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long noncoding Rnas

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https://www.readbyqxmd.com/read/28449042/long-noncoding-rna-a-crosslink-in-biological-regulatory-network
#1
Yuwei Zhang, Yang Tao, Qi Liao
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil...
April 24, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28446963/new-lncs-to-mesendoderm-specification
#2
REVIEW
Michael Alexanian, Thierry Pedrazzini, Samir Ounzain
Mammalian genomes are pervasively transcribed generating thousands of long noncoding RNAs (lncRNAs) with emergent regulatory roles. Many of these lncRNAs exhibit highly specialised expression patterns during development and typically flank and regulate key developmental factors. In this review, we discuss and summarise the latest advances in our understanding of the roles of lncRNAs during mesendoderm (ME) specification, a key step during gastrulation and the formation of the primitive streak (PS).
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446531/mining-exosomal-genes-for-pancreatic-cancer-targets
#3
Amy Makler, Ramaswamy Narayanan
BACKGROUND: Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. MATERIALS AND METHODS: Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28445933/the-long-noncoding-rna-hotair-promotes-parkinson-s-disease-by-upregulating-lrrk2-expression
#4
Sheng Wang, Xuan Zhang, Yuanyuan Guo, Han Rong, Tiebang Liu
Long noncoding RNAs (lncRNAs) have emerged recently as a new class of genes that regulate cellular processes. HOTAIR (Hox transcript antisense intergenic RNA), an approximately 2.2 kb long noncoding RNA transcribed from the HOXC locus, is upregulated in various diseases. However, the role of HOTAIR in Parkinson's disease (PD) remains unclear. A mouse model of PD was developed by intraperitoneal injection of MPTP. The expression of HOTAIR and LRRK2 were detected in the PD mice and in human neuroblastoma cell lines SH-SY5Y pretreated with MPP+...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444881/a-three-lncrna-expression-signature-associated-with-the-prognosis-of-gastric-cancer-patients
#5
Peng Song, Bo Jiang, Zhijian Liu, Jie Ding, Song Liu, Wenxian Guan
Long noncoding RNAs (lncRNAs) have emerged as essential players in gene regulation. An ever-increasing number of lncRNAs has been found to be associated with the biogenesis and prognosis of gastric cancer (GC). We aimed to develop an lncRNA signature with prognostic value for survival outcomes of GC. Using an lncRNA mining approach, we analyzed the lncRNA expression profiles of 492 GC patients from the Gene Expression Omnibus (GEO), which consisted of the GSE62254 set (N = 300) and the GSE15459 set (N = 192)...
April 26, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28444293/regulation-of-hematopoiesis-and-immune-responses-by-long-noncoding-rnas
#6
Wooseok Seo, Ichiro Taniuchi
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of noncoding RNAs...
April 22, 2017: International Immunology
https://www.readbyqxmd.com/read/28441948/over-expressed-long-noncoding-rna-hoxa11-as-promotes-cell-cycle-progression-and-metastasis-in-gastric-cancer
#7
Zhili Liu, Zhenyao Chen, Ruihua Fan, Bin Jiang, Xin Chen, Qinnan Chen, Fengqi Nie, Kaihua Lu, Ming Sun
BACKGROUND: Long noncoding RNAs (lncRNAs) have emerged as critical regulators in a variety of human cancers, including gastric cancer (GC). However, the function and mechanisms responsible for these molecules in GC are not fully understood. In our previous study, we found that GC associated lncRNA HOXA11-AS is significantly upregulated in GC tissues. Over-expressed HOXA11-AS promotes GC cells proliferation and invasion through scaffolding the chromatin modification factors PRC2, LSD1 and DNMT1...
April 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28441084/the-emergence-of-noncoding-rnas-as-heracles-in-autophagy
#8
Jian Zhang, Peiyuan Wang, Lin Wan, Shouping Xu, Da Pang
Macroautophagy/autophagy is a catabolic process that is widely found in nature. Over the past few decades, mounting evidence has indicated that noncoding RNAs, ranging from small noncoding RNAs to long noncoding RNAs (lncRNAs) and even circular RNAs (circRNAs), mediate the transcriptional and post-transcriptional regulation of autophagy-related genes by participating in autophagy regulatory networks. The differential expression of noncoding RNAs affects autophagy levels at different physiological and pathological stages, including embryonic proliferation and differentiation, cellular senescence, and even diseases such as cancer...
April 25, 2017: Autophagy
https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#9
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28438520/urinary-long-noncoding-rnas-in-nonmuscle-invasive-bladder-cancer-new-architects-in-cancer-prognostic-biomarkers
#10
REVIEW
Daniela Terracciano, Matteo Ferro, Sara Terreri, Giuseppe Lucarelli, Carolina D'Elia, Gennaro Musi, Ottavio de Cobelli, Vincenzo Mirone, Amelia Cimmino
Several reports over the last 10 years provided evidence that long noncoding RNAs (lncRNAs) are often altered in bladder cancers. lncRNAs are longer than 200 nucleotides and function as important regulators of gene expression, interacting with the major pathways of cell growth, proliferation, differentiation, and survival. A large number of lncRNAs has oncogenic function and is more expressed in tumor compared with normal tissues. Their overexpression may be associated with tumor formation, progression, and metastasis in a variety of tumors including bladder cancer...
