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Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae...
October 2016: PLoS Neglected Tropical Diseases
Hongwei Wang, Yan Wang, Shangqian Xie, Yizhi Liu, Zhi Xie
Advances in transcriptomics have led to the discovery of a large number of long intergenic non-coding RNAs (lincRNAs), which are now recognized as important regulators of diverse cellular processes. Although originally thought to be non-coding, recent studies have revealed that many lincRNAs are bound by ribosomes, with a few lincRNAs even having ability to generate micropeptides. The question arises: how widespread the translation of lincRNAs may be and whether such translation is likely to be functional. To better understand biological relevance of lincRNA translation, we systematically characterized lincRNAs with ribosome occupancy by the expression, structural, sequence, evolutionary and functional features for eight human cell lines, revealed that lincRNAs with ribosome occupancy have remarkably distinctive properties compared with those without ribosome occupancy, indicating that translation has important biological implication in categorizing and annotating lincRNAs...
October 13, 2016: Nucleic Acids Research
Hui Liu, Jie Lyu, Hongbo Liu, Yang Gao, Jing Guo, Hongjuan He, Zhengbin Han, Yan Zhang, Qiong Wu
As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5' ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features...
October 7, 2016: Scientific Reports
Pengxiang Yang, Yue Yang, Weiwei An, Jianyu Xu, Gan Zhang, Jing Jie, Qingyuan Zhang
BACKGROUND AND AIM: LincRNAs have critical roles in elevating efficacy of anticancer therapy and tumor progression. Recent studies show that long intergenic noncoding RNA-ROR (lincRNA-ROR) is aberrantly expressed in several types of cancer, including colorectal cancer (CRC). Radiotherapy is considered as a standard preoperative treatment. However, a considerable number of CRCs are resistant to radiotherapy. In this study, we evaluated the role of lincRNA-ROR in radiotherapy for CRC and detected the underlying molecular mechanism...
October 3, 2016: Journal of Gastroenterology and Hepatology
Emre Deniz, Batu Erman
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome...
September 28, 2016: Functional & Integrative Genomics
Jing Hu, Jinyuan Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Chun Xu, Yun Xiao, Xia Li
Schizophrenia (SZ) and bipolar disorder (BD) are severe neuropsychiatric disorders with serious impact on patients, together termed "major psychosis". Recently, long intergenic non-coding RNAs (lincRNAs) were reported to play important roles in mental diseases. However, little was known about their molecular mechanism in pathogenesis of SZ and BD. Here, we performed RNA sequencing on 82 post-mortem brain tissues from three brain regions (orbitofrontal cortex (BA11), anterior cingulate cortex (BA24) and dorsolateral prefrontal cortex (BA9)) of patients with SZ and BD and control subjects, generating over one billion reads...
September 19, 2016: Oncotarget
Airi Tiirats, Triin Viltrop, Margit Nõukas, Ene Reimann, Andres Salumets, Sulev Kõks
BACKGROUND: Despite extensive research the genetic component of extremely low birth weight (ELBW) in newborns has remained obscure. RESULTS: The aim of the case study was to identify candidate gene(s) causing ELBW in newborns and hypotrophy in infants. A family of four was studied: mother, father and two ELBW-phenotype children. Studies were made of the medical conditions of the second child at birth and post-partum - peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy and suspected metabolic and chromosomal abnormalities...
2016: BMC Genetics
Niraj Khemka, Vikash Kumar Singh, Rohini Garg, Mukesh Jain
Non-coding RNAs constitute a major portion of the transcriptome in most of eukaryotes. Long non-coding transcripts originating from the DNA segment present between the protein coding genes are termed as long intergenic non-coding RNAs (lincRNAs). Several evidences suggest the role of lincRNAs in regulation of various biological processes. In this study, we identified a total of 2248 lincRNAs in chickpea using RNA-seq data from eight successive stages of flower development and three vegetative tissues via an optimized pipeline...
