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Ying Chen, Zetian Shen, Yingru Zhi, Hao Zhou, Kai Zhang, Ting Wang, Bing Feng, Yitian Chen, Haizhu Song, Rui Wang, Xiaoyuan Chu
Radiotherapy plays a limited role in the treatment of hepatocellular carcinoma (HCC) due to the development of resistance. Therefore, further investigation of underlying mechanisms involved in HCC radioresistance is warranted. Increasing evidence shows that long non-coding RNAs (linc-RNAs) are involved in the pathology of various tumors, including HCC. Previously, we have shown that long noncoding RNA regulator of reprogramming (linc-ROR) promotes HCC metastasis via induction of epithelial-mesenchymal transition (EMT)...
March 17, 2018: Archives of Biochemistry and Biophysics
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
Dandan Yang, Jing Qiao, Guiying Wang, Yuanyuan Lan, Guoping Li, Xudong Guo, Jiajie Xi, Dan Ye, Songcheng Zhu, Wen Chen, Wenwen Jia, Ye Leng, Xiaoping Wan, Jiuhong Kang
Previous studies have revealed the critical roles of N6-methyladenosine (m6A) modification of mRNA in embryonic stem cells (ESCs), but the biological function of m6A in large intergenic noncoding RNA (lincRNA) is unknown. Here, we showed that the internal m6A modification of linc1281 mediates a competing endogenous RNA (ceRNA) model to regulate mouse ESC (mESC) differentiation. We demonstrated that loss of linc1281 compromises mESC differentiation and that m6A is highly enriched within linc1281 transcripts...
February 26, 2018: Nucleic Acids Research
Zhenjun Liu, Pei Zhao, Yuping Han, Song Lu
Long non-coding RNAs (lncRNA) have been reported to play important roles in tumorigenesis. In present study, we demonstrated long noncoding RNA (lncRNA) FEZF1 antisense RNA1 (FEZF1-AS1) is markedly upregulated in human lung adenocarcinoma (LAD) tissues, cell lines and associated with poor prognosis. Loss-of-function revealed that deletion of FEZF1-AS1 expression significantly inhibited the LAD cells proliferation, invasion and migration. Further studies revealed that downregulation of FEZF1-AS1 reduced mRNA and protein expression of its sense-cognate gene FEZF1 (forebrain embryonic zinc finger protein 1) in LAD cells, and vice versa...
March 6, 2018: Oncology Research
Ming-An Sun, Rihong Zhai, Qing Zhang, Yejun Wang
Long intergenic noncoding RNAs (lincRNAs) have caught increasing attention in recent years. The advance of RNA-Seq has greatly facilitated the discovery of novel lincRNAs. However, the computational analysis of lincRNAs is still challenging. In this protocol, we presented a step-by-step protocol for computational analyses of lincRNAs, including read processing and alignment, transcript assembly, lincRNA identification and annotation, and differential expression analysis.
2018: Methods in Molecular Biology
Jan Novak, Julie Bienertová Vašků, Miroslav Souček
The human genome contains about 22 000 protein-coding genes that are transcribed to an even larger amount of messenger RNAs (mRNA). Interestingly, the results of the project ENCODE from 2012 show, that despite up to 90 % of our genome being actively transcribed, protein-coding mRNAs make up only 2-3 % of the total amount of the transcribed RNA. The rest of RNA transcripts is not translated to proteins and that is why they are referred to as "non-coding RNAs". Earlier the non-coding RNA was considered "the dark matter of genome", or "the junk", whose genes has accumulated in our DNA during the course of evolution...
2018: Vnitr̆ní Lékar̆ství
Qiong Wu, Shihao Xiang, Jiali Ma, Pingping Hui, Ting Wang, Wenying Meng, Min Shi, Yugang Wang
Long non-coding RNAs (lncRNAs) are responsible for a diverse range of cellular functions, such as transcriptional and translational regulation and variance in gene expression. LncRNA CASC15 (cancer susceptibility candidate 15) is a lincRNA locus in chromosome 6p22.3. Previous researches show that lncRNA CASC15 is implicated in the biological behaviors of several cancers such as neuroblastoma and melanoma. Here, we aimed to explore in detail how CASC15 contributed to the growth of gastric cancer. As predicted, the expression of CASC15 was enriched in gastric cancer tissues and cell lines when compared to healthy tissues and cells using qRT-PCR...
