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https://www.readbyqxmd.com/read/28288321/phomopsis-longicolla-rna-virus-1-novel-virus-at-the-edge-of-myco-and-plant-viruses
#1
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)...
March 10, 2017: Virology
https://www.readbyqxmd.com/read/28235420/altered-expression-profiles-of-microrna-families-during-de-etiolation-of-maize-and-rice-leaves
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28174058/the-expression-of-lnc-il-7r-long-non-coding-rna-dramatically-correlated-with-soluble-and-membrane-bound-isoforms-of-il-7ra-gene-in-multiple-sclerosis-patients
#6
Parinaz Bina, Majid Pahlevan Kakhki, Mohammad Ali Sahraian, Mehrdad Behmanesh
BACKGROUND AND PURPOSE: Multiple sclerosis (MS) is a neurological disease of the central nervous system (CNS) that causes physical and cognitive impairments. IL-7Ra is a key non-MHC gene associated with MS. IL-7Ra is a likely functional candidate for this complex disease because it is involved in the development, maturation, and homeostasis of T and B cells. Our aim was to evaluate the expression level and controlling role of lnc-IL-7R in the expression of two variants of IL-7Ra in MS patients versus healthy controls and their correlation with certain clinical features...
March 6, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28157654/long-noncoding-rna-rp11-766n7-4-functions-as-a-tumor-suppressor-by-regulating-epithelial-mesenchymal-transition-in-esophageal-squamous-cell-carcinoma
#7
Guo-Liang Yao, Chun-Feng Pan, Hairong Xu, Ke Wei, Bin Liu, Rong Zhai, Yi-Jiang Chen
BACKGROUND: Numerous studies have proved that long non-coding RNAs participate in the initiation and metastasis of various cancers including esophageal squamous cell carcinoma (ESCC). Recently, a novel long non-coding RNA RP11-766N7.4 was discovered in a variety of human tissues. However, its role in oncogenesis and tumor metastasis remains unknown. METHODS: To investigate the function of long noncoding RNA RP11-766N7.4 in ESCC, RT-qPCR was used to monitor the expression level of long non-coding RNA RP11-766N7...
April 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28147217/ccg-an-integrative-resource-of-cancer-protein-coding-genes-and-long-noncoding-rnas
#8
Mengrong Liu, Yu-Cheng T Yang, Gang Xu, Chang Tan, Zhi John Lu
The identification of cancer genes remains a main aim of cancer research. With the advances of high-throughput sequencing technologies, thousands of novel cancer genes were identified through recurrent mutation analyses and differential expression analyses between normal tissues and tumors in large populations. Many databases were developed to document the cancer genes. However, no public database providing both cancer protein-coding genes and cancer lncRNAs is available presently. Here, we present the Catalogue of Cancer Genes (CCG) database (http://ccg...
December 2016: Discovery Medicine
https://www.readbyqxmd.com/read/28128738/clinical-significance-of-the-long-noncoding-rna-rp11-19p22-6-001-in-gastric-cancer
#9
Weiliang Sun, Xiaoyan Mo, Tianwen Li, Yi Xie, Junming Guo
BACKGROUND: Long non-coding RNAs (lncRNAs) play roles in carcinogenesis; however, the significance of most lncRNAs in gastric cancer is unclear. OBJECTIVE: To explore the diagnostic value of the long noncoding RNA RP11-19P22.6-001 in gastric cancer. METHODS: RP11-19P22.6-001 levels in gastric cancer tissues and paired non-tumor tissues were analyzed by quantitative reverse transcription-polymerase chain reaction. Since RP11-19P22.6-001 acts in cis to regulate nitric oxide synthase 2 (NOS2), we also analyzed NOS2 expression and its correlation with gastric cancer...
January 20, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28127595/small-rna-sequencing-revealed-dysregulated-pirnas-in-alzheimer-s-disease-and-their-probable-role-in-pathogenesis
#10
Jyoti Roy, Arijita Sarkar, Sibun Parida, Zhumur Ghosh, Bibekanand Mallick
PIWI-interacting RNAs (piRNAs), ∼23-36 nucleotide-long small non-coding RNAs, earlier believed to be germline-specific, have now been identified in somatic cells including neural cells. However, piRNAs have not yet been studied in the human brain (HB) and Alzheimer's disease (AD)-affected brain. In this study, by next-generation small RNA sequencing, 564 and 451 piRNAs were identified in the HB and AD-affected brain respectively. The majority of the neuronal piRNAs have intronic origin wherein primary piRNAs are mostly from the negative strand...
