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https://www.readbyqxmd.com/read/28220611/non-coding-rnas-emerging-regulatory-factors-in-the-derivation-and-differentiation-of-mammalian-parthenogenetic-embryonic-stem-cells
#1
REVIEW
Jihong Cui, Xin Xie
Parthenogenetic embryonic stem cells (PESCs) are ESCs derived from early parthenogenetic embryos. Haploid PESCs, containing haploid DNA, originate from a single sperm or occyte, while, diploid PESCs originate from two fused occytes. Most PESC lines used so far are diploid. PESCs exhibit representative pluripotent stem cell features, such as the capacity for self-renewal and the pariticular molecular signatures. Whereas, PESCs display distinctive properties, such as differential regulation of X-chromosome inactivation (XCI) and divergent monitor of genes involved in multiple biological processes...
February 21, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28217082/genomic-editing-of-non-coding-rna-genes-with-crispr-cas9-ushers-in-a-potential-novel-approach-to-study-and-treat-schizophrenia
#2
REVIEW
Chuanjun Zhuo, Weihong Hou, Lirong Hu, Chongguang Lin, Ce Chen, Xiaodong Lin
Schizophrenia is a genetically related mental illness, in which the majority of genetic alterations occur in the non-coding regions of the human genome. In the past decade, a growing number of regulatory non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified to be strongly associated with schizophrenia. However, the studies of these ncRNAs in the pathophysiology of schizophrenia and the reverting of their genetic defects in restoration of the normal phenotype have been hampered by insufficient technology to manipulate these ncRNA genes effectively as well as a lack of appropriate animal models...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28211799/increased-expression-of-long-non-coding-rna-glidr-in-prostate-cancer
#3
Yingyi Zhang, Zhe Kong, Yalong Zhang, Wenhua Huang, Hai Wu, Xuechao Wan, Yao Li
Prostate cancer (PCa) was one of the most common cancers in males in China. Long non-coding RNAs (lncRNA), a class of non-coding RNAs with more than 200 nucleotides, played key roles in the progression of prostate cancer. GLIDR, a novel long intergenic ncRNA, was found to be upregulated in tumors compared to normal tissues by using publically databases. In the clinical validation cohort, our results showed GLIDR was significantly up-regulated in prostate cancer samples and cell lines. To explore the potential functions of the GLIDR, we constructed gene co-expression networks and applied GO analysis...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28210621/circular-rnas-in-cardiovascular-disease-an-overview
#4
REVIEW
Ximin Fan, Xinyu Weng, Yifan Zhao, Wei Chen, Tianyi Gan, Dachun Xu
Circular RNA (circRNA), a novel type of endogenous noncoding RNA (ncRNA), has become a research hotspot in recent years. CircRNAs are abundant and stably exist in creatures, and they are found with covalently closed loop structures in which they are quite different from linear RNAs. Nowadays, an increasing number of scientists have demonstrated that circRNAs may have played an essential role in the regulation of gene expression, especially acting as miRNA sponges, and have described the potential mechanisms of several circRNAs in diseases, hinting at their clinical therapeutic values...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28195222/rna-seq-based-detection-of-differentially-expressed-genes-in-the-skeletal-muscle-of-duroc-pigs-with-distinct-lipid-profiles
#5
T F Cardoso, A Cánovas, O Canela-Xandri, R González-Prendes, M Amills, R Quintanilla
We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28192794/the-genetic-causes-of-nonsyndromic-congenital-retinal-detachment-a-genetic-and-phenotypic-study-of-pakistani-families
#6
Vafa Keser, Ayesha Khan, Sorath Siddiqui, Irma Lopez, Huanan Ren, Raheel Qamar, Javad Nadaf, Jacek Majewski, Rui Chen, Robert K Koenekoop
Purpose: To evaluate consanguineous pedigrees from Pakistan with a clinical diagnosis of nonsyndromic congenital retinal nonattachment (NCRNA) and identify genes responsible for the disease as currently only one NCRNA gene is known (atonal basic helix-loop-helix transcription factor 7: ATOH7). Methods: We implemented a three-step genotyping platform: single nucleotide polymorphism genotyping to identify loss of heterozygosity regions in patients, Retinal Information Network panel screening for mutations in currently known retinal genes...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28185557/reconstruction-of-ancestral-rna-sequences-under-multiple-structural-constraints
#7
Olivier Tremblay-Savard, Vladimir Reinharz, Jérôme Waldispühl
BACKGROUND: Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. METHODS: In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28177798/the-mals-5-utr-regulates-hisg-a-keygene-in-the-histidine-biosynthetic-pathway-in-salmonella-enterica-serovar-typhi
#8
Ying Zhang, Dongmei Yan, Lin Xia, Xin Zhao, George Osei-Adjei, Shungao Xu, Xiumei Sheng, Xinxiang Huang
Bacterial noncoding RNAs regulate diverse cellular processes, including virulence and environmental fitness. The malS-5'UTR was identified as a regulatory ncRNA that increases the invasive capacity of Salmonella enterica serovar Typhi. An IntaRNA search suggested base pairing between malS-5'UTR and hisG mRNA, a key gene in the histidine biosynthetic pathway. Overexpression of malS-5'UTR markly reduced bacterial growth in minimal medium without histidine. Overexpression of malS-5'UTR increased mRNA from his operon genes, independently of the bax gene, and decreased HisG protein in S...
