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https://www.readbyqxmd.com/read/28523007/transcriptomic-identification-of-drought-related-genes-and-ssr-markers-in-sudan-grass-based-on-rna-seq
#1
Yongqun Zhu, Xia Wang, Linkai Huang, Chaowen Lin, Xinquan Zhang, Wenzhi Xu, Jianhua Peng, Zhou Li, Haidong Yan, Fuxiang Luo, Xie Wang, Li Yao, Dandan Peng
Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28516000/role-of-a-dual-splicing-and-amino-acid-code-in-myopia-cone-dysfunction-and-cone-dystrophy-associated-with-l-m-opsin-interchange-mutations
#2
Scott H Greenwald, James A Kuchenbecker, Jessica S Rowlan, Jay Neitz, Maureen Neitz
PURPOSE: Human long (L) and middle (M) wavelength cone opsin genes are highly variable due to intermixing. Two L/M cone opsin interchange mutants, designated LIAVA and LVAVA, are associated with clinical diagnoses, including red-green color vision deficiency, blue cone monochromacy, cone degeneration, myopia, and Bornholm Eye Disease. Because the protein and splicing codes are carried by the same nucleotides, intermixing L and M genes can cause disease by affecting protein structure and splicing...
May 2017: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/28507281/high-expression-of-long-non-coding-rna-neat1-indicates-poor-prognosis-of-human-cancer
#3
Jian Fang, Fuhao Qiao, Jingjing Tu, Jinfeng Xu, Fangfang Ding, Yun Liu, Bufugdi Andreas Akuo, Jianpeng Hu, Shihe Shao
The nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA. Many studies have reported that NEAT1 plays critical oncogenic roles and facilitates tumorigenesis of various human cancers. High NEAT1 expression is associated with a poor prognosis in cancer patients. This meta-analysis was conducted to assess the association between NEAT1 levels and survival times of cancer patients. Overall survival (OS) was the primary endpoint. Thirteen publications with 1,496 cancer patients from 5 databases (PubMed, EMBASE, Cochrane Library, Wiley Online Library, and Medline) met the criteria for this meta-analysis...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28506253/genome-wide-identification-of-lncrnas-associated-with-chlorantraniliprole-resistance-in-diamondback-moth-plutella-xylostella-l
#4
Bin Zhu, Manyu Xu, Haiyan Shi, Xiwu Gao, Pei Liang
BACKGROUND: Long noncoding RNAs (lncRNAs) are now considered important regulatory factors, with a variety of biological functions in many species including insects. Some lncRNAs have the ability to show rapid responses to diverse stimuli or stress factors and are involved in responses to insecticide. However, there are no reports to date on the characterization of lncRNAs associated with chlorantraniliprole resistance in Plutella xylostella. RESULTS: Nine RNA libraries constructed from one susceptible (CHS) and two chlorantraniliprole-resistant P...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28498454/identification-of-setd2-nf1-fusion-gene-in-a-pediatric-spindle-cell-tumor-with-the-chromosomal-translocation-t-3-17-p21-q12
#5
Ioannis Panagopoulos, Ludmila Gorunova, Ingvild Lobmaier, Bodil Bjerkehagen, Sverre Heim
Spindle cell tumors are clinically heterogeneous but morphologically similar neoplasms. The term refers to the tumor cells' long and slender microscopic appearance. Distinct subgroups of spindle cell tumors are characterized by chromosomal translocations and also fusion genes. Other spindle cell tumors exist that have not yet been found to have characteristic, let alone pathognomonic, genetic or pathogenetic features. Continuous examination of spindle cell tumors is likely to reveal other subgroups that may, in the future, be seen to correspond to meaningful clinical differences and may even be therapeutically decisive...
