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long noncoding Rnas

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https://www.readbyqxmd.com/read/28106309/transposable-elements-tes-contribute-to-stress-related-long-intergenic-noncoding-rnas-in-plants
#1
Dong Wang, Zhipeng Qu, Lan Yang, Qingzhu Zhang, Zhi-Hong Liu, Trung Do, David L Adelson, Zhen-Yu Wang, Iain Searle, Jian-Kang Zhu
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown...
January 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28106228/expression-of-long-non-coding-rna-pandar-and-its-prognostic-value-in-colorectal-cancer-patients
#2
Xiangke Li, Feng Wang, Yan Sun, Qingxia Fan, Guangfei Cui
BACKGROUND: Long noncoding RNAs (lncRNAs) are emerging as key molecules in human cancer. In the present study, we explored the role of the lncRNA PANDAR in colorectal cancer (CRC). METHODS: The relative expression level of lncRNA PANDAR in CRC tissues and cell lines was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The associations between PANDAR expression and clinicopathological features of CRC patients were further analyzed. Kaplan-Meier survival analysis was performed to evaluate the value of PANDAR in the prognosis of CRC patients...
January 20, 2017: International Journal of Biological Markers
https://www.readbyqxmd.com/read/28105536/a-long-noncoding-rna-uca1-promotes-proliferation-and-predicts-poor-prognosis-in-glioma
#3
W Zhao, C Sun, Z Cui
BACKGROUND: Acting as a proto-oncogene, long noncoding RNAs (lncRNAs) urothelial carcinoembryonic antigen 1 (UCA1) plays a key role in the occurrence and development of several human tumors. However, the expression and biological functions of UCA1 in glioma are less known. This study discussed the expression of UCA1 in glioma and its effect on the proliferation and cell cycle of glioma cells. METHOD: LncRNA UCA1 expressions in 64 glioma samples (Grade I-II in 22 cases and Grade III-IV in 42 cases, according to WHO criteria) and 10 normal brain samples were detected using real-time fluorescence quantitative PCR...
January 19, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28105167/cisplatin-induces-hepg2-cell-cycle-arrest-through-targeting-specific-long-noncoding-rnas-and-the-p53-signaling-pathway
#4
Ping Wang, Jiayue Cui, Jihong Wen, Yunhui Guo, Liangzi Zhang, Xia Chen
Cisplatin has been used effectively in the treatment of hepatocellular carcinoma (HCC). Long noncoding RNAs (lncRNAs) were recently reported to contribute to the pathogenesis and progression of HCC. Their molecular mechanism related to cisplatin treatment remains unclear. The purpose of this study is to identify specific lncRNAs and to clarify their functions in HCC after cisplatin exposure. Reannotation and identification of differentially expressed lncRNAs were performed using the microarray data set GSE38122 in the Gene Expression Omnibus database...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28104771/circulating-noncoding-rnas-as-biomarkers-of-cardiovascular-disease-and-injury
#5
REVIEW
Janika Viereck, Thomas Thum
The discovery of thousands of noncoding RNAs (ncRNAs) has expanded our view on mammalian genomes and transcriptomes, as well as their organization and regulation. Accumulating evidence on aberrantly regulated ncRNAs, including short microRNAs, long ncRNAs and circular RNAs, across various heart diseases indicates that ncRNAs are critical contributors to cardiovascular pathophysiology. In addition, ncRNAs are released into the circulation where they are present in concentration levels that differ between healthy subjects and diseased patients...
January 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28104764/long-noncoding-rnas-in-pathological-cardiac-remodeling
#6
Janika Viereck, Thomas Thum
A novel long noncoding RNA Chaer acts as noncoding epigenetic regulator at the onset of cardiac hypertrophy and enables an improved understanding about the complex mechanisms in cardiovascular disease.
January 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#7
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#8
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#9
Gerald Arthur, Md Almamun, Kristen Taylor
AIM: Long noncoding RNAs serve critical regulatory functions highly specific for a tissue and its developmental stage. Antisense long ncRNA (AS-lncRNA) methylation changes in acute lymphoblastic leukemia (ALL) versus normal pre-B-cell lymphoblasts were evaluated to identify potential differential methylation in this group of genes. MATERIALS & METHODS: The methylome of ALL and normal lymphoblasts was examined by the methylated CpG island recovery assay followed by NGS...
