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long no coding rna

Awa Diop, Saber Khelaifia, Nicholas Armstrong, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Matthieu Million
BACKGROUND: Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. METHODS: By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined. RESULTS: Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp...
2016: Microbial Ecology in Health and Disease
Peng-Cheng Fu, Yan-Zhao Zhang, Hui-Min Geng, Shi-Long Chen
BACKGROUND: The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). METHODS: Using high throughput sequencing technology, we got the complete nucleotide sequence of the G...
2016: PeerJ
Hui Li, Yuting Wang, Meirong Chen, Peng Xiao, Changxing Hu, Zhiyong Zeng, Chaogang Wang, Jiangxin Wang, Zhangli Hu
Microalgae are regarded as the most promising biofuel candidates and extensive metabolic engineering were conducted but very few improvements were achieved. Long non-coding RNA (lncRNA) investigation and manipulation may provide new insights for this issue. LncRNAs refer to transcripts that are longer than 200 nucleotides, do not encode proteins but play important roles in eukaryotic gene regulation. However, no information of potential lncRNAs has been reported in eukaryotic alga. Recently, we performed RNA sequencing in Chlamydomonas reinhardtii, and obtained totally 3,574 putative lncRNAs...
2016: Scientific Reports
Jörg Ellinger, Heidrun Gevensleben, Stefan C Müller, Dimo Dietrich
Bodily fluids like serum and plasma contain significant amounts of tumor-derived circulating cell-free RNA, which holds the potential to serve as diagnostic biomarker. Consequently, liquid biopsies comprising circulating cell-free RNA might help to facilitate personalized treatment strategies for patients with renal cell carcinoma (RCC). Areas covered: The present review provides a summary of the literature obtained by a PubMed search and covers the current knowledge on circulating non-coding cell-free RNA in patients with RCC...
October 2016: Expert Review of Molecular Diagnostics
Nan Song, Shiheng An, Xinming Yin, Wanzhi Cai, Hu Li
Hemiptera make up the largest nonholometabolan insect assemblage. Despite previous efforts to elucidate phylogeny within this group, relationships among the major sub-lineages remain uncertain. In particular, mitochondrial genome (mitogenome) data are still sparse for many important hemipteran insect groups. Recent mitogenomic analyses of Hemiptera have usually included no more than 50 species, with conflicting hypotheses presented. Here, we determined the nearly complete nucleotide sequence of the mitogenome for the aphid species of Rhopalosiphum padi using RNA-seq plus gap filling...
2016: Scientific Reports
Catrin Stutika, Mario Mietzsch, Andreas Gogol-Döring, Stefan Weger, Madlen Sohn, Wei Chen, Regine Heilbronn
Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter...
2016: PloS One
Boris Novakovic, Christine E Napier, Regan Vryer, Eva Dimitriadis, Ursula Manuelpillai, Andrew Sharkey, Jeffrey M Craig, Roger R Reddel, Richard Saffery
STUDY QUESTION: What factors regulate elongated telomere length in the human placenta? SUMMARY ANSWER: Hypomethylation of TERRA promoters in the human placenta is associated with high expression TERRA genes, however, no clear mechanistic link between these phenomena and elongated telomere length in the human placenta was found. WHAT IS KNOWN ALREADY: Human placenta tissue and trophoblasts show longer telomere lengths compared to gestational age-matched somatic cells...
September 7, 2016: Molecular Human Reproduction
J Liu, J Wang, Y Song, Y Yang, Y Hu, P Gao, J Sun, X Chen, Y Xu, Z Wang
Long non-coding RNAs (lncRNAs) occupy the majority of the human genome. Their dysregulation is usually related with the procession of diseases, including tumors. Abnormally expressed lncRNAs have been found in colorectal cancer (CRC), but are not fully understood. In the current study, we determined the expression level of a novel lncRNA-RP1-13P20.6 in 99 pairs of CRC tissues compared to their matched normal adjacent tissues, using real time polymerase chain reaction. We further assessed the correlation between their expression levels and their clinicopathological parameters, and determined the potential of RP1-13P20...
September 6, 2016: Neoplasma
C H Li, Y Chen
Long noncoding RNA (LncRNA) is a large class of RNA molecules with size larger than 200 nucleotides. They exhibit cellular functions although having no protein-coding capability. Accumulating evidence suggests that long noncoding RNA play crucial roles in cancer biology. Studies showed that deregulation of lncRNA was frequently observed in various types of cancers which contributed heavily to malignant phenotypical changes. Aberration of lncRNA can be induced by a number of factors such as dysregulated signaling pathway, response to catastrophic effect, viral infection, and contact with carcinogens...
2016: International Review of Cell and Molecular Biology
Juliane Colditz, Benjamin Rupf, Caroline Maiwald, Aria Baniahmad
Inhibition of the androgen receptor (AR) is a major target of prostate cancer (PCa) therapy. However, prolonged androgen deprivation results eventually in castration-resistant PCa (CRPC) with metastasis and poor survival. Emerging evidence suggests that epithelial-mesenchymal transition (EMT) may facilitate castration-resistance and cancer metastasis in PCa. The human androgen-dependent, castration-sensitive prostate cancer (CSPC) cell line LNCaP and the CRPC cell line C4-2 are often used as a model system for human PCa...
October 2016: Molecular and Cellular Biochemistry
Jia-Jun Qiu, Zhao-Rui Ren, Jing-Bin Yan
Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data...