May 4, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28454518/transcriptome-wide-n-6-methyladenosine-methylome-profiling-of-porcine-muscle-and-adipose-tissues-reveals-a-potential-mechanism-for-transcriptional-regulation-and-differential-methylation-pattern
#6
Xuelian Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Yan Chen, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen, Qin Wang, Guangxiang Zhu, Meng Xie, Jiayun Wu, Tao He, Chunyu Huang, Xiang Gao, Xuewei Li
BACKGROUND: N (6) -methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth...
April 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28442991/a-novel-long-non-coding-rna-durga-modulates-dendrite-density-and-expression-of-kalirin-in-zebrafish
#7
Mayuresh A Sarangdhar, Divya Chaubey, Abhishek Bhatt, Monisha Km, Manish Kumar, Shashi Ranjan, Beena Pillai
Kalirin, a key player in axonal development, nerve growth and synaptic re-modeling, is implicated in many pathological conditions like schizophrenia and autism-spectrum disorders. Alternative promoters and splicing lead to functionally distinct isoforms, but the post-transcriptional regulation of Kalirin has not been studied. Here, we report a novel non-coding RNA, which we name durga, arising from the first exon of kalirin a (kalrna) in the antisense orientation in zebrafish. The kalrna and durga transcripts are barely detectable during early development, but steadily increase by 24 hours post-fertilization (hpf) as the brain develops...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28412742/association-of-the-long-non-coding-rna-malat1-with-the-polycomb-repressive-complex-pathway-in-t-and-nk-cell-lymphoma
#8
Soo Hee Kim, Se Hoon Kim, Woo Ick Yang, Soo Jeong Kim, Sun Och Yoon
Recently, various long non-coding RNAs (lncRNAs) have been reported to have significant therapeutic or prognostic value. However, the expression of lncRNAs has not been investigated in T and NK cell lymphoma. Thus, we evaluated the biological and prognostic role of lncRNAs related to the polycomb repressive complex (PRC) and PRC markers in tissue samples and cell lines of T and NK cell lymphoma. Among the tested lncRNAs, MALAT1 was most highly expressed in clinical samples and cell lines. High expression of MALAT1 as well as BMI1 was related to poor prognosis in patients with mature T cell lymphoma...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28404885/significant-association-between-lncrna-h19-polymorphisms-and-cancer-susceptibility-a-meta-analysis
#9
Xue-Feng Li, Xin-Hai Yin, Jun-Wei Cai, Ming-Ju Wang, Yu-Qin Zeng, Min Li, Yu-Ming Niu, Ming Shen
Previous epidemiological research suggests polymorphisms in long non-coding RNA (lncRNA) H19 are associated with an increased risk of cancer, but the results are inconsistent. We therefore conducted a meta-analysis to more accurately determine the association between lncRNA H19 polymorphisms and cancer risk. The PubMed, Embase, and Science Citation Index online databases were searched and 11 relevant studies involving a total of 33,209 participants were identified. Odds ratios (ORs) and corresponding 95% confidence interval (CIs) from these studies were used to detect associations between H19 polymorphisms and cancer risk using five genetic models...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28396580/p53-regulation-association-long-non-coding-rna-lncrna-pral-inhibits-cell-proliferation-by-regulation-of-p53-in-human-lung-cancer
#10
Pengxiao Su, Fengqin Wang, Bin Qi, Ting Wang, Shaobo Zhang
BACKGROUND Lung cancer is among the most common causes of cancer-related deaths worldwide, but its tumorigenic mechanisms are largely unknown. Long non-coding RNAs (LncRNAs) have been shown to have significant roles in multiple cancers. Herein, we aimed to elucidate the detailed effects of a newly-discovered LncRNA, termed PRAL, on cell proliferation in lung cancer. MATERIAL AND METHODS A total of 100 lung cancer patients were subjected to RT-PCR analysis to detect the expressions of PRAL. Western blot analysis was performed to examine P53 protein levels...
