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https://www.readbyqxmd.com/read/28637296/omixcore-a-web-server-for-prediction-of-protein-interactions-with-large-rna
#1
Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia
Summary: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction; (ii) pre-compiled library for exploration of human long intergenic RNAs (lincRNAs) interactions; (iii) prediction of binding sites. Results: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation (eCLIP) data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#2
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/28592847/tgf-%C3%AE-induced-hepatocyte-lincrna-p21-contributes-to-liver-fibrosis-in-mice
#3
Xiaolong Tu, Yuanyuan Zhang, Xiuxiu Zheng, Jia Deng, Huanan Li, Zhiqian Kang, Zhipeng Cao, Zhen Huang, Zhi Ding, Lei Dong, Jiangning Chen, Yuhui Zang, Junfeng Zhang
Hepatocyte death, as well as the following inflammatory and fibrogenic signaling cascades, is the key trigger of liver fibrosis. Here, we isolated hepatocytes from CCl4-induced fibrotic liver and found that hepatocyte lincRNA-p21 significantly increased during liver fibrosis. The increase of hepatocyte lincRNA-p21 was associated with the loss of miR-30, which can inhibit TGF-β signaling by targeting KLF11. We revealed that lincRNA-p21 modulated miR-30 availability by acting as a competing endogenous RNA (ceRNA)...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28580169/endogenous-mirna-sponge-lincrna-ror-promotes-proliferation-invasion-and-stem-cell-like-phenotype-of-pancreatic-cancer-cells
#4
Zhiqiang Fu, Guolin Li, Zhihua Li, Yingxue Wang, Yue Zhao, Shangyou Zheng, Huilin Ye, Yuming Luo, Xiaohui Zhao, Lusheng Wei, Yimin Liu, Qing Lin, Quanbo Zhou, Rufu Chen
The long intergenic non-coding RNA, regulator of reprogramming (linc-ROR) is an oncogene and plays a key role in the embryonic stem cell maintenance and is involved in cancer progression. The objective of this study was to analyze linc-ROR expression in pancreatic ductal adenocarcinoma (PDAC) and determine the regulation effects of linc-ROR on proliferation and invasion of cancer cells, as well as properties of cancer stem-like cells (CSLCs). In this study, we found that linc-ROR was up-regulated in PDAC tissues and related to poor prognosis...
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/28536600/evolinc-a-tool-for-the-identification-and-evolutionary-comparison-of-long-intergenic-non-coding-rnas
#5
Andrew D L Nelson, Upendra K Devisetty, Kyle Palos, Asher K Haug-Baltzell, Eric Lyons, Mark A Beilstein
Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28516515/interaction-of-lincrna-ror-and-p53-mir-145-correlates-with-lung-cancer-stem-cell-signatures
#6
Fan Xia, Ye Xiong, Qiang Li
ROR is one of large intergenic non-coding RNAs (lincRNAs) and acts as a strong negative regulator of p53 and a sponge for miR-145 to regulate diverse cancer progression. However, the interaction of ROR, p53 and miR-145 in lung cancer and its correlation with lung cancer stem cell (LCSC) signatures were not fully understood. Here, qRT-PCR analysis revealed that p53 and ROR were upregulated while miR-145 was downregulated in non-small cell lung cancer (NSCLC) tissues and LCSCs compared to their paired adjacent normal tissues and lung cancer cells (LCCs)...
May 18, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28499146/rna-sequencing-reveals-pronounced-changes-in-the-noncoding-transcriptome-of-aging-synaptosomes
#7
Bei Jun Chen, Uwe Ueberham, James D Mills, Ludmil Kirazov, Evgeni Kirazov, Mara Knobloch, Jana Bochmann, Renate Jendrek, Konii Takenaka, Nicola Bliim, Thomas Arendt, Michael Janitz
Normal aging is associated with impairments in cognitive functions. These alterations are caused by diminutive changes in the biology of synapses, and ineffective neurotransmission, rather than loss of neurons. Hitherto, only a few studies, exploring molecular mechanisms of healthy brain aging in higher vertebrates, utilized synaptosomal fractions to survey local changes in aging-related transcriptome dynamics. Here we present, for the first time, a comparative analysis of the synaptosomes transcriptome in the aging mouse brain using RNA sequencing...