August 16, 2016: Oncotarget
Abigail F Groff, Diana B Sanchez-Gomez, Marcela M L Soruco, Chiara Gerhardinger, A Rasim Barutcu, Eric Li, Lara Elcavage, Olivia Plana, Lluvia V Sanchez, James C Lee, Martin Sauvageau, John L Rinn
The Linc-p21 locus, encoding a long non-coding RNA, plays an important role in p53 signaling, cell-cycle regulation, and tumor suppression. However, despite extensive study, confusion exists regarding its mechanism of action: is activity driven by the transcript acting in trans, in cis, or by an underlying functional enhancer? Here, using a knockout mouse model and a massively parallel enhancer assay, we delineate the functional elements at this locus. We observe that, even in tissues with no detectable Linc-p21 transcript, deletion of the locus significantly affects local gene expression, including of the cell-cycle regulator Cdkn1a...
August 23, 2016: Cell Reports
Usha Panchapakesan, Carol Pollock
Diabetic kidney disease (DKD) is escalating and is the major cause of end stage kidney failure. There is increasing evidence to support the role of epigenetic factors and metabolic memory in linking the environmental and genetic causes of this disease. Although our understanding of this disease has improved, there has been no significant efficacious therapeutic translation in the last decade. Current sequencing technology has allowed interrogation of the human transcriptome. It is evident that although approximately 80% of the genome is transcribed, only 1-2% is read and coded into protein...
September 1, 2016: Clinical Science (1979-)
Sandrine Sallé-Lefort, Stéphanie Miard, Marc-André Nolin, Louise Boivin, Marie-Ève Paré, Richard Debigaré, Frédéric Picard
Increased expression levels of the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (Malat1) have been associated with enhanced proliferation and metastasis of several cancer cell types. Hypoxia, a hallmark characteristic of solid tumors, has been linked to an increase in the activity of the ATP-generating AMPK protein. Since Malat1 was recently shown to be upregulated during hypoxia, the objective of this study was to determine the contribution of AMPK in the mechanistic pathways regulating Malat1 expression in low oxygen conditions...
October 2016: International Journal of Oncology
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
Feng Liu, Fu Yang, Xia Wu, Jin-Feng Huang, Ji-Hang Yuan, Qi-Fei Tao, Gui-Hua Jiang, Jia-Sheng Zheng, Shu-Han Sun
Sexual dimorphism is a major issue in hepatocellular carcinoma (HCC), with significantly higher incidence in males. We screened male specific Y chromosome transcripts through RNA sequence and discovered a long non-coding RNA RBMY2FP (RNA binding motif protein, Y-linked, family 2, member F pseudogene, lnc-RBMY2FP) that is specifically expressed in about 1/3 male HCC tissues, with no expression in adjacent livers. Positive expression of lnc-RBMY2FP in male HCC is related to poor patient survival. Lnc-RBMY2FP enhances HCC cell growth, proliferation and tumor stemness both in vitro and in vivo...
July 30, 2016: Oncotarget
Susanne M Rittig, Maik Haentschel, Katrin J Weimer, Annkristin Heine, Martin R Müller, Wolfram Brugger, Marius S Horger, Olga Maksimovic, Arnulf Stenzl, Ingmar Hoerr, Hans-Georg Rammensee, Tobias A Holderried, Lothar Kanz, Steve Pascolo, Peter Brossart
Renal cell carcinoma (RCC) is an immunogenic tumor for which immunotherapeutic approaches could be associated with clinically relevant responses. It was recently shown, that induction of T-cell responses against multiple tumor-associated antigen (TAA) epitopes results in prolonged overall survival in RCC patients. In 2003-2005, we performed a phase I/II trial testing an mRNA-based vaccine formulation consisting of a mixture of in vitro transcribed RNA coding for six different TAAs (MUC1, CEA, Her2/neu, telomerase, survivin, MAGE-A1) in 30 metastatic RCC (mRCC) patients...
May 2016: Oncoimmunology
Guangcun Cheng, Jie He, Leilei Zhang, Shengfang Ge, He Zhang, Xianqun Fan
Uveal melanoma (UM) is the most common primary intraocular cancer in adults. Although the diagnosis modality of primary UM was improved significantly, there are currently no effective therapies for metastatic UM. Hypermethylated in cancer 1 (HIC1) is frequently deleted or epigenetically silenced in various human cancers. However, the role and mechanism of HIC1 in UM is still unclear. In this study, we found that HIC1 acted as a tumor suppressor and that its expression was downregulated in UM. Functional studies demonstrated that ectopic expression of HIC1 in UM cells inhibited cell proliferation and invasion...
July 23, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Albert Busch, Suzanne M Eken, Lars Maegdefessel
Non-coding RNA (ncRNA) is a class of genetic, epigenetic and translational regulators, containing short and long transcripts with intriguing abilities for use as biomarkers due to their superordinate role in disease development. In the past five years many of these have been investigated in cardiovascular diseases (CVD), mainly myocardial infarction (MI) and heart failure. To extend this view, we summarize the existing data about ncRNA as biomarker in the whole entity of CVDs by literature-based review and comparison of the identified candidates...
June 2016: Annals of Translational Medicine
E Seck, S I Traore, S Khelaifia, M Beye, C Michelle, C Couderc, S Brah, P-E Fournier, D Raoult, G Dubourg
A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7(T) (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.
September 2016: New Microbes and New Infections
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