April 11, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28381186/the-expression-pattern-of-long-non-coding-rna-pvt1-in-tumor-tissues-and-in-extracellular-vesicles-of-colorectal-cancer-correlates-with-cancer-progression
#11
Kai Guo, Jie Yao, Qiang Yu, Zijian Li, Hu Huang, Jianguo Cheng, Zhigang Wang, Yunfeng Zhu
The plasmacytoma variant translocation 1 gene (PVT1) is a large non-coding locus at adjacent of c-Myc, and long non-coding RNA PVT1 is now recognized as a cancerous gene co-amplified with c-Myc in various cancers. But the expression and functional role of PVT1 in colorectal cancer are still unelucidated. In addition, all the reported long non-coding RNAs so far are discovered in either cells or tissues, but no research about long non-coding RNAs detection in extracellular vesicles has been reported yet. In the present study, we firstly investigated the expression of PVT1 in colorectal cancer specimens and its correlation with the expression of c-Myc and other related genes by real-time polymerase chain reaction...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28358873/whole-genome-analysis-of-papillary-kidney-cancer-finds-significant-noncoding-alterations
#12
Shantao Li, Brian M Shuch, Mark B Gerstein
To date, studies on papillary renal-cell carcinoma (pRCC) have largely focused on coding alterations in traditional drivers, particularly the tyrosine-kinase, Met. However, for a significant fraction of tumors, researchers have been unable to determine a clear molecular etiology. To address this, we perform the first whole-genome analysis of pRCC. Elaborating on previous results on MET, we find a germline SNP (rs11762213) in this gene predicting prognosis. Surprisingly, we detect no enrichment for small structural variants disrupting MET...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28352334/long-non-coding-rna-asncmtrna-2-is-upregulated-in-diabetic-kidneys-and-high-glucose-treated-mesangial-cells
#13
Yan Gao, Zhao-Yu Chen, Yan Wang, Yan Liu, Jian-Xia Ma, Yu-Kun Li
Diabetic nephropathy (DN) is one of the most frequent complications associated with type I and II diabetes mellitus. Kidneys from patients with DN are characterized by mesangial matrix expansion and increased thickness of the glomerular basement membrane, which are induced by reactive oxygen species (ROS) production. Previous studies have been conducted to investigate this; however, the detailed mechanism of DN progression remains to be elucidated. The present study evaluated the expression of antisense mitochondrial non-coding RNA-2 (ASncmtRNA-2) in an experimental DN model and cultured human mesangial cells...
February 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28347715/preeclampsia-novel-insights-from-global-rna-profiling-of%C3%A2-trophoblast-subpopulations
#14
Matthew Gormley, Katherine Ona, Mirhan Kapidzic, Tamara Garrido-Gomez, Tamara Zdravkovic, Susan J Fisher
BACKGROUND: The maternal signs of preeclampsia, which include the new onset of high blood pressure, can occur because of faulty placentation. We theorized that transcriptomic analyses of trophoblast subpopulations in situ would lend new insights into the role of these cells in preeclampsia pathogenesis. OBJECTIVE: Our goal was to enrich syncytiotrophoblasts, invasive cytotrophoblasts, or endovascular cytotrophoblasts from the placentas of severe preeclampsia cases...
March 24, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28342449/a-systematic-review-and-meta-analysis-of-the-association-between-long-non-coding-rna-polymorphisms-and-cancer-risk
#15
REVIEW
Zhi Lv, Qian Xu, Yuan Yuan
It has been suggested that long non-coding RNA (lncRNA) gene polymorphisms are associated with cancer risk. In this article, we conducted a systematic review related to studies on the association between lncRNA single-nucleotide polymorphisms (SNPs) and the overall risk of cancer. A total 17 SNPs in four common lncRNA genes were included in the meta-analysis. In the lncRNA H19, the rs2735971 A/G, rs2839698C/T, and rs3024270 G/C polymorphisms, but not rs217727C/T, were correlated with overall cancer risk. The results also suggested that other SNPs were correlated with overall cancer risk, namely, two in HOTAIR (HOX transcript antisense RNA: rs920778C/T and rs7958904 G/C) and two in PRNCR1 (rs1016343C/T and rs16901946 A/G)...