April 18, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28492554/the-novel-long-intergenic-noncoding-rna-ucc-promotes-colorectal-cancer-progression-by-sponging-mir-143
#8
Feng-Ting Huang, Wen-Ying Chen, Zhi-Qiang Gu, Yan-Yan Zhuang, Chu-Qiang Li, Ling-Yun Wang, Juan-Fei Peng, Zhe Zhu, Xin Luo, Yuan-Hua Li, He-Rui Yao, Shi-Neng Zhang
The human genome contains thousands of long intergenic noncoding RNAs (lincRNAs). However, the functional roles of these transcripts and the mechanisms responsible for their deregulation in colorectal cancer (CRC) remain elusive. A novel lincRNA termed upregulated in CRC (UCC) was found to be highly expressed in human CRC tissues and cell lines. UCC levels correlated with lymph node metastasis, Dukes' stage, and patient outcomes. In SW480 and SW620 cells, knockdown of UCC inhibited proliferation, invasion, and cell cycle progression and induced apoptosis in vitro...
May 11, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28472271/annotating-function-to-differentially-expressed-lincrnas-in-myelodysplastic-syndrome-using-a-network-based-method
#9
Keqin Liu, Dominik Beck, Julie A I Thoms, Liang Liu, Weiling Zhao, John E Pimanda, Xiaobo Zhou
Motivation: Long non-coding RNAs (lncRNAs) have been implicated in the regulation of diverse biological functions. The number of newly identified lncRNAs has increased dramatically in recent years but their expression and function have not yet been described from most diseases. To elucidate lncRNA function in human disease, we have developed a novel network based method (NLCFA) integrating correlations between lncRNA, protein coding genes and noncoding miRNAs. We have also integrated target gene associations and protein-protein interactions and designed our model to provide information on the combined influence of mRNAs, lncRNAs and miRNAs on cellular signal transduction networks...
May 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28455512/systematic-identification-and-characterization-of-cardiac-long-intergenic-noncoding-rnas-in-zebrafish
#10
Lei Wang, Xiao Ma, Xiaolei Xu, Yuji Zhang
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as potential key regulators of heart development and related diseases, but their identities and functions remain elusive. In this study, we sought to identify and characterize the cardiac lincRNA transcriptome in the experimentally accessible zebrafish model by integrating bioinformatics analysis with experimental validation. By conducting genome-wide RNA sequencing profiling of zebrafish embryonic hearts, adult hearts, and adult muscle, we generated a high-confidence set of 813 cardiac lincRNA transcripts, 423 of which are novel...
April 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425074/lincrna-p21-function-and-mechanism-in-cancer
#11
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/28423633/novel-lincrna-slinky-is-a-prognostic-biomarker-in-kidney-cancer
#12
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/28422321/aberrantly-expressed-long-non-coding-rnas-in-cd8-t-cells-response-to-active-tuberculosis
#13
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/28391277/lincrna-p21-inhibits-the-wnt-%C3%AE-catenin-pathway-in-activated-hepatic-stellate-cells-via-sponging-microrna-17-5p
#14
Fujun Yu, Yong Guo, Bicheng Chen, Liang Shi, Peihong Dong, Mengtao Zhou, Jianjian Zheng
BACKGROUND/AIMS: It is known that the activation of hepatic stellate cells (HSCs) is a pivotal step in the initiation and progression of liver fibrosis. Aberrant activated Wnt/β-catenin pathway is known to accelerate the development of liver fibrosis. microRNAs (miRNAs)-mediated Wnt/β-catenin pathway has been reported to be involved in HSC activation during liver fibrosis. However, whether long noncoding RNAs (lncRNAs) regulate Wnt/β-catenin pathway during HSC activation still remains unclear...