December 2, 2016: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28138357/genome-sequence-of-a-high-agarase-producing-strain-flammeovirga-sp-sjp92
#9
Qi Dong, Lingwei Ruan, Hong Shi
Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated strain that belongs to the family Flammeovirgaceae of the class Cytophagia. The strain was isolated from the intestine of abalone, which produces many extracellular agarases and exhibits efficient degradation activities on various polysaccharides, especially agarose. Here we present the high-quality draft genome of Flammeovirga sp. SJP92, together with its phenotypic characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one chromosome and no plasmid...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28131900/non-coding-rnas-and-neuroprotection-after-acute-cns-injuries
#10
Raghavendar Chandran, Suresh L Mehta, Raghu Vemuganti
Accumulating evidence indicates that various classes of non-coding RNAs (ncRNAs) including microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and long non-coding RNAs (lncRNAs) play important roles in normal state as well as the diseases of the CNS. Interestingly, ncRNAs have been shown to interact with messenger RNA, DNA and proteins, and these interactions could induce epigenetic modifications and control transcription and translation, thereby adding a new layer of genomic regulation. The ncRNA expression profiles are known to be altered after acute CNS injuries including stroke, traumatic brain injury and spinal cord injury that are major contributors of morbidity and mortality worldwide...
January 26, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28125557/o-009-long-ncrna-landscape-in-the-ileum-of-treatment-na%C3%A3-ve-early-onset-crohn-disease
#11
Yael Haberman, Marina Ben-Shoshan, Ayelet Di-Segni, Phillip Dexheimer, Tzipi Klein, Batya Weiss, Thomas Walters, Robert Baldassano, Joshua Noe, James Markowitz, Mel Heyman, Joel Rosh, Anne Griffiths, Wallace Crandall, Bruce Aronow, Yair Anikster, Jeffrey Hyams, Subra Kugathasan, Lee Denson
BACKGROUND: Long non-coding RNAs (lncRNA) regulate gene transcription and diverse cellular functions. We have recently reported a core inflammatory and metabolic ileal gene signature in treatment naïve pediatric Crohn Disease (CD), but the potential role of lncRNA was not known. We hypothesized that differences in ileal lncRNA would be associated with differences in protein-coding gene expression, suggesting a role for lncRNA in regulating those gene signatures. METHODS: Poly-A selected RNA-seq and Ensembl annotation were used to define differentially expressed ileal genes with false discovery rate correction of 0...
February 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28125025/inhaled-pollutants-the-molecular-scene-behind-respiratory-and-systemic-diseases-associated-with-ultrafine-particulate-matter
#12
REVIEW
Hussein Traboulsi, Necola Guerrina, Matthew Iu, Dusica Maysinger, Parisa Ariya, Carolyn J Baglole
Air pollution of anthropogenic origin is largely from the combustion of biomass (e.g., wood), fossil fuels (e.g., cars and trucks), incinerators, landfills, agricultural activities and tobacco smoke. Air pollution is a complex mixture that varies in space and time, and contains hundreds of compounds including volatile organic compounds (e.g., benzene), metals, sulphur and nitrogen oxides, ozone and particulate matter (PM). PM0.1 (ultrafine particles (UFP)), those particles with a diameter less than 100 nm (includes nanoparticles (NP)) are considered especially dangerous to human health and may contribute significantly to the development of numerous respiratory and cardiovascular diseases such as chronic obstructive pulmonary disease (COPD) and atherosclerosis...