2016: Scientific Reports
Fujun Yu, Zhongqiu Lu, Bicheng Chen, Peihong Dong, Jianjian Zheng
Previously, we found that long intergenic noncoding RNA-p21 (lincRNA-p21) inhibits hepatic stellate cell (HSC) activation and liver fibrosis via p21. However, the underlying mechanism of the antifibrotic role of lincRNA-p21 in liver fibrosis remains largely unknown. Here, we found that lincRNA-p21 expression was significantly downregulated during liver fibrosis. In LX-2 cells, the reduction of lincRNA-p21 induced by TGF-β1 was in a dose- and time-dependent manner. lincRNA-p21 expression was reduced in liver tissues from patients with liver cirrhosis when compared with that of healthy controls...
2016: Mediators of Inflammation
Lijie Han, Shengnan Liu, Jia Liang, Yanli Guo, Supeng Shen, Xin Guo, Zhiming Dong, Wei Guo
Esophageal squamous cell carcinoma (ESCC) may be caused by a combination of environmental factors and genetic variants. The present study was to evaluate the association between haplotype-tagging SNPs (htSNPs) of lincRNA-NR_024015 and the risk of ESCC. We selected htSNPs across the whole 1469 bp lincRNA-NR_024015 locus and 2 kb upstream as well as 2 kb downstream regions of the gene and conducted a case-control study in 581 ESCC cases and 677 healthy controls to test the effects of functional lincRNA-NR_024015 htSNPs on ESCC susceptibility...
September 1, 2016: Molecular Carcinogenesis
Maoshan Chen, Hongxing Zhao, Sara Bergström Lind, Ulf Pettersson
Expression of cellular long non-coding RNAs (lncRNAs) in human primary lung fibroblasts (IMR-90) during the course of adenovirus type 2 (Ad2) infection was studied by strand-specific whole transcriptome sequencing. In total, 645 cellular lncRNAs were expressed at a significant level and 398 of them were changed more than 2-fold. The changes in expression followed a distinct temporal pattern. Significantly, 80% of the changes occurred at the late phase and 80% of the de-regulated lncRNAs were up-regulated. The three largest groups of deregulated lncRNAs were 125 antisense RNAs, 111 pseudogenes and 85 long intergenic non-coding RNAs (lincRNAs)...
September 2016: Data in Brief
Stanford Kwenda, Paul R J Birch, Lucy N Moleleki
BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues...
2016: BMC Genomics
Jiaqiang Wang, Xin Li, Leyun Wang, Jingyu Li, Yanhua Zhao, Gerelchimeg Bou, Yufei Li, Guanyi Jiao, Xinghui Shen, Renyue Wei, Shichao Liu, Bingteng Xie, Lei Lei, Wei Li, Qi Zhou, Zhonghua Liu
Endogenous retroviruses (ERVs) are transcriptionally active in cleavage stage embryos, yet their functions are unknown. ERV sequences are present in the majority of long intergenic noncoding RNAs (lincRNAs) in mouse and humans, playing key roles in many cellular processes and diseases. Here, we identify LincGET as a nuclear lincRNA that is GLN-, MERVL-, and ERVK-associated and essential for mouse embryonic development beyond the two-cell stage. LincGET is expressed in late two- to four-cell mouse embryos. Its depletion leads to developmental arrest at the late G2 phase of the two-cell stage and to MAPK signaling pathway inhibition...
October 2016: EMBO Reports
Joan J Castellano, Alfons Navarro, Nuria Viñolas, Ramon M Marrades, Jorge Moises, Anna Cordeiro, Adela Saco, Carmen Muñoz, Dolors Fuster, Laureano Molins, Josep Ramirez, Mariano Monzo
INTRODUCTION: Long intergenic noncoding RNA-p21 (lincRNA-p21) is a long noncoding RNA transcriptionally activated by tumor protein p53 (TP53) and hypoxia inducible factor 1 alpha subunit (HIF1A). It is involved in the regulation of TP53-dependent apoptosis and the Warburg effect. We have investigated the role of lincRNA-p21 in NSCLC. METHODS: LincRNA-p21 expression was assessed in tumor and normal tissue from 128 patients with NSCLC and correlated with time to relapse and cancer-specific survival (CSS)...