February 28, 2018: Molecular Oncology
Jorge Melendez-Zajgla, Gabriela E Mercado-Celis, Javier Gaytan-Cervantes, Amada Torres, Nayeli Belem Gabiño, Martha Zapata-Tarres, Luis Enrique Juarez-Villegas, Pablo Lezama, Vilma Maldonado, Karen Ruiz-Monroy, Elvia Mendoza-Caamal
Ovarian fibrosarcomas are extremely rare tumors with little genomic information available to date. In the present report we present the tumoral exome and transcriptome and the germinal exome of an ovarian fibrosarcoma from a 9-years old child. We found a paucity of mutations (0.77/Mb) and CNV alterations. Of these, the most relevant were a point mutation in the metal-binding site of the microRNA-processing DICER1 enzyme and a frame-shift alteration in the tumor suppressor gene NF1. We validated a germinal truncating mutation in DICER1, which was consistent with a DICER1 Syndrome diagnosis, providing the first example of an ovarian fibrosarcoma as the presenting neoplasia in this syndrome...
February 19, 2018: Scientific Reports
Alberto Lopez-Ezquerra, Andreas Mitschke, Erich Bornberg-Bauer, Gerrit Joop
BACKGROUND: Microsporidia are obligate parasites that possess some of the smallest eukaryotic genomes. Several insect species are susceptible to infections by microsporidian parasites. Paranosema whitei frequently infects young larvae of Tribolium castaneum and obligately kills the host whereupon transmission to subsequent hosts is accomplished via spores. P. whitei infection results in developmental arrest of T. castaneum, preventing larvae from pupation. The mechanisms underlying P...
February 13, 2018: Journal of Invertebrate Pathology
Harshavardhan Janga, Marina Aznaourova, Fabian Boldt, Katrin Damm, Arnold Grünweller, Leon N Schulte
CRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes...
2018: PloS One
Muhe Shang, Xianghu Wang, Ying Zhang, Zhikui Gao, Tian Wang, Ran Liu
Background and objective: In an attempt to discover a new biomarker for early diagnosis and prognosis of esophageal squamous cell carcinoma (ESCC), the regulation mechanism of large intergenic non-coding RNA-regulator of reprogramming (lincRNA-ROR) as a microRNA (miRNA) sponge was studied. Patients and methods: ROR expression in 91 pairs of ESCC tissue samples and matched adjacent tissues was quantified with real-time fluorescent quantitative polymerase chain reaction (qRT-PCR)...
2018: OncoTargets and Therapy
Viorel Simion, Stefan Haemmig, Mark W Feinberg
Accumulating studies indicate that long non-coding RNAs (lncRNAs) play important roles in the regulation of diverse biological processes involved in homeostatic control of the vessel wall in health and disease. However, our knowledge of the mechanisms by which lncRNAs control gene expression and cell signaling pathways is still nascent. Furthermore, only a handful of lncRNAs has been functionally evaluated in response to pathophysiological stimuli or in vascular disease states. For example, lncRNAs may regulate endothelial dysfunction by modulating endothelial cell proliferation (e...
February 6, 2018: Vascular Pharmacology
Verena Sailer, Arthur Charpentier, Joern Dietrich, Timo J Vogt, Alina Franzen, Friedrich Bootz, Dimo Dietrich, Andreas Schroeck
BACKGROUND: Patients with squamous cell cancer of the head and neck region (HNSCC) are at risk for disease recurrence and metastases, even after initial successful therapy. A tissue-based biomarker could be beneficial to guide treatment as well as post-treatment surveillance. Gene methylation status has been recently identified as powerful prognostic biomarker in HNSCC. We therefore evaluated the methylation status of the homeobox gene PITX1 and the adjacent long intergenic non-coding RNA (lincRNA) C5orf66-AS1 in publicly available datasets...
