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Long noncoding rna

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https://www.readbyqxmd.com/read/29035442/long-noncoding-rna-pvt1-as-a-potent-predictor-of-prognosis-in-cancers-a-meta-analysis
#1
Xuefeng Pan, Baohui Li, Naijun Fan, Juntang Li, Fengbo Cai, Guang Zhao, Guobao Zheng, Chunfang Gao
BACKGROUND: Plasmacytoma variant translocation 1 (PVT1), an oncogenic long noncoding RNA located in a recognized cancer-risk gene region-8q24, is significantly overexpressed in various cancers. Many studies have found that high expression of PVT1 was correlated with poor prognosis. METHODS: This meta-analysis was performed by searching electronic databases Pubmed, Web of Science, Chinese National Knowledge Infrastructure, WanFang, and ChongQing VIP for eligible papers on the prognostic impact and clinicopathological characteristics of PVT1 expression in cancer from inception to January 31, 2017...
October 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/29033588/hoxd-as1-functions-as-an-oncogenic-cerna-to-promote-nsclc-cell-progression-by-sequestering-mir-147a
#2
Qinghua Wang, Shujun Jiang, Anying Song, Siyuan Hou, Qinfeng Wu, Longju Qi, Xiang Gao
Non-small cell lung cancer (NSCLC) is one of the most common malignancies worldwide, and it occurs at a higher frequency in males. HOXD-AS1, an important cancer-associated long noncoding RNA (lncRNA), contributes to the development and progression of several cancers. However, the exact roles of HOXD-AS1 in NSCLC progression are still unknown. Here, we investigated the underlying mechanisms of HOXD-AS1 in human NSCLC tissues. We found that lncRNA HOXD-AS1 was specifically upregulated (P<0.001) in NSCLC tissues and promoted cancer cell growth by targeting miR-147a...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29030825/analysis-of-lncrna-protein-interactions-by-rna-protein-pull-down-assays-and-rna-immunoprecipitation-rip
#3
Holger Bierhoff
Long noncoding RNAs (lncRNAs) have important roles in shaping chromatin by targeting chromatin-modifying enzymes to distinct genomic sites. This section covers two methods to analyze lncRNA-protein interactions. The RNA-protein pull-down assays use either bead-bound proteins to capture in vitro transcripts, or immobilized synthetic RNAs to bind proteins from cell lysates. In the RNA immunoprecipitation (RIP) assay, endogenous RNAs are co-immunoprecipitated with a protein of interest. Both the methods can be applied to material from proliferating and quiescent cells, thus providing insights into how lncRNA-protein interactions are altered between these two cellular states...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029483/the-long-noncoding-rna-tug1-acts-as-a-competing-endogenous-rna-to-regulate-the-hedgehog-pathway-by-targeting-mir-132-in-hepatocellular-carcinoma
#4
Jingjing Li, Qinghui Zhang, Xiaoming Fan, Wenhui Mo, Weiqi Dai, Jiao Feng, Liwei Wu, Tong Liu, Sainan Li, Shizan Xu, Wenwen Wang, Xiya Lu, Qiang Yu, Kan Chen, Yujing Xia, Jie Lu, Yingqun Zhou, Ling Xu, Chuanyong Guo
Emerging evidence shows that the Hedgehog pathway and the long noncoding RNA TUG1 play pivotal roles in cell proliferation, migration, and invasion in tumors. However, the mechanism underlying the effect of TUG1 and the Hedgehog pathway in hepatoma remains undefined. In the present study, we showed that the expression of TUG1 was negatively correlated with that of microRNA (miR)-132, and depletion of TUG1 inhibited the activation of the Hedgehog pathway in vitro and in vivo. We showed that TUG1 functions as a competing endogenous (ceRNA) by competing with miR-132 for binding to the sonic hedgehog protein in HCC, thereby suppressing the activation of Hedgehog signaling and its tumorigenic effect...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029454/long-noncoding-rna-ab073614-promotes-the-malignance-of-glioma-by-activating-wnt-%C3%AE-catenin-signaling-through-downregulating-sox7
#5
Yuqian Li, Gang Zhu, Wen Zeng, Jiancai Wang, Zhihong Li, Bao Wang, Bo Tian, Dan Lu, Xingye Zhang, Guodong Gao, Lihong Li
