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https://www.readbyqxmd.com/read/28430163/long-non-coding-rnas-key-regulators-of-epithelial-mesenchymal-transition-tumour-drug-resistance-and-cancer-stem-cells
#1
REVIEW
Richard Heery, Stephen P Finn, Sinead Cuffe, Steven G Gray
Epithelial mesenchymal transition (EMT), the adoption by epithelial cells of a mesenchymal-like phenotype, is a process co-opted by carcinoma cells in order to initiate invasion and metastasis. In addition, it is becoming clear that is instrumental to both the development of drug resistance by tumour cells and in the generation and maintenance of cancer stem cells. EMT is thus a pivotal process during tumour progression and poses a major barrier to the successful treatment of cancer. Non-coding RNAs (ncRNA) often utilize epigenetic programs to regulate both gene expression and chromatin structure...
April 21, 2017: Cancers
https://www.readbyqxmd.com/read/28428833/complete-genome-sequence-of-kosakonia-oryzae-type-strain-ola-51-t
#2
Yuanyuan Li, Shuying Li, Mingyue Chen, Guixiang Peng, Zhiyuan Tan, Qianli An
Strain Ola 51(T) (=LMG 24251(T) = CGMCC 1.7012(T)) is the type strain of the species Kosakonia oryzae and was isolated from surface-sterilized roots of the wild rice species Oryza latifolia grown in Guangdong, China. Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. The genome contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content, 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48 pseudo genes, and 1 CRISPR array...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28424679/linking-diet-to-colorectal-cancer-the-emerging-role-of-microrna-in-the-communication-between-plant-and-animal-kingdoms
#3
REVIEW
Manuela Del Cornò, Gloria Donninelli, Lucia Conti, Sandra Gessani
Environmental and lifestyle factors, including diet and nutritional habits have been strongly linked to colorectal cancer (CRC). Of note, unhealthy dietary habits leading to adiposity represent a main risk factor for CRC and are associated with a chronic low-grade inflammatory status. Inflammation is a hallmark of almost every type of cancer and can be modulated by several food compounds exhibiting either protective or promoting effects. However, in spite of an extensive research, the underlying mechanisms by which dietary patterns or bioactive food components may influence tumor onset and outcome have not been fully clarified yet...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#4
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28414973/regulation-of-antibiotic-resistance-by-non-coding-rnas-in-bacteria
#5
REVIEW
Daniel Dar, Rotem Sorek
Antibiotic resistance genes are commonly regulated by sophisticated mechanisms that activate gene expression in response to antibiotic exposure. Growing evidence suggest that cis-acting non-coding RNAs play a major role in regulating the expression of many resistance genes, specifically those which counteract the effects of translation-inhibiting antibiotics. These ncRNAs reside in the 5'UTR of the regulated gene, and sense the presence of the antibiotics by recruiting translating ribosomes onto short upstream open reading frames (uORFs) embedded in the ncRNA...
April 14, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28412522/small-non-coding-rnas-in-adipocyte-biology-and-obesity
#6
REVIEW
Ez-Zoubir Amri, Marcel Scheideler
Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs...
April 12, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28407081/isolation-of-early-responsive-microrna-from-diuraphis-noxia-hemiptera-aphididae-resistant-wheat
#7
Vittorio F Nicolis, Sonia-Mari Greyling, Eduard Venter
The Russian wheat aphid (Diuraphis noxia Kurdjumov) is an economically important pest of small grains in many countries. The past decades have seen the deployment of resistance-carrying wheat (Triticum aestivum L.) cultivars to control D. noxia. However, the emergence of resistance-breaking biotypes is negating this strategy. The role that noncoding RNA (ncRNA) molecules play in the wheat-D. noxia interaction has not been studied to date. This study aimed to isolate differentially regulated microRNA from a resistant and susceptible near-isogenic wheat line after aphid infestation...