2018: PloS One
Nilgün Çekin, Arzu Özcan, Sabahattin Göksel, Serdal Arslan, Ergün Pınarbaşı, Öcal Berkan
OBJECTIVE: Cardiovascular diseases are the most important cause of mortality worldwide, particularly atherosclerosis. Recently, lncRNAs affecting atherosclerotic progression have been reported in vascular smooth muscle cells, endothelial cells, and monocytes, suggesting that lncRNAs play an important role in atherosclerosis. METHODS: In recent clinical studies, nowadays, it was determined that internal mammary bypass grafts are closest to ideal grafts in coronary artery bypass surgery...
February 2018: Anatolian Journal of Cardiology
Richard W Zealy, Mikhail Fomin, Sylvia Davila, Daniel Makowsky, Haley Thigpen, Catherine H McDowell, James C Cummings, Edward S Lee, Sang-Ho Kwon, Kyung-Won Min, Je-Hyun Yoon
Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly. To address that research gap, our lab investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA expression...
February 5, 2018: Biochimica et Biophysica Acta
Santanu Biswas, Mohan Haleyurgirisetty, Viswanath Ragupathy, Xue Wang, Sherwin Lee, Indira Hewlett, Krishnakumar Devadas
Non-coding RNAs and mRNAs have been implicated in replication, pathogenesis and host response in HIV infection. However, the impact of long intergenic non-coding RNAs (lincRNAs) on HIV-1 and HIV-2 infection is not known. In this study, we have analyzed expression profiles of lincRNAs and mRNAs in monocyte derived macrophages (MDMs) infected with HIV-1/HIV-2 using microarrays. Our study identified many differentially expressed lincRNAs and mRNAs in MDMs infected with HIV-1/HIV-2 compared to uninfected MDMs. Genes involved in glutathione metabolism and lysine degradation were differentially regulated only in HIV-1 infected MDMs...
February 7, 2018: Scientific Reports
Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L Thomas, Alessandra Stella, John L Williams, Paolo Ajmone Marsan, Hasan Khatib
BACKGROUND: Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets altered the transcriptome of fetal tissues. However, the mechanisms underlying transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle that generate the methyl group donor, SAM...
February 6, 2018: BMC Genomics
Saleh Al-Quraishy, Mohamed A Dkhil, Abdel Azeem S Abdel-Baki, Denis Delic, Frank Wunderlich
Current knowledge about liver responses to blood-stage malaria and their modulation by vaccination is still unclear. This study investigated effects of protective vaccination on liver gene and lincRNA expression of Balb/c mice at early prepatency of Plasmodium chabaudi blood-stage malaria. When a blood-stage vaccine was used to induce > 80% survival of otherwise lethal malaria, significant differences (p < 0.01) were detectable in global liver gene expression between vaccination-protected (potentially surviving) and non-protected non-vaccinated mice on day 1 p...
February 5, 2018: Parasitology Research
Sylvain Fauquenoy, Valerie Migeot, Olivier Finet, Carlo Yague-Sanz, Olga Khorosjutina, Karl Ekwall, Damien Hermand
The cell fate decision leading to gametogenesis requires the convergence of multiple signals on the promoter of a master regulator. In fission yeast, starvation-induced signaling leads to the transcriptional induction of the ste11 gene, which encodes the central inducer of mating and gametogenesis, known as sporulation. We find that the long intergenic non-coding (linc) RNA rse1 is transcribed divergently upstream of the ste11 gene. During vegetative growth, rse1 directly recruits a Mug187-Lid2-Set1 complex that mediates cis repression at the ste11 promoter through SET3C-dependent histone deacetylation...
January 18, 2018: Current Biology: CB
Haibing Xiao, Lin Bao, Wen Xiao, Hailong Ruan, Zhengshuai Song, Yan Qu, Ke Chen, Xiaoping Zhang, Hongmei Yang
Background: Many long intergenic noncoding RNAs (lincRNAs) are encoded in the human genome. However, their biological functions, molecular mechanisms and prognostic values associated with clear cell renal cell carcinoma (ccRCC) have yet to be elucidated. Methods: We screened the lncRNAs' profile in ccRCC from The Cancer Genome Atlas (TCGA) database, and selected Lucat1 for further study. MTS, colony formation assay and transwell assay were performed to examine the effect of Lucat1 on proliferation and metastasis of ccRCC...
December 26, 2017: Oncotarget
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