January 2017: Mutation Research
https://www.readbyqxmd.com/read/28288321/phomopsis-longicolla-rna-virus-1-novel-virus-at-the-edge-of-myco-and-plant-viruses
#16
Lenka Hrabáková, Igor Koloniuk, Karel Petrzik
The complete nucleotide sequence of a new RNA mycovirus in the KY isolate of Phomopsis longicolla Hobbs 1985 and its protoplasts subcultures p5, p9, and ME711 was discovered. The virus, provisionally named Phomopsis longicolla RNA virus 1 (PlRV1), was localized in mitochondria and was determined to have a genome 2822 nucleotides long. A single open reading frame could be translated in silico by both standard and mitochondrial genetic codes into a product featuring conservative domains for an RNA-dependent RNA polymerase (RdRp)...
June 2017: Virology
https://www.readbyqxmd.com/read/28235420/altered-expression-profiles-of-microrna-families-during-de-etiolation-of-maize-and-rice-leaves
#17
Jiajia Xu, Yuanyuan Li, Yaling Wang, Xinyu Liu, Xin-Guang Zhu
BACKGROUND: MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009). RESULTS: In this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C3) and Zea mays (C4) to explore conserved and species-specific characteristics of miRNAs between these two species...
February 24, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28215748/long-non-coding-rna-snhg14-promotes-microglia-activation-by-regulating-mir-145-5p-pla2g4a-in-cerebral-infarction
#18
Xu Qi, Ming Shao, Hongjing Sun, Yue Shen, Delong Meng, Wei Huo
Activated microglia cells (MCs) are able to release a large amount of inflammatory cytokines after ischemic stroke, which exacerbates neuron damage. In this study, we explored the functional involvement of long non-coding RNA (lncRNA) SNHG14 and its potential regulatory mechanism in the activation of MCs. The mouse model of middle cerebral artery occlusion (MCAO) and microglia cell model of oxygen/glucose deprivation (OGD) were made. The expression of SNHG14, miR-145-5p and PLA2G4A protein expression was determined by quantitative real time PCR and western blot, respectively...
February 16, 2017: Neuroscience
https://www.readbyqxmd.com/read/28208661/differential-binding-of-three-major-human-adar-isoforms-to-coding-and-long-non-coding-transcripts
#19
Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
RNA editing by deamination of adenosine to inosine is an evolutionarily conserved process involved in many cellular pathways, from alternative splicing to miRNA targeting. In humans, it is carried out by no less than three major adenosine deaminases acting on RNA (ADARs): ADAR1-p150, ADAR1-p110, and ADAR2. However, the first two derive from alternative splicing, so that it is currently impossible to delete ADAR1-p110 without also knocking out ADAR1-p150 expression. Furthermore, the expression levels of ADARs varies wildly among cell types, and no study has systematically explored the effect of each of these isoforms on the cell transcriptome...
February 11, 2017: Genes
https://www.readbyqxmd.com/read/28187749/identification-of-a-large-intronic-transposal-insertion-in-slc17a5-causing-sialic-acid-storage-disease
#20
Maja Tarailo-Graovac, Britt I Drögemöller, Wyeth W Wasserman, Colin J D Ross, Ans M W van den Ouweland, Niklas Darin, Gittan Kollberg, Clara D M van Karnebeek, Maria Blomqvist
BACKGROUND: Sialic acid storage diseases are neurodegenerative disorders characterized by accumulation of sialic acid in the lysosome. These disorders are caused by mutations in SLC17A5, the gene encoding sialin, a sialic acid transporter located in the lysosomal membrane. The most common form of sialic acid storage disease is the slowly progressive Salla disease, presenting with hypotonia, ataxia, epilepsy, nystagmus and findings of cerebral and cerebellar atrophy. Hypomyelination and corpus callosum hypoplasia are typical as well...
February 10, 2017: Orphanet Journal of Rare Diseases
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