April 7, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28433650/long-noncoding-rna-malat1-is-a-potent-autophagy-inducer-protecting-brain-microvascular-endothelial-cells-against-oxygen-glucose-deprivation-reoxygenation-induced-injury-by-sponging-mir-26b-and-upregulating-ulk2-expression
#11
Zhijun Li, Jing Li, Na Tang
Brain microvascular endothelial cell (BMEC) injury induced by ischemia-reperfusion (I/R) is the initial stage of blood-brain barrier (BBB) disruption, which results in a poor prognosis in ischemic stroke patients. Autophagy has been shown to have protective effects on BMECs against cerebral ischemic insults. However, molecular mechanism of BMEC autophagy during I/R is unclear. Long noncoding RNAs (lncRNAs) are emerging as new factors involved in cell autophagy. LncRNA Malat1 is one of the most highly upregulated I/R or OGD/R-responsive endothelial lncRNA and plays a protective role in BMECs against cerebral ischemic insults...
April 20, 2017: Neuroscience
https://www.readbyqxmd.com/read/28431855/relationship-between-long-noncoding-rnas-and-physiological-risk-factors-of-cardiovascular-disease
#12
REVIEW
Moshen Mazidi, Peter Penson, Anna Gluba-Brzozka, Jacek Rysz, Maciej Banach
Long noncoding ribonucleic acids (lncRNAs) are an important category of noncoding RNAs that play crucial roles in controlling the expression of genes in health and in a range of illnesses including cardiovascular disease. A large body of genetic, experimental, and epidemiologic evidence suggests roles for an increasing number of lncRNAs in the regulation of metabolism, lipid profile, inflammation, and glucose metabolism in type II diabetes. Importantly, it has been suggested that lncRNAs can regulate chromatin alteration, messenger RNA stability, microRNA action, and can control transcription factors...
March 27, 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/28430799/diagnostic-and-prognostic-value-of-long-noncoding-rnas-as-biomarkers-in-urothelial-carcinoma
#13
Johanna Droop, Tibor Szarvas, Wolfgang A Schulz, Christian Niedworok, Günter Niegisch, Kathrin Scheckenbach, Michèle J Hoffmann
Many long noncoding RNAs (lncRNAs) are deregulated in cancer and contribute to oncogenesis. In urothelial carcinoma (UC), several lncRNAs have been reported to be overexpressed and proposed as biomarkers. As most reports have not been confirmed independently in large tissue sets, we aimed to validate the diagnostic and prognostic value of lncRNA upregulation in independent cohorts of UC patients. Thus, expression of seven lncRNA candidates (GAS5, H19, linc-UBC1, MALAT1, ncRAN, TUG1, UCA1) was measured by RT-qPCR in cell lines and tissues and correlated to clinicopathological parameters including follow-up data (set 1: N n = 10; T n = 106)...
2017: PloS One
https://www.readbyqxmd.com/read/28428329/visualization-of-rna-structure-models-within-the-integrative-genomics-viewer
#14
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/28428004/long-noncoding-rna-awpph-promotes-hepatocellular-carcinoma-progression-through-ybx1-and-serves-as-a-prognostic-biomarker
#15
Xiaodong Zhao, Yanbo Liu, Shuo Yu
Long noncoding RNAs (lncRNAs) have been shown to play important roles in various cancers. However, the clinical significances and biological roles of lncRNAs in hepatocellular carcinoma (HCC) remain largely unknown. In this study, using online-available data sets and quantitative real-time PCR, we identified a novel lncRNA termed lncRNA-AWPPH, which is highly expressed in HCC tissues. Its upregulation is correlated with encapsulation incomplete, microvascular invasion, advanced TNM stage and BCLC stage. Cox proportional hazards regression analysis revealed that high lncRNA-AWPPH expression is an independent prognostic factor for poor recurrence-free and overall survival...
April 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28427159/genome-wide-analysis-of-long-noncoding-rna-and-mrna-co-expression-profile-in-intrahepatic-cholangiocarcinoma-tissue-by-rna-sequencing
#16
Wenhui Yang, Yuan Li, Xia Song, Jun Xu, Jun Xie
Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA).We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues...
February 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425074/lincrna-p21-function-and-mechanism-in-cancer
#17
REVIEW
Shaoyun Chen, Hairong Liang, Hui Yang, Kairu Zhou, Longmei Xu, Jiaxian Liu, Bei Lai, Li Song, Hao Luo, Jianming Peng, Zhidong Liu, Yongmei Xiao, Wen Chen, Huanwen Tang
In view of the rapid development of gene chips and high-throughput sequencing technology, noncoding RNAs (ncRNas) form a high percentage of the mammalian genome. Two major subgroups of ncRNAs that have been identified are the long ncRNAs (lncRNas) and the microRNAs. A number of studies in the past few years have showed crucial functions for lncRNas in cancer. LincRNa-p21 as a p53-dependent transcriptional target gene and a potential diagnostic marker is involved in proliferation, cell cycle, metabolism and reprogramming...
May 2017: Medical Oncology
https://www.readbyqxmd.com/read/28423732/long-intergenic-noncoding-rna-00673-promotes-non-small-cell-lung-cancer-metastasis-by-binding-with-ezh2-and-causing-epigenetic-silencing-of-hoxa5
#18
Chenhui Ma, Guannan Wu, Qingqing Zhu, Hongbing Liu, Yanwen Yao, Dongmei Yuan, Yafang Liu, Tangfeng Lv, Yong Song
Metastasis of cancer cells is a key impediment to favorable outcomes of cancer treatment. Functional roles of long noncoding RNAs in several biological processes, including metastasis, have recently been discovered. In our previous work, we reported a positive correlation of increased expression of linc00673 in NSCLC tissues with tumor size, lymph node metastasis, TNM stage, and increased proliferation of NSCLC cells, both, in vitro and in vivo. In this study, we demonstrate that ectopic expression of linc00673 promotes migration and invasion of NSCLC cells...
March 13, 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
#19
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
#20
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
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