCUT and FOXC1 in nasopharyngeal carcinoma tissues were significantly higher than those observed in chronic nasopharyngitis tissues and that FOXCUT expression was positively correlated with FOXC1 expression...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28635106/long-noncoding-rna-and-its-contribution-to-autism-spectrum-disorders
#8
REVIEW
Jie Tang, Yizhen Yu, Wei Yang
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome...
June 20, 2017: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/28634418/long-noncoding-rnas-as-biomarkers-in-cancer
#9
REVIEW
Luka Bolha, Metka Ravnik-Glavač, Damjan Glavač
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer...
2017: Disease Markers
https://www.readbyqxmd.com/read/28632999/long-noncoding-rna-lnc-sox5-modulates-crc-tumorigenesis-by-unbalancing-tumor-microenvironment
#10
Wu Kaiming, Zhenxian Zhao, Kuanzhi Liu, Jian Zhang, Guanghua Li, Liang Wang
Long non-coding RNAs (LncRNAs) have been recently regarded as systemic regulators in multiple biological processes including tumorigenesis. In this study, we observed the expression of lncRNA lnc-sox5 was significantly increased in colorectal cancer (CRC). Despite the CRC cell growth, cell cycle and cell apoptosis was not affected by lnc-sox5 knock-down, lnc-sox5 knock-down suppressed CRC cell migration and invasion. In addition, xenograft animal model suggested that lnc-sox5 knock-down significantly suppressed the CRC tumorigenesis...
June 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28630135/inhibition-of-the-cardiac-fibroblast-enriched-lncrna-meg3-prevents-cardiac-fibrosis-and-diastolic-dysfunction
#11
Maria-Teresa Piccoli, Shashi Gupta, Janika Viereck, Ariana Foinquinos, Sabine Samolovac, Freya Kramer, Ankita Garg, Janet Remke, Karina Zimmer, Sandor Batkai, Thomas Thum
Rationale: Cardiac fibroblasts (CFs) drive extracellular matrix (ECM) remodeling following pressure overload, leading to fibrosis and diastolic dysfunction. Recent studies described the role of long noncoding RNAs (lncRNAs) in cardiac pathologies. Nevertheless, detailed reports on lncRNAs regulating CF biology and describing their implication in cardiac remodeling are still missing. Objective: Here, we aimed at characterizing lncRNA expression in murine CFs following chronic pressure overload, in order to identify CF-enriched lncRNAs and investigate their function and contribution to cardiac fibrosis and diastolic dysfunction...
June 19, 2017: Circulation Research
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#12
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#13
Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M Ibeagha-Awemu, Xin Zhao
BACKGROUND: Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. RESULTS: Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28628087/chromatin-enriched-lncrnas-can-act-as-cell-type-specific-activators-of-proximal-gene-transcription
#14
Michael S Werner, Matthew A Sullivan, Rohan N Shah, Rangarajan D Nadadur, Adrian T Grzybowski, Vasiliy Galat, Ivan P Moskowitz, Alexander J Ruthenburg
We recently described a new class of long noncoding RNAs (lncRNAs) that are distinguished by especially tight chromatin association and whose presence is strongly correlated to expression of nearby genes. Here, we examine the cis-enhancer mechanism of this class of chromatin-enriched RNA (cheRNA) across multiple human cell lines. cheRNAs are largely cell type specific and provide the most reliable chromatin signature to predict cis-gene transcription in every human cell type examined. Targeted depletion of three cheRNAs decreases expression of their neighboring genes, indicating potential co-activator function, and single-molecule fluorescence in situ hybridization (smFISH) of one cheRNA-distal target gene pair suggests a spatial overlap consistent with a role in chromosome looping...
June 19, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28626066/cytoplasmic-form-of-carlr-lncrna-facilitates-inflammatory-gene-expression-upon-nf-%C3%AE%C2%BAb-activation
#15
Ainara Castellanos-Rubio, Radomir Kratchmarov, Maialen Sebastian, Koldo Garcia-Etxebarria, Liher Garcia, Iñaki Irastorza, Sankar Ghosh
Long noncoding RNAs (lncRNAs) have emerged as critical regulators of inflammation. To further understand the interaction between inflammatory signaling pathways and lncRNAs, we characterized the function of cardiac and apoptosis-related lncRNA (Carlr), an lncRNA expressed in both mouse and human cells of diverse tissues. Carlr expression is increased following NF-κB signaling in macrophages, with concomitant translocation to, and enrichment of, the transcript in the cytoplasm. Knockdown of Carlr results in impaired expression of NF-κB pathway genes and influences the interaction between macrophages and intestinal cells in an inflammatory environment...
