keyword
MENU ▼
Read by QxMD icon Read
search

Noncoding RNA

keyword
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#1
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/28095922/long-noncoding-rna-braveheart-promotes-cardiogenic-differentiation-of-mesenchymal-stem-cells-in-vitro
#2
Jingying Hou, Huibao Long, Changqing Zhou, Shaoxin Zheng, Hao Wu, Tianzhu Guo, Quanhua Wu, Tingting Zhong, Tong Wang
BACKGROUND: Mesenchymal stem cells (MSCs) have limited potential of cardiogenic differentiation. In this study, we investigated the influence of long noncoding RNA Braveheart (lncRNA-Bvht) on cardiogenic differentiation of MSCs in vitro. METHODS: MSCs were obtained from C57BL/6 mice and cultured in vitro. Cells were divided into three groups: blank control, null vector control, and lncRNA-Bvht. All three groups experienced exposure to hypoxia (1% O2) and serum deprivation for 24 h, and 24 h of reoxygenation (20% O2)...
January 17, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#3
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/28092449/long-noncoding-rna-as-an-indicator-differentiating-schizophrenia-from-major-depressive-disorder-and-generalized-anxiety-disorder-in-nonpsychiatric-hospital
#4
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/28090356/long-noncoding-rna-noncoding-and-not-coded
#5
EDITORIAL
Debra Toiber, Gabriel Leprivier, Barak Rotblat
No abstract text is available yet for this article.
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/28089750/long-noncoding-rna-ccat2-can-predict-metastasis-and-poor-prognosis-a-meta-analysis
#6
REVIEW
Yang-Hua Fan, Hua Fang, Chen-Xing Ji, Huan Xie, Bing Xiao, Xin-Gen Zhu
BACKGROUND: It has been reported that Colon cancer-associated transcript 2 (CCAT2) is dysregulated in various cancers. We performed this meta-analysis to clarify its promising functions as a prognosis marker in malignant tumors. METHODS: Electronic databases, including PubMed, Medline, OVID, Cochrane Library, and Web of Science, were searched from inception to October 20, 2016. The hazard ratio (HR) and 95% confidence interval (CI) were calculated to explore the relationship between CCAT2 expression and survival, which were extracted from the eligible studies...
January 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28088836/upregulation-of-long-noncoding-rna-tug1-promotes-cervical-cancer-cell-proliferation-and-migration
#7
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/28087943/rna-interference-in-fungi-retention-and-loss
#8
Francisco E Nicolás, Victoriano Garre
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087167/lingering-questions-about-enhancer-rna-and-enhancer-transcription-coupled-genomic-instability
#9
REVIEW
Gerson Rothschild, Uttiya Basu
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes...
January 10, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28079712/a-comprehensive-review-of-genomics-and-noncoding-rna-in-gliomas
#10
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/28079130/association-of-nsv823469-copy-number-loss-with-decreased-risk-of-chronic-obstructive-pulmonary-disease-and-pulmonary-function-in-chinese
#11
Xiaoliang Chen, Xiaoxiao Lu, Jiansong Chen, Di Wu, Fuman Qiu, Huali Xiong, Zihua Pan, Lei Yang, Binyao Yang, Chenli Xie, Yifeng Zhou, Dongsheng Huang, Yumin Zhou, Jiachun Lu
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077601/a-new-rna-based-adjuvant-enhances-virus-specific-vaccine-responses-by-locally-triggering-tlr-and-rlh-dependent-effects
#12
Annett Ziegler, Claudia Soldner, Stefan Lienenklaus, Julia Spanier, Stephanie Trittel, Peggy Riese, Thomas Kramps, Siegfried Weiss, Regina Heidenreich, Edith Jasny, Carlos A Guzmán, Karl-Josef Kallen, Mariola Fotin-Mleczek, Ulrich Kalinke
Among innovative adjuvants conferring a Th1-shift, RNAdjuvant is a promising candidate. This adjuvant consists of a 547-nt uncapped noncoding ssRNA containing polyU repeats that is stabilized by a cationic carrier peptide. Whereas vaccination of mice with an influenza subunit vaccine induced moderate virus-specific IgG1, vaccination together with RNAdjuvant significantly enhanced this IgG1 and additionally promoted the formation of IgG2b/c, which is indicative of Th1 responses. Furthermore, such sera neutralized influenza virus, whereas this effect was not detected upon vaccination with the subunit vaccine alone...