Long noncoding RNA (lncRNA) AB073614 has recently shown to be aberrantly increased and identified as a poor prognostic biomarker in human glioma. However, the potential mechanisms remain unknown. This study demonstrated that AB073614 expression was significantly upregulated in both glioma tissues and cell lines, and glioma patients with high AB073614 expression had lower overall survival rates. Importantly, silencing AB073614 expression remarkably inhibited U251 cell proliferation, migration, and invasion in vitro, as well as suppressed tumor formation in vivo...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029323/lncrnal20992-regulates-apoptotic-proteins-to-promote-lead-induced-neuronal-apoptosis
#6
Aruo Nan, Yangyang Jia, Xin Li, Meiling Liu, Nan Zhang, Lijian Chen, Ti Yang, Yiqin Xu, Xin Dai, Ying Cheng, Zhenzhong Liu, Yihui Ling, Yiguo Jiang
Lead is a heavy metal pollutant that is widely present in the environment and can seriously harm human health, especially the nervous system. Long noncoding RNAs (lncRNAs) play important roles in many physiological and pathological processes; however, there remains a lack of in-depth studies on the molecular mechanisms associated with lead neurotoxicity. Here, our results showed that lead exposure inhibited cell proliferation and promoted cell apoptosis. We observed that lncRNAL20992 was significantly upregulated in a lead-induced neuronal-injury cell model according to quantitative reverse transcription polymerase chain reaction...
September 25, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29028415/crispr-cas9-mediated-noncoding-rna-editing-in-human-cancers
#7
Jie Yang, Xiaodan Meng, Jinchang Pan, Nan Jiang, Chengwei Zhou, Zhenhua Wu, Zhaohui Gong
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system...
October 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29027165/chromatin-rna-immunoprecipitation-chrip
#8
Tanmoy Mondal, Santhilal Subhash, Chandrasekhar Kanduri
Researchers have recently had a growing interest in understanding the functional role of long noncoding RNAs (lncRNAs) in chromatin organization. Accumulated evidence suggests lncRNAs could act as interphase molecules between chromatin and chromatin remodelers to define the epigenetic code. However, it is not clear how lncRNAs target chromatin remodelers to specific chromosomal regions in order to establish a functionally distinct epigenetic state of chromatin. We developed and optimized chromatin RNA immunoprecipitation (ChRIP) technology to characterize the lncRNAs associated with active and inactive chromatin compartments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29025584/regulatory-mechanisms-of-long-noncoding-rnas-on-gene-expression-in-cancers
#9
REVIEW
Weiliang Sun, Yunben Yang, Chunjing Xu, Junming Guo
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. HOTAIR and ANRIL function in chromatin remodeling...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29024030/melatonin-prevents-endothelial-cell-pyroptosis-via-regulation-of-long-noncoding-rna-meg3-mir-223-nlrp3-axis
#10
Yong Zhang, Xin Liu, Xue Bai, Yuan Lin, Zhange Li, Jiangbo Fu, Mingqi Li, Tong Zhao, Huan Yang, Ranchen Xu, Jiamin Li, Jin Ju, Benzhi Cai, Chaoqian Xu, Baofeng Yang
Atherosclerosis (AS) is an inflammatory disease linked to endothelial dysfunction. Melatonin is reported to possess substantial anti-inflammatory properties, which has proven to be effective in AS. Emerging literature suggests that pyroptosis plays a critical role during AS progression. However, whether pyroptosis contributes to endothelial dysfunction and the underlying molecular mechanisms remained unexploited. This study was designed to investigate the anti-pyroptotic effects of melatonin in atherosclerotic endothelium and to elucidate the potential mechanisms...
October 11, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/29022892/the-lncrna-hulc-functions-as-an-oncogene-by-targeting-atg7-and-itgb1-in-epithelial-ovarian-carcinoma
#11
Shuo Chen, Dan-Dan Wu, Xiu-Bo Sang, Li-Li Wang, Zhi-Hong Zong, Kai-Xuan Sun, Bo-Liang Liu, Yang Zhao
Highly upregulated in liver cancer (HULC) is a long noncoding RNA (lncRNA), which has recently been identified as a key regulator in the progression of hepatocellular carcinoma, gliomas and gastric cancer. However, its role in epithelial ovarian carcinoma (EOC) remains unknown. In this study, HULC expression was examined in EOC, borderline and benign ovarian tumors, and normal ovarian tissues by RT-PCR. Ovarian cancer cell phenotypes, as well as autophagy-associated proteins were examined after HULC overexpression or downregulation by plasmid or small interfering RNA (siRNA) transfection, respectively...
