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long non-coding RNAs

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https://www.readbyqxmd.com/read/28431932/zbed3-as1-induces-chondrogenesis-of-human-synovial-fluid-mesenchymal-stem-cells
#1
Farong Ou, Kai Su, Jiadong Sun, Wenting Liao, Yu Yao, Youhua Zheng, Zhiguang Zhang
Human synovial fluid-derived mesenchymal stem cells (SFMSCs) have great potential for cartilage induction and are promising for cell-based strategies for articular cartilage repair. Many long non-coding RNAs (lncRNAs) regulate chondrogenesis of MSCs. We hypothesized that the divergent lncRNA ZBED3-AS1, which binds locally to chromatin, could promote the expression of zbed3, a novel Axin-interacting protein that activates Wnt/β-catenin signaling, involved in chondrogenesis. However, the function of ZBED3-AS1 in SFMSCs is unclear...
April 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28430163/long-non-coding-rnas-key-regulators-of-epithelial-mesenchymal-transition-tumour-drug-resistance-and-cancer-stem-cells
#2
REVIEW
Richard Heery, Stephen P Finn, Sinead Cuffe, Steven G Gray
Epithelial mesenchymal transition (EMT), the adoption by epithelial cells of a mesenchymal-like phenotype, is a process co-opted by carcinoma cells in order to initiate invasion and metastasis. In addition, it is becoming clear that is instrumental to both the development of drug resistance by tumour cells and in the generation and maintenance of cancer stem cells. EMT is thus a pivotal process during tumour progression and poses a major barrier to the successful treatment of cancer. Non-coding RNAs (ncRNA) often utilize epigenetic programs to regulate both gene expression and chromatin structure...
April 21, 2017: Cancers
https://www.readbyqxmd.com/read/28428329/visualization-of-rna-structure-models-within-the-integrative-genomics-viewer
#3
Steven Busan, Kevin M Weeks
Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist...
April 20, 2017: RNA
https://www.readbyqxmd.com/read/28427943/high-density-lipoprotein-from-coronary-artery-disease-patients-cause-abnormal-expression-of-long-non-coding-rnas-in-vascular-endothelial-cells
#4
Xiang Liu, Tian-Tian Wang, Yan Li, Mao-Mao Shi, Hua-Ming Li, Hao-Xiang Yuan, Zhi-Wei Mo, Jing Chen, Bin Zhang, Yang-Xin Chen, Jing-Feng Wang, Wei-Ping Dai, Ying-Qi Xu, Zhi-Ping Wang, Xi Zhang, Zhi-Jun Ou, Jing-Song Ou
Increased evidence showed that normal high density lipoprotein (HDL) can convert to dysfunction HDL in diseases states including coronary artery disease (CAD), which regulates vascular endothelial cell function differently. Long non-coding RNAs (lncRNAs) play an extensive role in various important biological processes including endothelial cell function. However, whether lncRNAs involved in the regulation of HDL metabolism and HDL-induced changes of vascular endothelial function remains unclear. Cultured human umbilical vein endothelial cells (HUVECs) were treated with HDL from healthy subjects and patients with CAD and hypercholesterolemia for 24 h, then the cells were collected for lncRNA-Seq and the expressions of lncRNAs, genes and mRNAs were identified...
April 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28427191/down-regulation-of-long-non-coding-rna-rp11-708h21-4-is-associated-with-poor-prognosis-for-colorectal-cancer-and-promotes-tumorigenesis-through-regulating-akt-mtor-pathway
#5
Longci Sun, Chunhui Jiang, Chunjie Xu, Hanbing Xue, Hong Zhou, Lei Gu, Ye Liu, Qing Xu
Long non-coding RNAs (lncRNAs) serve critical roles in cancer development and progression. Herein, through next generation RNA sequencing and experimental validations, we determined the expression status of RP11-708H21.4 in colorectal cancer (CRC) and explored its clinical significance and biological functions in CRC. Differentially expressed lncRNAs from CRC samples and corresponding normal mucosa tissues was screened through RNA sequencing, and RP11-708H21.4 was selected for further experimental validation...