January 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28107589/serum-lincrna-p21-as-a-potential-biomarker-of-liver-fibrosis-in-chronic-hepatitis-b-patients
#11
Fujun Yu, Guangyao Zhou, Kate Huang, XuFei Fan, Guojun Li, Bicheng Chen, Peihong Dong, Jianjian Zheng
Serum long non-coding RNAs (lncRNAs) are emerging as promising biomarkers for various human diseases. The aim of this study was to investigate the feasibility of using serum long intergenic non-coding RNA-p21 (lincRNA-p21) as a biomarker for chronic hepatitis B patients. Serum lincRNA-p21 levels were quantified using real-time PCR in 417 CHB patients and 363 healthy controls. The promoter methylation level of lincRNA-p21 was detected using bisulphite-sequencing analysis in primary hepatic stellate cells (HSCs)...
January 20, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28073183/a-liver-specific-long-non-coding-rna-with-a-role-in-cell-viability-is-elevated-in-human-non-alcoholic-steatohepatitis
#12
Biljana Atanasovska, Sander S Rensen, Marijke R van der Sijde, Glenn Marsman, Vinod Kumar, Iris Jonkers, Sebo Withoff, Ronit Shiri-Sverdlov, Jan Willem M Greve, Klaas Nico Faber, Han Moshage, Cisca Wijmenga, Bart van de Sluis, Marten H Hofker, Jingyuan Fu
Hepatocyte apoptosis in non-alcoholic steatohepatitis (NASH) can lead to fibrosis and cirrhosis, which permanently damage the liver. Understanding the regulation of hepatocyte apoptosis is therefore important to identify therapeutic targets that may prevent the progression of NASH to fibrosis. Recently, increasing evidence has shown that lncRNAs are involved in various biological processes and that their dysregulation underlies a number of complex human diseases. By performing gene expression profiling of 4,383 lncRNAs in 82 liver samples from individuals with NASH (n=48), simple steatosis but no NASH (n=11) and healthy controls (n=23), we discovered a liver-specific lncRNA (RP11-484N16...
January 10, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28069890/apobec1-complementation-factor-a1cf-is-dispensable-for-c-to-u-rna-editing-in-vivo
#13
Elizabeth M Snyder, Christopher McCarty, Adrienne Mehalow, Karen L Svenson, Stephen A Murray, Ron Korstanje, Robert E Braun
Editing of the human and murine ApoB mRNA by APOBEC1, the catalytic enzyme of the protein complex that catalyzes C-to-U RNA editing, creates an internal stop codon within the APOB coding sequence, generating two protein isoforms. It has been long held that APOBEC1-mediated editing activity is dependent on the RNA binding protein A1CF. The function of A1CF in adult tissues has not been reported because a previously reported null allele displays embryonic lethality. This work aimed to address the function of A1CF in adult mouse tissues using a conditional A1cf allele...
April 2017: RNA
https://www.readbyqxmd.com/read/28053272/transgenerational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-noncoding-rna-loci
#14
Brian M Farley, Kathleen Collins
Transgenerational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of transgenerational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of transgenerational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated transgenerational regulation to include unique noncoding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction...
April 2017: RNA
https://www.readbyqxmd.com/read/28051255/down-regulation-of-long-non-coding-rna-meg3-serves-as-an-unfavorable-risk-factor-for-survival-of-patients-with-breast-cancer
#15
J-J Zhang, S-H Guo, B-Q Jia
OBJECTIVE: The downregulation of Long non-coding RNA MEG3 (MEG3) has been observed in breast cancer (BC). However, there is no previous study of the relationship between MEG3 and patient prognosis in BC. Accordingly, this study investigated the prognostic values of MEG3 in BC patients. MATERIALS AND METHODS: we performed RT-qPCR to detect the expression of MEG3 in 207 paired BC tissues and adjacent noncancerous tissues. The association of MEG3 expression with clinicopathological factors or prognosis was statistically analyzed...