January 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28109476/a-three-lncrna-signature-derived-from-the-atlas-of-ncrna-in-cancer-tanric-database-predicts-the-survival-of-patients-with-head-and-neck-squamous-cell-carcinoma
#13
Wei Cao, Jian-Nan Liu, Zeqi Liu, Xu Wang, Ze-Guang Han, Tong Ji, Wan-Tao Chen, Xin Zou
OBJECTIVE: Long non-coding RNAs (lncRNAs) have important biological functions and can be used as prognostic biomarkers in cancer. To identify a lncRNA prognostic signature for head and neck squamous cell carcinoma (HNSCC). METHOD: We analysed RNA-seq data derived from the TANRIC database to identify a lncRNA prognostic signature model using the orthogonal partial least squares discrimination analysis (OPLS-DA) and 1.5-fold expression change criterion methods. The prognosis prediction model based on the lncRNA signatures and clinical parameters were evaluated using the 5-fold cross validation method...
February 2017: Oral Oncology
https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#14
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#15
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/28090611/performance-of-nano-assembly-logic-gates-with-a-dna-multi-hairpin-motif
#16
Lulu Zhang, Annie M Bluhm, Kuan-Jen Chen, Nicholas E Larkey, Sean M Burrows
DNA nano-assemblies have far-reaching implications for molecular computers. Boolean logic gates made from DNA respond to specific combinations of chemical or molecular inputs. In complex samples an assortment of other chemicals and molecules may interfere with the gate's recognition and response mechanisms. For logic gates to accept an increasing number of inputs, while maintaining selectivity, their design must only respond when specific input combinations are available simultaneously. Here we present proof-of-principle for a fluorescent-based nano-assembly logic gate for three inputs...
January 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/28077569/rain-rna-protein-association-and-interaction-networks
#17
Alexander Junge, Jan C Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T Workman, Lars Juhl Jensen, Jan Gorodkin
Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28069878/malat1-is-associated-with-poor-response-to-oxaliplatin-based-chemotherapy-in-colorectal-cancer-patients-and-promotes-chemoresistance-through-ezh2
#18
Peilong Li, Xin Zhang, Haiyan Wang, Lili Wang, Tong Liu, Lutao Du, Yongmei Yang, Chuanxin Wang
A major reason for oxaliplatin chemoresistance in colorectal cancer (CRC) is the acquisition of epithelial-mesenchymal transition (EMT) in cancer cells. The long non-coding RNA, MALAT1, is a highly conserved nuclear ncRNA and a key regulator of metastasis development in several cancers. However, its role in oxaliplatin-induced metastasis and chemo-resistance is not well known. In this study, we aim to investigate the prognostic and therapeutic role of MALAT1 in CRC patients receiving oxaliplatin-based therapy, and further explore the potential transcriptional regulation through interaction with EZH2 based on the established HT29 oxaliplatin-resistant cells...
January 9, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28058582/genome-wide-dna-methylation-patterns-analysis-of-noncoding-rnas-in-temporal-lobe-epilepsy-patients
#19
Wenbiao Xiao, Yuze Cao, Hongyu Long, Zhaohui Luo, Shuyu Li, Na Deng, Jianjian Wang, Xiaoyan Lu, Tianfeng Wang, Shangwei Ning, Lihua Wang, Bo Xiao
Temporal lobe epilepsy (TLE) is the most common form of adult epilepsy and frequently evolving drug resistance. Although there is growing consensus that noncoding ribonucleic acids (ncRNAs) are modulators of TLE, the knowledge about the deoxyribonucleic acid (DNA) methylation patterns of ncRNAs in TLE remains limited. In the current study, we constructed DNA methylation profiles from 30 TLE patients and 30 healthy controls for ncRNAs, primarily focusing on long ncRNAs (lncRNAs) and microRNAs (miRNAs), by reannotating data of DNA methylation BeadChip...
January 5, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28029658/the-inhibition-of-45a-ncrna-expression-reduces-tumor-formation-affecting-tumor-nodules-compactness-and-metastatic-potential-in-neuroblastoma-cells
#20
Ilaria Penna, Arianna Gigoni, Delfina Costa, Serena Vella, Debora Russo, Alessandro Poggi, Federico Villa, Antonella Brizzolara, Claudio Canale, Andrea Mescola, Antonio Daga, Claudio Russo, Mario Nizzari, Tullio Florio, Paola Menichini, Aldo Pagano
We recently reported the in vitro over-expression of 45A, a RNA polymerase III-transcribed non-coding (nc)RNA, that perturbs the intracellular content of FE65L1 affecting cell proliferation rate, short-term response to genotoxic stress, substrate adhesion capacity and, ultimately, increasing the tumorigenic potential of human neuroblastoma cells. In this work, to deeply explore the mechanism by which 45A ncRNA contributes to cancer development, we targeted in vitro and in vivo 45A levels by the stable overexpression of antisense 45A RNA...
January 31, 2017: Oncotarget
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