March 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425476/lncrnas2pathways-identifying-the-pathways-influenced-by-a-set-of-lncrnas-of-interest-based-on-a-global-network-propagation-method
#6
Junwei Han, Siyao Liu, Zeguo Sun, Yunpeng Zhang, Fan Zhang, Chunlong Zhang, Desi Shang, Haixiu Yang, Fei Su, Yanjun Xu, Chunquan Li, Huan Ren, Xia Li
Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, we have developed a novel computational method, LncRNAs2Pathways, to identify the functional pathways influenced by the combinatorial effects of a set of lncRNAs of interest based on a global network propagation algorithm...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#7
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28423944/emerging-roles-of-long-non-coding-rnas-in-plant-response-to-biotic-and-abiotic-stresses
#8
Naghmeh Nejat, Nitin Mantri
Spectacular progress in high-throughput transcriptome sequencing and expression profiling using next-generation sequencing technologies have recently revolutionized molecular biology and allowed massive advances in identifying the genomic regions and molecular mechanisms underlying transcriptional regulation of growth, development, and stress response. Through recent research, non-coding RNAs, in particular long non-coding RNAs, have emerged as key regulators of transcription in eukaryotes. Long non-coding RNAs are vastly heterogeneous groups of RNAs that execute a broad range of essential roles in various biological processes at the epigenetic, transcriptional, and post-transcriptional levels...
April 20, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28423735/the-long-non-coding-rna-nonhsag026900-predicts-prognosis-as-a-favorable-biomarker-in-patients-with-diffuse-large-b-cell-lymphoma
#9
Shuangtao Zhao, Shuangsang Fang, Yanhua Liu, Xixi Li, Shengyou Liao, Jinwen Chen, Jingjia Liu, Lianhe Zhao, Hui Li, Wei Zhou, Wenzhi Shen, Xiaoli Dong, Rong Xiang, Luhua Wang, Yi Zhao
Long non-coding RNAs are known to be involved in cancer progression, but their biological functions and prognostic values are still largely unexplored in diffuse large B-cell lymphoma. In this study, long non-coding RNAs expression was characterized in 1,403 samples including normal and diffuse large B-cell lymphoma by repurposing 7 microarray datasets. Compared with any stage of normal B cells, NONHSAG026900 expression was significantly decreased in tumor samples. And in germinal center B-cell subtype, the significantly higher expression of NONHSAG026900 indicated it was a favorable prognosis biomarker...
March 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423699/long-non-coding-rna-lucat1-is-associated-with-poor-prognosis-in-human-non-small-lung-cancer-and-regulates-cell-proliferation-via-epigenetically-repressing-p21-and-p57-expression
#10
Yue Sun, Shi-Dai Jin, Quan Zhu, Liang Han, Jing Feng, Xi-Yi Lu, Wei Wang, Feng Wang, Ren-Hua Guo
Recently, long non-coding RNAs (lncRNAs) have been recognized as playing key roles in regulating cellular processes, such as proliferation, invasion, and metastasis. These lncRNAs have been shown to be abnormally expressed in tumorigenic processes. However, the role and clinical relevance of LUCAT1 in non-small-cell lung cancer (NSCLC) remain unclear. In this study, we found that the expression of LUCAT1 was significantly up-regulated in NSCLC tissues compared to non-tumor tissues, and its expression was associated with tumor size, tumor-node-metastasis (TNM) stage and overall survival (OS)...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423633/novel-lincrna-slinky-is-a-prognostic-biomarker-in-kidney-cancer
#11
Xue Gong, Zurab Siprashvili, Okyaz Eminaga, Zhewei Shen, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Paul A Khavari, Jonathan R Pollack, James D Brooks
Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423601/a-novel-lncrna-gasl1-inhibits-cell-proliferation-and-restricts-e2f1-activity
#12
Lital Gasri-Plotnitsky, Aviv Ovadia, Katerina Shamalov, Tali Nizri-Megnaji, Shimrit Meir, Irit Zurer, Cyrille J Cohen, Doron Ginsberg
The human genome encodes thousands of unique long non-coding RNAs (lncRNAs), many of which are emerging as critical regulators of cell fate. However, their functions as well as their transcriptional regulation are only partially understood. The E2F1 transcription factor induces both proliferation and apoptosis, and is a critical downstream target of the tumor suppressor, RB. Here, we provide evidence that a novel lncRNA named GASL1 is transcriptionally regulated by E2F1; GASL1 levels are elevated upon activation of exogenous E2F1 or endogenous E2Fs...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423571/predictive-analysis-of-long-non-coding-rna-expression-profiles-in-diffuse-large-b-cell-lymphoma
#13
Danxia Zhu, Cheng Fang, Xiaodong Li, Yiting Geng, Ruiqi Li, Chen Wu, Jingting Jiang, Changping Wu