December 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28039689/long-non-coding-rna-potential-diagnostic-and-therapeutic-biomarker-for-major-depressive-disorder
#16
Xuelian Cui, Xinyang Sun, Wei Niu, Lingming Kong, Mingjun He, Aifang Zhong, Shengdong Chen, Kunhong Jiang, Liyi Zhang, Zaohuo Cheng
BACKGROUND The criteria for diagnosing depression are based on behavioral observation and self-reporting of symptoms by the patients or guardians without any biological validation of the disease. This study aimed to identify long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) as robust and predictive biomarkers for diagnosis and therapy response in major depressive disorder (MDD). MATERIAL AND METHODS We used human lncRNA 3.0 microarray profiling (which covers 30,586 human lncRNAs), using PBMCs from five MDD patients and five controls...
December 31, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/27974853/human-cellular-cyba-utr-sequences-increase-mrna-translation-without-affecting-the-half-life-of-recombinant-rna-transcripts
#17
Mehrije Ferizi, Manish K Aneja, Elizabeth R Balmayor, Zohreh Sadat Badieyan, Olga Mykhaylyk, Carsten Rudolph, Christian Plank
Modified nucleotide chemistries that increase the half-life (T1/2) of transfected recombinant mRNA and the use of non-native 5'- and 3'-untranslated region (UTR) sequences that enhance protein translation are advancing the prospects of transcript therapy. To this end, a set of UTR sequences that are present in mRNAs with long cellular T1/2 were synthesized and cloned as five different recombinant sequence set combinations as upstream 5'-UTR and/or downstream 3'-UTR regions flanking a reporter gene. Initial screening in two different cell systems in vitro revealed that cytochrome b-245 alpha chain (CYBA) combinations performed the best among all other UTR combinations and were characterized in detail...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27966488/long-non-coding-rna-hotair-regulates-proliferation-and-invasion-via-activating-notch-signalling-pathway-in-retinoblastoma
#18
Changxia Dong, Shaoyi Liu, Yongbin Lv, Chunping Zhang, Heying Gao, Lixia Tan, Hong Wang
Retinoblastoma is the most frequently occurring tumour in the eyes in early childhood. Novel targets that are important for the diagnosis or treatment of retinoblastoma could be valuable in increasing the survival rate of patients affected by this disease. Long non-coding RNAs (lncRNAs) are a recently discovered type of RNAs with no proteincoding function; yet it has become increasingly clear that lncRNAs are responsible for important gene regulatory functions in various diseases. In this study, the expression of lncRNA HOTAIR was measured by qRT-PCR, and HOTAIR expression was found to be significantly upregulated in human retinoblastomas tissues as compared with that in paracancerous tissues...
December 2016: Journal of Biosciences
https://www.readbyqxmd.com/read/27966450/upregulated-nnt-as1-a-long-noncoding-rna-contributes-to-proliferation-and-migration-of-colorectal-cancer-cells-in-vitro-and-in-vivo
#19
Qian Wang, Lei Yang, Xin Hu, Yuliang Jiang, Yizhang Hu, Zhe Liu, Jian Liu, Tao Wen, Yingmin Ma, Guangyu An, Guosheng Feng
The expression patterns of the long non-coding RNA Nicotinamide Nucleotide Transhydrogenase-antisense RNA1 (NNT-AS1) have not been investigated in the context of cancer. In this study, we aim to investigate the NNT-AS1 expression level in colorectal cancer (CRC) patients and its potential roles in tumor biology. We measured the expression of NNT-AS1 in 70 paired tumor tissues and adjacent normal tissues. NNT-AS1 was expressed higher in tumor tissues than that in adjacent noncancer tissues, and higher expression of NNT-AS1 was significantly correlated with lymph node metastasis (Yes vs...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/27955882/melanoma-long-non-coding-rna-signature-predicts-prognostic-survival-and-directs-clinical-risk-specific-treatments
#20
Xijia Chen, Wenna Guo, Xin-Jian Xu, Fangchu Su, Yi Wang, Yingzheng Zhang, Qiang Wang, Liucun Zhu
BACKGROUND: Various studies have demonstrated that the Breslow thickness, tumor ulceration and mitotic index could serve as prognostic markers in patients with cutaneous melanoma. Recently, however, as these clinicopathological biomarkers lack efficient interpretation of endogenous mechanism of melanoma, the emphasis on the prognosis of melanoma has transformed to molecular tumor markers. OBJECTIVE: This study was designed to identify survival-related long non-coding RNAs (lncRNAs), and based on the different expressions of these lncRNAs, clinical risk-specific diagnosis and adjuvant therapy could be employed on melanoma patients, especially patients in the early course of disease or patients with a Breslow thickness no more than 2mm...
December 5, 2016: Journal of Dermatological Science
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