April 12, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28387604/des-ncrna-a-knowledgebase-for-exploring-information-about-human-micro-and-long-noncoding-rnas-based-on-literature-mining
#8
Adil Salhi, Magbubah Essack, Tanvir Alam, Vladan P Bajic, Lina Ma, Aleksandar Radovanovic, Benoit Marchand, Sebastian Schmeier, Zhang Zhang, Vladimir B Bajic
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www...
April 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28385563/evidence-of-putative-non-coding-rnas-from-leishmania-untranslated-regions
#9
Felipe Freitas Castro, Patricia C Ruy, Karina Nogueira Zeviani, Ramon Freitas Santos, Juliano Simões Toledo, Angela Kaysel Cruz
Non-coding RNAs (ncRNAs) are regulatory elements present in a wide range of organisms, including trypanosomatids. ncRNAs transcribed from the untranslated regions (UTRs) of coding genes have been described in the transcriptomes of several eukaryotes, including Trypanosoma brucei. To uncover novel putative ncRNAs in two Leishmania species, we examined a L. major cDNA library and a L. donovani non-polysomal RNA library. Using a combination of computational analysis and experimental approaches, we classified 26 putative ncRNA in L...
April 3, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28380027/evaluation-of-a-short-rna-within-prostate-cancer-gene-3-in-the-predictive-role-for-future-cancer-using-non-malignant-prostate-biopsies
#10
Karl H Pang, Derek J Rosario, Susan L Morgan, James W F Catto
BACKGROUND: Prostate Cancer 3 (PCA3) is a long non-coding RNA (ncRNA) upregulated in prostate cancer (PCa). We recently identified a short ncRNA expressed from intron 1 of PCA3. Here we test the ability of this ncRNA to predict the presence of cancer in men with a biopsy without PCa. METHODS: We selected men whose initial biopsy did not identify PCa and selected matched cohorts whose subsequent biopsies revealed PCa or benign tissue. We extracted RNA from the initial biopsy and measured PCA3-shRNA2, PCA3 and PSA (qRT-PCR)...
2017: PloS One
https://www.readbyqxmd.com/read/28361713/the-joint-nettab-integrative-bioinformatics-2015-meeting-aims-topics-and-outcomes
#11
EDITORIAL
Paolo Romano, Ralf Hofestädt, Matthias Lange, Domenica D'Elia
The 15(th) International NETTAB workshop and the 11(th) Integrative Bioinformatics Symposium were held together in Bari, on October 14-16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was "Bioinformatics for ncRNA", but the traditional topics of both meetings series were also included in the event.About 60 scientific contributions were presented, including six keynote lectures, one special guest lecture, and many oral communications and posters. A "Two-Day Hands-on Tutorial" event was organised before the workshop...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28358390/microrna-exocytosis-by-large-dense-core-vesicle-fusion
#12
Alican Gümürdü, Ramazan Yildiz, Erden Eren, Gökhan Karakülah, Turgay Ünver, Şermin Genç, Yongsoo Park
Neurotransmitters and peptide hormones are secreted into outside the cell by a vesicle fusion process. Although non-coding RNA (ncRNA) that include microRNA (miRNA) regulates gene expression inside the cell where they are transcribed, extracellular miRNA has been recently discovered outside the cells, proposing that miRNA might be released to participate in cell-to-cell communication. Despite its importance of extracellular miRNA, the molecular mechanisms by which miRNA can be stored in vesicles and released by vesicle fusion remain enigmatic...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28338834/comparative-genomics-of-microsporidian-genomes-reveals-a-minimal-non-coding-rna-set-and-new-insights-for-transcription-in-minimal-eukaryotic-genomes
#13
Abdel Belkorchia, Jean-François Pombert, Valérie Polonais, Nicolas Parisot, Frédéric Delbac, Jean-François Brugère, Pierre Peyret, Christine Gaspin, Eric Peyretaillade
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments...