October 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29021209/transcription-profiling-suggests-that-mitochondrial-topoisomerase-ib-acts-as-a-topological-barrier-and-regulator-of-mitochondrial-dna-transcription
#12
Ilaria Dalla Rosa, Hongliang Zhang, Salim Khiati, Xiaolin Wu, Yves Pommier
Mitochondrial DNA (mtDNA) is essential for cell viability because it encodes subunits of the respiratory chain complexes. Mitochondrial topoisomerase IB (TOP1MT) facilitates mtDNA replication by removing DNA topological tensions produced during mtDNA transcription, but appears to be dispensable. To test whether cells lacking TOP1MT have aberrant mtDNA transcription, we performed mitochondrial transcriptome profiling. To that end, we designed and implemented a customized tiling array, which enabled genome-wide, strand-specific, and simultaneous detection of all mitochondrial transcripts...
October 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29017417/aberrant-expression-of-lncrna-hoxa11-as1-and-homeobox-a-hoxa9-hoxa10-hoxa11-and-hoxa13-genes-in-infertile-women-with-endometriosis
#13
Meimei Wang, Cuifang Hao, Xin Huang, Hongchu Bao, Qinglan Qu, Zhenteng Liu, Huangguan Dai, Shunzhi He, Wei Yan
This study aimed to study the expression of homeobox (HOX)A11-AS1 ( HOXA11 antisense RNA) long noncoding RNA (lncRNA) and the expression of homeobox A ( HOXA9, HOXA10, HOXA11, and HOXA13) genes in the eutopic (EU) and ectopic (EC) endometria of women with peritoneal endometriosis. A total of 30 women undergoing laparoscopic surgery for peritoneal endometriosis and 15 infertile women without endometriosis were enrolled in this study. Peritoneal EC tissue samples were obtained through surgery. The EU tissues were obtained by curettage...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/29016307/the-differential-expression-and-possible-function-of-long-noncoding-rnas-in-liver-cells-infected-by-dengue-virus
#14
Xiao-Jun Wang, Shi-Chen Jiang, Hai-Xia Wei, Sheng-Qun Deng, Cheng He, Hong-Juan Peng
The function of long noncoding RNAs (lncRNAs) in liver injury resulted by dengue virus (DENV) infection have not yet been explored. The differential expression profiles of lncRNAs coupled with mRNAs in L-02 liver cells in the DENV1 infected, DENV2 infected, and untreated control group were analyzed after high throughput RNA sequencing, the significantly upregulated and downregulated lncRNAs or mRNAs comparing with the control group were identified with a cutoff value at log2 (ratio) ≥ 1.5 and log2 (ratio) ≤ -1...
October 2, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28993514/the-nf-%C3%AE%C2%BAb-responsive-long-noncoding-rna-firre-regulates-posttranscriptional-regulation-of-inflammatory-gene-expression-through-interacting-with-hnrnpu
#15
Yajing Lu, Xu Liu, Minghong Xie, Mingjia Liu, Mengling Ye, Mingxuan Li, Xian-Ming Chen, Xiaoqing Li, Rui Zhou
Long noncoding RNAs, a newly identified class of noncoding RNAs, are important regulators of gene expression in innate immunity. We report in this study that the transcription of FIRRE, a conserved long noncoding RNA between humans and mice, is controlled by NF-κB signaling in macrophages and intestinal epithelial cells. Functionally, FIRRE appears to positively regulate the expression of several inflammatory genes in macrophages or intestinal epithelial cells in response to LPS stimulation via posttranscriptional mechanisms...