2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28389524/de-novo-rna-sequence-assembly-during-in-vivo-inflammatory-stress-reveals-hundreds-of-unannotated-lincrnas-in-human-blood-cd14-monocytes-and-in-adipose-tissue
#15
Chenyi Xue, Xuan Zhang, Hanrui Zhang, Jane F Ferguson, Ying Wang, Christine Hinkle, Mingyao Li, Muredach P Reilly
Long intergenic noncoding RNAs (lincRNAs) have emerged as key regulators of cellular functions and physiology. Yet functional lincRNAs often have low, context-specific and tissue-specific expression. We hypothesized that many human monocyte and adipose lincRNAs would be absent in current public annotations due to lincRNA tissue specificity, modest sequencing depth in public data, limitations of transcriptome assembly algorithms and lack of dynamic physiological contexts. Deep RNA-seq was performed in peripheral blood CD14+ monocytes (monocytes; average ~247 million reads per sample) and adipose tissue (average ~378 million reads per sample) collected before and after human experimental endotoxemia, an in vivo inflammatory stress, to identify tissue-specific and clinically relevant lincRNAs...
April 7, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28388536/long-noncoding-rna-ror-regulates-chemoresistance-in-docetaxel-resistant-lung-adenocarcinoma-cells-via-epithelial-mesenchymal-transition-pathway
#16
Yan Pan, Jing Chen, Leilei Tao, Kai Zhang, Rui Wang, Xiaoyuan Chu, Longbang Chen
Emerging evidence indicates that the dysregulation of long non-coding RNAs (lncRNAs) contributes to the development and progression of lung adenocarcinoma (LAD), however the underlying mechanism of action of lncRNAs remains unclear. It is well known that the effective treatment of cancers has been hindered by drug resistance in the clinical setting. Epithelial-mesenchymal transition (EMT) has been recognized to be involved in acquiring drug resistance, cell migration and invasion properties in several types of cancer...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28388302/genome-wide-association-and-replication-study-of-hepatotoxicity-induced-by-antiretrovirals-alone-or-with-concomitant-anti-tuberculosis-drugs
#17
Zelalem Petros, Ming Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo, Eleni Aklillu
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28385713/genome-wide-top2a-dna-cleavage-is-biased-towards-translocated-and-highly-transcribed-loci
#18
Xiang Yu, James W Davenport, Karen A Urtishak, Marie L Carillo, Sager J Gosai, Christos P Kolaris, Jo Ann W Byl, Eric F Rappaport, Neil Osheroff, Brian D Gregory, Carolyn Ann Felix
Type II topoisomerases orchestrate proper DNA topology and they are the targets of anticancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single base precision and use the technology to characterize TOP2A cleavage genome-wide in the human K562 leukemia cell line. We find that TOP2A cleavage has functionally conserved local sequence preferences, occurs in cleavage cluster regions (CCRs) and is enriched in introns and lincRNA loci...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28376483/long-non-coding-rnas-in-cardiac-remodeling
#19
REVIEW
Shutong Shen, Huimin Jiang, Yihua Bei, Junjie Xiao, Xinli Li
Cardiac remodeling occurs after stress to the heart, manifested as pathological processes, including hypertrophy and apoptosis of cardiomyocytes, dysfunction of vascular endothelial cells and vascular smooth muscle cells as well as differentiation and proliferation of fibroblasts, ultimately resulting in progression of cardiovascular diseases. Emerging evidence has revealed that long non-coding RNAs (lncRNAs) acted as powerful and dynamic modifiers of cardiac remodeling. LncRNAs including Chaer, Chast, Mhrt, CHRF, ROR, H19, and MIAT have been implicated in cardiac hypertrophy while NRF, H19, APF, CARL, UCA, Mhrt and several other lncRNAs (n379599, n379519, n384640, n380433 and n410105) in cardiomyocyte loss and extracellular matrix remodeling...
2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28370091/genotyping-by-sequencing-reveals-a-new-locus-for-pig-teat-number
#20
L Wang, Y Zhang, T Zhang, L Zhang, H Yan, X Liu, L Wang
Teat number is an extremely valuable trait for sow reproduction performance and piglet survival. Here, we used genotyping-by-sequencing and a general liner model to carry out genome-wide analysis of sow total teat number in an Erhualian population. The results indicated that eight SNPs on chromosomes 4, 5, 9 and 10 were significant genome wide (Bonferroni method, P < 2.85E-7) for sow total teat number. Validation analyses were performed in 298 Erhualian and 904 Large White sows using these significant SNPs and the general liner model procedure in sas...
April 3, 2017: Animal Genetics
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