June 16, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28625897/differential-expression-of-long-noncoding-rnas-in-congenital-microtia
#16
Ling Zhang, Lin Lin, Yu-Peng Song, Bo Pan, Qing-Hua Yang, Hai-Yue Jiang
OBJECTIVE: To analyse lncRNA expression profiles in microtia using bioinformatics analysis. METHODS: We examined lncRNA expression profiles in residual ear cartilage and normal ear cartilage from individual congenital microtia patients. RESULTS: The gene chips used in this study included 30586 lncRNAs and 26109 mRNA probes. Intotal, 180 lncRNAs with differential expression weredetected in the residual ear cartilage compared with the normal cartilage, including 74 up-regulated and 106down-regulated lncRNAs...
June 15, 2017: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/28621149/identification-and-evaluation-of-lncrna-and-mrna-integrative-modules-in-human-peripheral-blood-mononuclear-cells
#17
Xing-Bo Mo, Long-Fei Wu, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Fei-Yan Deng, Shu-Feng Lei
AIM: To identify sets of functionally related long noncoding RNAs (lncRNAs) and mRNAs and to evaluate the importance of lncRNAs in an lncRNA-mRNA network. METHODS: We carried out weighted gene co-expression network analysis and enrichment analyses to identify functional modules of co-expressed lncRNAs and mRNAs in human peripheral blood mononuclear cells of 43 females. RESULTS: We identified seven modules and found hub lncRNAs in each module...
June 16, 2017: Epigenomics
https://www.readbyqxmd.com/read/28620265/panel-of-seven-long-noncoding-rna-as-a-candidate-prognostic-biomarker-for-ovarian-cancer
#18
Xiaohui Zhan, Chuanpeng Dong, Gang Liu, Yixue Li, Lei Liu
Ovarian cancer is one of the most common and lethal gynecological malignancies. The diagnosis of ovarian cancer is often at an advanced stage. Accumulated evidence suggests that long noncoding RNAs (lncRNAs) play important roles during ovarian tumorigenesis. In this study, using the lncRNA-mining approach, we analyzed lncRNA expression profiles of 493 ovarian cancer patients from Gene Expression Omnibus datasets, and identified a signature group of seven lncRNAs (BC037530, AK021924, AK094536, AK094536, BC062365, BC004123 and BC007937) associated with patient survival in the training dataset GSE9891...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28620127/prognostic-and-diagnostic-significance-of-lncrnas-expression-in-cervical-cancer-a-systematic-review-and-meta-analysis
#19
Shuqi Chi, Lina Shen, Teng Hua, Shuangge Liu, Guobing Zhuang, Xiaoxiao Wang, Xing Zhou, Guozhen Wang, Hongbo Wang
Long noncoding RNAs (lncRNAs) have been reported to be abnormally expressed in cervical cancer (CC) and presumably serve as diagnostic or prognostic markers. We thus performed a systematic review and meta-analysis to evaluate the clinical values of dysregulated lncRNAs in CC. A literature search was performed using the electronic databases PubMed, Embase, and Web of Science. A total of 22 relevant studies were eligible, including 21 on clinicopathological features, 18 on prognosis, and 4 on diagnosis. For clinicopathological features, HOTAIR expression was positively associated with tumor size (odds ratio [OR]=2...
May 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28620042/long-noncoding-rnas-lincs-between-human-health-and-disease
#20
REVIEW
Zhi Hao Kwok, Yvonne Tay
Long noncoding RNAs (lncRNAs) represent one of the largest classes of transcripts and are highly diverse in terms of characteristics and functions. Advances in high-throughput sequencing platforms have enabled the rapid discovery and identification of lncRNAs as key regulatory molecules involved in various cellular processes and their dysregulation in various human diseases. Here, we summarize the current knowledge of the functions and underlying mechanisms of lncRNA activity with a particular focus on cancer biology...
June 15, 2017: Biochemical Society Transactions
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