October 9, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28993096/altered-expression-of-malat1-lncrna-in-nonalcoholic-steatohepatitis-fibrosis-regulates-cxcl5-in-hepatic-stellate-cells
#16
Fatjon Leti, Christophe Legendre, Christopher D Still, Xin Chu, Anthony Petrick, Glenn S Gerhard, Johanna K DiStefano
In the present study, we sought to identify long noncoding RNA (lncRNA) expression profiles in nonalcoholic steatohepatitis (NASH) patients with histologic evidence of lobular inflammation and advanced fibrosis. We profiled lncRNA expression using RNA-sequencing of wedge liver biopsies from 24 nonalcoholic fatty liver disease (NAFLD) patients with normal liver histology, 53 NAFLD patients with lobular inflammation, and 65 NAFLD patients with advanced fibrosis. Transcript profiling identified 4432 and 4057 differentially expressed lncRNAs in comparisons of normal tissue with lobular inflammation and fibrosis samples, respectively...
September 19, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28986790/holistic-and-affordable-analyses-of-microrna-expression-profiles-using-tagged-cdna-libraries-and-a-multiplex-sequencing-strategy
#17
Patrick P Weil, Yan Jaszczyszyn, Anne Baroin-Tourancheau, Jan Postberg, Laurence Amar
Small and long noncoding RNAs (ncRNAs) are key regulators of gene expression. Variations in ncRNA expression patterns can consequently affect the control of many cellular processes. Not just since 2006, when Andrew Z Fire and Craig C Mello were jointly awarded The Nobel Prize in Physiology or Medicine for their discovery of RNA interference, great efforts were undertaken to unleash the biomedical applicability of small noncoding RNAs, in particular microRNAs. With the technological evolution of massive parallel sequencing technologies over the last years, which now are available for an increasing number of scientists, there is a demand for comprehensible and efficient workflows reliable even for unique and valuable clinical specimens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28986780/rna-function-prediction
#18
Yongsheng Li, Juan Xu, Tingting Shao, Yunpeng Zhang, Hong Chen, Xia Li
Recent studies have shown that a considerable proportion of eukaryotic genomes are transcribed as noncoding RNA (ncRNA), and regulatory ncRNAs have attracted much attention from researchers in many fields, especially of microRNA (miRNA) and long noncoding RNA (lncRNA). However, most ncRNAs are functionally uncharacterized due to the difficulty to accurately identify their targets. In this chapter, we first summarize the most recent advances in ncRNA research and their primary function. We then discuss the current state-of-the-art computational methods for predicting RNA functions, which comprise three different categories: miRNA function prediction approaches using target genes, lncRNA function prediction based on the guilt-by-association principle, and RNA function prediction approaches based on competing endogenous RNA partners...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28985553/lncrnas-hif1a-as2-facilitates-the-up-regulation-of-hif-1%C3%AE-by-sponging-to-mir-153-3p-whereby-promoting-angiogenesis-in-huvecs-in-hypoxia
#19
Lingjuan Li, Mingyue Wang, Zhujun Mei, Wenfeng Cao, Yun Yang, Yanmei Wang, An Wen
Angiogenesis serves as an important protective mechanism against ischemic stroke, because angiogenesis promotes the generation of collateral circulation and consequently improves the blood supply to cerebral infraction areas. Long noncoding RNAs (lncRNAs), which can act as a competing endogenous RNA, mediate protein-coding gene expression by sponging miRNA. Based on previous studies, the present study hypothesized that lncRNAs HIF1A-AS2 by sponging to miR-153-3p might regulate expression of HIF-1α and its down-stream targets, thereby influencing angiogenesis in hypoxia...
October 3, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28984197/circular-rna-expression-profiles-and-features-in-human-tissues-a-study-using-rna-seq-data
#20
Tianyi Xu, Jing Wu, Ping Han, Zhongming Zhao, Xiaofeng Song
BACKGROUND: Circular RNA (circRNA) is one type of noncoding RNA that forms a covalently closed continuous loop. Similar to long noncoding RNA (lncRNA), circRNA can act as microRNA (miRNA) 'sponges' to regulate gene expression, and its abnormal expression is related to diseases such as atherosclerosis, nervous system disorders and cancer. So far, there have been no systematic studies on circRNA abundance and expression profiles in human adult and fetal tissues. RESULTS: We explored circRNA expression profiles using RNA-seq data for six adult and fetal normal tissues (colon, heart, kidney, liver, lung, and stomach) and four gland normal tissues (adrenal gland, mammary gland, pancreas, and thyroid gland)...
October 3, 2017: BMC Genomics
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