January 17, 2017: Epigenomics
https://www.readbyqxmd.com/read/28093235/expression-profile-of-lncrna-in-human-bronchial-epithelial-cells-response-to-talaromyces-marneffei-infection-a-microarray-analysis
#10
Yinghua Li, Meihua Li, Honglin Luo, Xiuwan Lan, Jianquan Zhang, Xiaoning Zhong, Jing Bai, Zhiyi He
Talaromyces marneffei is an important opportunistic pathogenic fungus capable of causing systemic lethal infection through inhalation of its conidia. However, little is known about the pathogenesis and interactions between Talaromyces marneffei and host. The aim of this study was to identify potential long noncoding RNAs (lncRNAs) and genes associated with interactions between airway epithelial cell and Talaromyces marneffei conidia. We carried out a microarray analysis to determine the expression profile of lncRNA and mRNA in human bronchial epithelial cell in response to Talaromyces marneffei infection...
January 13, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28092449/long-noncoding-rna-as-an-indicator-differentiating-schizophrenia-from-major-depressive-disorder-and-generalized-anxiety-disorder-in-nonpsychiatric-hospital
#11
Xuelian Cui, Wei Niu, Lingming Kong, Mingjun He, Kunhong Jiang, Shengdong Chen, Aifang Zhong, Qiaoli Zhang, Wanshuai Li, Jim Lu, Liyi Zhang
AIM: Depression and anxiety are common symptoms for schizophrenia (SZ) in the early onset. This study aimed to determine whether long noncoding RNAs (lncRNAs) can be indicators for diagnosing SZ in nonpsychiatric hospitals. MATERIALS & METHODS: Three upregulated SZ lncRNAs, six downregulated major depressive disorder (MDD) lncRNAs and three upregulated generalized anxiety disorder (GAD) lncRNAs were cross-validated in 45 SZ patients, 48 MDD patients, 52 GAD patients and 40 controls by reverse transcription-PCR...
January 16, 2017: Biomarkers in Medicine
https://www.readbyqxmd.com/read/28088836/upregulation-of-long-noncoding-rna-tug1-promotes-cervical-cancer-cell-proliferation-and-migration
#12
Yingying Hu, Xiangwei Sun, Chenchen Mao, Gangqiang Guo, Sisi Ye, Jianfeng Xu, Ruanmin Zou, Jun Chen, Ledan Wang, Ping Duan, Xiangyang Xue
Long noncoding RNAs (lncRNAs), a novel class of transcripts that have critical roles in carcinogenesis and progression, have emerged as important gene expression modulators. Recent evidence indicates that lncRNA taurine-upregulated gene 1 (TUG1) functions as an oncogene in numerous types of human cancers. However, its function in the development of cervical cancer remains unknown. The aim of this research was to investigate the clinical significance and biological functions of TUG1 in cervical cancer. TUG1 was found to be significantly upregulated in cervical cancer tissues and four cervical cancer cell lines by quantitative real-time polymerase chain reaction (qRT-PCR)...
January 15, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28086904/the-lncrna-crnde-promotes-colorectal-cancer-cell-proliferation-and-chemoresistance-via-mir-181a-5p-mediated-regulation-of-wnt-%C3%AE-catenin-signaling
#13
Peng Han, Jing-Wen Li, Bo-Miao Zhang, Jia-Chen Lv, Yong-Min Li, Xin-Yue Gu, Zhi-Wei Yu, Yun-He Jia, Xue-Feng Bai, Li Li, Yan-Long Liu, Bin-Bin Cui
BACKGROUND: With more than 600,000 mortalities each year, colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide. Recently, mechanisms involving noncoding RNAs have been implicated in the development of CRC. METHODS: We examined expression levels of lncRNA CRNDE and miR-181a-5p in 64 cases of CRC tissues and cell lines by qRT-PCR. Gain-of-function and loss-of-function assays were performed to examine the effect of CRNDE and miR-181a-5p on proliferation and chemoresistance of CRC cells...
January 13, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28079712/a-comprehensive-review-of-genomics-and-noncoding-rna-in-gliomas
#14
Ahmed Hassan, Jennifer Mosley, Sanjay Singh, Pascal Olivier Zinn
Glioblastoma (GBM) is the most malignant primary adult brain tumor. In spite of our greater understanding of the biology of GBMs, clinical outcome of GBM patients remains poor, as their median survival with best available treatment is 12 to 18 months. Recent efforts of The Cancer Genome Atlas (TCGA) have subgrouped patients into 4 molecular/transcriptional subgroups: proneural, neural, classical, and mesenchymal. Continuing efforts are underway to provide a comprehensive map of the heterogeneous makeup of GBM to include noncoding transcripts, genetic mutations, and their associations to clinical outcome...