Long non-coding RNAs (lncRNAs) are implicated in many tumors. To find novel targets for study of diffuse large B-cell lymphoma (DLBCL), our team performed genome-wide analyses of lncRNA expression in 5 DLBCL cell lines using the 4*180K Agilent lncRNA Chip system, and in normal B cells. Five lncRNAs were validated by quantitative reverse transcription polymerase chain reaction. The differentially expressed lncRNAs and mRNAs were identified via false discovery rate and fold-change filtering. Potential targets correlated with DLBCL were recognized via gene ontology and pathway analysis...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423570/identification-of-long-non-coding-rnas-gas5-linc0597-and-lnc-dc-in-plasma-as-novel-biomarkers-for-systemic-lupus-erythematosus
#14
Guo-Cui Wu, Jun Li, Rui-Xue Leng, Xiang-Pei Li, Xiao-Mei Li, De-Guang Wang, Hai-Feng Pan, Dong-Qing Ye
Despite increasing evidence that long non-coding RNAs (lncRNAs) widely take part in human diseases, the role of lncRNAs in systemic lupus erythematosus (SLE) is largely unknown. In this study, we performed a two-stage study to explore the plasma levels of five lncRNAs (GAS5, linc0949, linc0597, HOTAIRM1 and lnc-DC) and their potential as SLE biomarkers. Compared with healthy controls, plasma levels of GAS5 and lnc-DC were significantly decreased (P < 0.001 and P = 0.002, respectively) while linc0597 were overexpressed in SLE patients (P < 0...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423525/the-combination-of-circulating-long-noncoding-rnas-ak001058-inhba-as1-mir4435-2hg-and-cebpa-as1-fragments-in-plasma-serve-as-diagnostic-markers-for-gastric-cancer
#15
Dong Ke, Hanwei Li, Yi Zhang, Yinghong An, Hanjiang Fu, Xuedong Fang, Xiaofei Zheng
BACKGROUND: Suitable diagnostic markers for cancers are urgently required in clinical practice. Long non-coding RNAs, which have been reported in many cancer types, are a potential new class of biomarkers for tumor diagnosis. RESULTS: Five lncRNAs, including AK001058, INHBA-AS1, MIR4435-2HG, UCA1 and CEBPA-AS1 were validated to be increased in gastric cancer tissues. Furthermore, we found that plasma level of these five lncRNAs were significantly higher in gastric cancer patients compared with normal controls...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422321/aberrantly-expressed-long-non-coding-rnas-in-cd8-t-cells-response-to-active-tuberculosis
#16
Yurong Fu, Kunshan Gao, Enxue Tao, Ruifang Li, Zhengjun Yi
Dysregulated expression of long noncoding RNAs (lncRNAs) has been demonstrated as being implicated in a variety of human diseases. In the study we aimed to determine lncRNA profile in CD8(+) T cells response to active tuberculosis (TB). We examined the lncRNA expression by microarray in circulating CD8(+) T cells isolated from patients with active TB and healthy controls. Change predictions to analysis was used to address functional roles of the deregulated mRNAs. Real-time quantitative PCR (RT-qPCR) was used to validate the microarray result...
April 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#17
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28420874/therapeutic-targeting-using-tumor-specific-peptides-inhibits-long-non-coding-rna-hotair-activity-in-ovarian-and-breast-cancer
#18
Ali R Özeş, Yinu Wang, Xingyue Zong, Fang Fang, Jay Pilrose, Kenneth P Nephew
Long non-coding RNAs (lncRNAs) play key roles in human diseases, including cancer. Functional studies of the lncRNA HOTAIR (HOX transcript antisense RNA) provide compelling evidence for therapeutic targeting of HOTAIR in cancer, but targeting lncRNAs in vivo has proven to be difficult. In the current study, we describe a peptide nucleic acids (PNA)-based approach to block the ability of HOTAIR to interact with EZH2 and subsequently inhibit HOTAIR-EZH2 activity and resensitize resistant ovarian tumors to platinum...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420615/the-mechanism-and-clinical-significance-of-long-noncoding-rna-mediated-gene-expression-via-nuclear-architecture
#19
Shi Jian, Li Yanming, Fang Xiangdong
Long noncoding RNAs (lncRNAs) are a class of non-protein coding transcripts exceeding 200 nucleotides in length. Accumulating evidence achieved by several sophisticated techniques such as chromatin conformation capture and RNA-seq has led to new questions concerning correlations between lncRNAs and chromatin structures. Many studies have revealed that lncRNAs exert great influences on gene expression through regulating chromatin 3D structures. In addition, lncRNAs play a crucial role in tumorigenesis and therefore hold great promises in disease diagnosis and prognosis...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420548/expression-of-long-non-coding-rnas-in-autoimmunity-and-linkage-to-enhancer-function-and-autoimmune-disease-risk-genetic-variants
#20
T M Aune, P S Crooke, A E Patrick, J T Tossberg, N J Olsen, C F Spurlock
Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk. Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear. The majority of the human genome is transcribed yet its biologic significance is incompletely understood. We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders...
April 15, 2017: Journal of Autoimmunity
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