January 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28075173/tgf%C3%AE-1-induced-lncrna-uca1-upregulation-promotes-gastric-cancer-invasion-and-migration
#13
Zhong-Kun Zuo, Yi Gong, Xiang-Heng Chen, Fei Ye, Zheng-Ming Yin, Qian-Ni Gong, Jiang-Sheng Huang
According to recent studies, long noncoding RNA urothelial carcinoma associated 1 (UCA1) is involved in the development and progression of many malignant tumors, including gastric cancer (GC). We validated the detailed role of UCA1 in human GC cell lines and GC tissues so as to determine its exact function and the underlying mechanism of GC invasion and migration. In our research, lncRNA-UCA1 was specifically upregulated in GC tissues and cell lines, and augmented GC cell proliferation, and invasive and migratory capabilities...
January 11, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28075045/interplay-between-long-noncoding-rna-zeb1-as1-and-mir-200s-regulates-osteosarcoma-cell-proliferation-and-migration
#14
Chibo Liu, Chunqin Pan, Yanqun Cai, Haibao Wang
In our previous study we found long noncoding RNA ZEB1-AS1 is upregulated and functions as an oncogene in osteosarcoma. MiR-200 family (miR-200s) functions as tumor suppressor via directly targeting ZEB1 in various cancers. In this study we further investigate the potential interplay between ZEB1-AS1, miR-200s, and ZEB1 in osteosarcoma. Our results showed that ZEB1-AS1 functions as a molecular sponge for miR-200s and relieves the inhibition of ZEB1 caused by miR-200s. ZEB1-AS1 and miR-200s reciprocally negatively regulate each other...
January 11, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28074027/a-unique-cis-encoded-small-noncoding-rna-is-regulating-legionella-pneumophila-hfq-expression-in-a-life-cycle-dependent-manner
#15
Giulia Oliva, Tobias Sahr, Monica Rolando, Maike Knoth, Carmen Buchrieser
: Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires' disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#16
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28073357/long-noncoding-rna-repertoire-in-chicken-liver-and-adipose-tissue
#17
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/28073110/relationship-between-the-pathogenesis-of-glaucoma-and-mirna
#18
Ruru Guo, Wencui Shen, Chang Su, Shaoyun Jiang, Jiantao Wang
Small RNA (microRNA or miRNA) is a kind of small noncoding single-stranded RNA that regulates complementary mRNA at the posttranscriptional level in eukaryotic organisms. As important regulatory factors, miRNAs play an important role in the occurrence and development of glaucoma and widely participate in regulating biological processes of glaucoma-related genes. This article reviews the connection between the aqueous humor, trabecular meshwork, the apoptosis of retinal ganglion cells, and miRNA.
January 11, 2017: Ophthalmic Research
https://www.readbyqxmd.com/read/28069548/long-noncoding-rna-hulc-promotes-cell-proliferation-by-regulating-pi3k-akt-signaling-pathway-in-chronic-myeloid-leukemia
#19
Yinghao Lu, Yan Li, Xiao Chai, Qian Kang, Peng Zhao, Jie Xiong, Jishi Wang
Aberrant expression of long noncoding RNA (lncRNA) HULC is associated with various human cancers. However, the role of HULC in chronic myeloid leukemia (CML) is unknown. In this study, we found that HULC was remarkably overexpressed in both leukemia cell lines and primary hematopoietic cells derived from CML patients. The increase in HULC expression was positively correlated with clinical stages in CML. Moreover, the knockdown of HULC significantly inhibited CML cell proliferation and induced apoptosis by repressing c-Myc and Bcl-2...
January 6, 2017: Gene
https://www.readbyqxmd.com/read/28068310/visualizing-the-secondary-and-tertiary-architectural-domains-of-lncrna-repa
#20
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
keyword
keyword
40722
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"