January 11, 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28076325/identification-of-long-noncoding-rnas-for-the-detection-of-early-stage-lung-squamous-cell-carcinoma-by-microarray-analysis
#15
Zule Cheng, Yanan Bai, Ping Wang, Zhenhua Wu, Lin Zhou, Ming Zhong, Qinghui Jin, Jianlong Zhao, Hailei Mao, Hongju Mao
The aberrant expressions of long noncoding RNAs have been reported in numerous cancers, which have facilitated the cancer diagnosis. However, the expression profile of lncRNAs in early stage lung squamous cell carcinoma has not been well discussed. The present study aimed to examine the expression profile of lncRNAs in early stage lung squamous cell carcinoma and identify lncRNA biomarkers for diagnosis. Through high-throughput lncRNA microarray, we screened thousands of aberrantly expressed lncRNAs and mRNAs in early stage lung squamous cell carcinoma tissues compared to their corresponding adjacent nontumorous tissues...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28073357/long-noncoding-rna-repertoire-in-chicken-liver-and-adipose-tissue
#16
Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Sandrine Lagarrigue
BACKGROUND: Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity...
January 10, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28068310/visualizing-the-secondary-and-tertiary-architectural-domains-of-lncrna-repa
#17
Fei Liu, Srinivas Somarowthu, Anna Marie Pyle
Long noncoding RNAs (lncRNAs) are important for gene expression, but little is known about their structures. RepA is a 1.6-kb mouse lncRNA comprising the same sequence as the 5' region of Xist, including A and F repeats. It has been proposed to facilitate the initiation and spread of X-chromosome inactivation, although its exact role is poorly understood. To gain insight into the molecular mechanism of RepA and Xist, we determined a complete phylogenetically validated secondary-structural map of RepA through SHAPE and DMS chemical probing of a homogeneously folded RNA in vitro...
January 9, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28066612/elevated-hotair-expression-associated-with-cisplatin-resistance-in-non-small-cell-lung-cancer-patients
#18
Ming-Yue Liu, Xi-Qing Li, Tian-Hui Gao, Yao Cui, Ning Ma, Yun Zhou, Guo-Jun Zhang
BACKGROUND: This study investigated the mechanism of drug resistance in non-small cell lung cancer (NSCLC) patients. We specifically studied whether long noncoding RNAs influence drug resistance in NSCLC to discover new therapeutic targets to increase the survival rate of drug-resistant NSCLC patients. METHODS: Tissue samples were collected from NSCLC patients, and total RNA was isolated for assessment of HOTAIR expression and drug resistance status. MTT assays, tumor sphere formation assays, and western blot were performed to cytologically determine the relationship between HOTAIR expression and cisplatin resistance, as well as to elucidate the potential molecular mechanism involved...
November 2016: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28063931/long-noncoding-rna-h19-derived-mir-675-aggravates-restenosis-by-targeting-pten
#19
Junyuan Lv, Lei Wang, Jin Zhang, Ruoran Lin, Lun Wang, Weifeng Sun, Huize Wu, Shijie Xin
Restenosis is mainly attributed to excessive proliferation of vascular smooth muscle cells (VSMCs). Noncoding RNAs have been identified as key regulators of diverse pathological processes. We reported that the long noncoding RNA H19 (LncRNA H19) and LncRNA H19-derived microRNA (miR-675) are overexpressed in neointima of balloon-injured artery. Thus, the present study aims to evaluate the role of LncRNA H19 on VSMCs proliferation. To determine the changes of LncRNA H19 and miR-675 expression in the injured arterial wall, the standard rat carotid artery balloon injury model was used...
January 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28061329/not-just-noise-genomics-and-genetics-bring-long-noncoding-rnas-into-focus
#20
L Stirling Churchman
Thousands of long noncoding RNAs (lncRNAs) have been annotated, yet their functions remain unclear. Recent studies-including Schlackow et al. (2017) in this issue of Molecular Cell-using orthogonal methods investigated the expression and functions of lncRNAs, resulting in deeper appreciation for the salient differences between lncRNAs and mRNAs and the roles lncRNAs serve.
January 5, 2017: Molecular Cell
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