February 28, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28335259/lipid-nanovectors-to-deliver-rna-oligonucleotides-in-cancer
#14
REVIEW
Virginia Campani, Giuseppina Salzano, Sara Lusa, Giuseppe De Rosa
The growing knowledge on the mechanisms of gene silencing and gene regulation by non-coding RNAs (ncRNA), mainly small interfering RNA (siRNA) and microRNA (miRNA), is providing a significant boost to the development of new therapeutic strategies for the treatment of cancer. However, the design of RNA-based therapeutics is hampered by biopharmaceutical issues, thus requiring the use of suitable delivery strategies. In this regards, lipid nanovectors have been successfully investigated to deliver RNA in different forms of cancer...
July 9, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334976/a-sensitivity-analysis-of-rna-folding-nearest-neighbor-parameters-identifies-a-subset-of-free-energy-parameters-with-the-greatest-impact-on-rna-secondary-structure-prediction
#15
Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain McFadyen, David H Mathews
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334257/fast-clash-free-rna-conformational-morphing-using-molecular-junctions
#16
Amélie Héliou, Dominik Budday, Rasmus Fonseca, Henry van den Bedem
Motivation: Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble...
March 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28329687/impact-of-dietary-interventions-on-noncoding-rna-networks-and-mrnas-encoding-chromatin-related-factors
#17
Christopher D Green, Yi Huang, Xiaoyang Dou, Liu Yang, Yong Liu, Jing-Dong J Han
Dietary interventions dramatically affect metabolic disease and lifespan in various aging models. Here, we profiled liver microRNA (miRNA), coding, and long non-coding RNA (lncRNA) expression by high-throughput deep sequencing in mice across multiple energy intake and expenditure interventions. Strikingly, three dietary intervention network design patterns were uncovered: (1) lifespan-extending interventions largely repressed the expression of miRNAs, lncRNAs, and transposable elements; (2) protein-coding mRNAs with expression positively correlated with long lifespan are highly targeted by miRNAs; and (3) miRNA-targeting interactions mainly target chromatin-related functions...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28327113/low-cell-number-single-tube-amplification-sta-of-total-rna-revealed-transcriptome-changes-from-pluripotency-to-endothelium
#18
Yi-Hsuan Lee, Ya-Wen Hsueh, Yao-Hung Peng, Kung-Chao Chang, Kuen-Jer Tsai, H Sunny Sun, Ih-Jen Su, Po-Min Chiang
BACKGROUND: In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28322921/linking-deregulation-of-non-coding-rna-to-the-core-pathophysiology-of-alzheimer-s-disease-an-integrative-review
#19
REVIEW
Mark J Millan
The human genome encodes a vast repertoire of protein non-coding RNAs (ncRNA), some specific to the brain. MicroRNAs, which interfere with the translation of target mRNAs, are of particular interest since their deregulation has been implicated in neurodegenerative disorders like Alzheimer's disease (AD). However, it remains challenging to link the complex body of observations on miRNAs and AD into a coherent framework. Using extensive graphical support, this article discusses how a diverse panoply of miRNAs convergently and divergently impact (and are impacted by) core pathophysiological processes underlying AD: neuroinflammation and oxidative stress; aberrant generation of β-amyloid-42 (Aβ42); anomalies in the production, cleavage and post-translational marking of Tau; impaired clearance of Aβ42 and Tau; perturbation of axonal organisation; disruption of synaptic plasticity; endoplasmic reticulum stress and the unfolded protein response; mitochondrial dysfunction; aberrant induction of cell cycle re-entry; and apoptotic loss of neurons...
March 17, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28320778/the-epitranscriptome-of-noncoding-rnas-in-cancer
#20
REVIEW
Manel Esteller, Pier Paolo Pandolfi
The activity of RNA is controlled by different types of post-transcriptional modifications, such as the addition of methyl groups and other chemical and structural changes, that have been recently described in human cells by high-throughput sequencing. Herein, we will discuss how the so-called epitranscriptome is disrupted in cancer and what the contribution of its writers, readers, and erasers to the process of cellular transformation is, particularly focusing on the epigenetic modifications of ncRNAs.Significance: Chemical modifications of RNA play a central role in the control of messenger and ncRNA activity and, thus, are tightly regulated in cells...
March 20, 2017: Cancer Discovery
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