August 2, 2016: Journal of Thoracic Oncology
Jun Wang, Ying Wang, Weidong Gu, Buqing Ni, Haoliang Sun, Tong Yu, Wanjun Gu, Liang Chen, Yongfeng Shao
RNA sequencing (RNA-seq) has revolutionary roles in transcriptome identification and quantification of different types of tissues and cells in many organisms. Although numerous RNA-seq data derived from many types of human tissues and cell lines, little is known on the transcriptome repertoire of human aortic valve. In this study, we sequenced the total RNA prepared from two calcified human aortic valves and reported the whole transcriptome of human aortic valve. Integrating RNA-seq data of 13 human tissues from Human Body Map 2 Project, we constructed a transcriptome repertoire of human tissues, including 19,505 protein-coding genes and 4,948 long intergenic noncoding RNAs (lincRNAs)...
2016: Evolutionary Bioinformatics Online
Ruimin Gao, Peng Liu, Nadia Irwanto, De Rong Loh, Sek-Man Wong
A long intergenic noncoding RNA LINC - AP2 is upregulated and negatively correlated with AP2 gene expression with Turnip crinkle virus infection in Arabidopsis. Plant vegetative growth and floral reproductive structure were severely retarded and distorted in Turnip crinkle virus (TCV)-infected Arabidopsis thaliana. Compared to mock-inoculated plants, the stamen filaments were shorter in flowers of TCV-infected plants. However, TCV-infected plants can still produce normal seeds through artificial pollination, indicating both its pollen and stigma were biologically functional...
November 2016: Plant Cell Reports
Saleh A Al-Quraishy, Mohamed A Dkhil, Abdel-Azeem A Abdel-Baki, Denis Delic, Frank Wunderlich
Protective vaccination induces self-healing of otherwise fatal blood-stage malaria of Plasmodium chabaudi in female Balb/c mice. To trace processes critically involved in self-healing, the liver, an effector against blood-stage malaria, is analyzed for possible changes of its transcriptome in vaccination-protected in comparison to non-protected mice toward the end of the crisis phase. Gene expression microarray analyses reveal that vaccination does not affect constitutive expression of mRNA and lincRNA. However, malaria induces significant (p < 0...
2016: Frontiers in Microbiology
Daniel D Bikle, Yan Jiang, Thai Nguyen, Yuko Oda, Chia-Ling Tu
1,25 dihydroxyvitamin D (1,25(OH)2D), the active metabolite of vitamin D, and calcium regulate epidermal differentiation. 1,25(OH)2D exerts its effects through the vitamin D receptor (VDR), a transcription factor in the nuclear hormone receptor family, whereas calcium acts through the calcium sensing receptor (Casr), a membrane bound member of the G protein coupled receptor family. We have developed mouse models in which the Vdr and Casr have been deleted in the epidermis ((epid) Vdr (-∕-) and (epid) Casr (-∕-))...
2016: Frontiers in Physiology
Callie R Merry, Sarah McMahon, Megan E Forrest, Cynthia F Bartels, Alina Saiakhova, Courtney A Bartel, Peter C Scacheri, Cheryl L Thompson, Mark W Jackson, Lyndsay N Harris, Ahmad M Khalil
Approximately, 25-30% of early-stage breast tumors are classified at the molecular level as HER2-positive, which is an aggressive subtype of breast cancer. Amplification of the HER2 gene in these tumors results in a substantial increase in HER2 mRNA levels, and consequently, HER2 protein levels. HER2, a transmembrane receptor tyrosine kinase (RTK), is targeted therapeutically by a monoclonal antibody, trastuzumab (Tz), which has dramatically improved the prognosis of HER2-driven breast cancers. However, ~30% of patients develop resistance to trastuzumab and recur; and nearly all patients with advanced disease develop resistance over time and succumb to the disease...
July 16, 2016: Oncotarget
Andrew D L Nelson, Evan S Forsythe, Upendra K Devisetty, David S Clausen, Asher K Haug-Batzell, Ari M R Meldrum, Michael R Frank, Eric Lyons, Mark A Beilstein
Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs...
2016: G3: Genes—Genomes—Genetics
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