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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28299719/the-non-coding-transcriptome-of-prostate-cancer-implications-for-clinical-practice
#9
REVIEW
Irene V Bijnsdorp, Martin E van Royen, Gerald W Verhaegh, Elena S Martens-Uzunova
Prostate cancer (PCa) is the most common type of cancer and the second leading cause of cancer-related death in men. Despite extensive research, the molecular mechanisms underlying PCa initiation and progression remain unclear, and there is increasing need of better biomarkers that can distinguish indolent from aggressive and life-threatening disease. With the advent of advanced genomic technologies in the last decade, it became apparent that the human genome encodes tens of thousands non-protein-coding RNAs (ncRNAs) with yet to be discovered function...
March 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28289554/non-coding-rnas-new-players-in-skin-wound-healing
#10
REVIEW
Eva K Herter, Ning Xu Landén
Significance: Wound healing is a basic physiological process that is utilized to keep the integrity of the skin. Impaired wound repair, such as chronic wounds and pathological scars, presents a major health and economic burden worldwide. To date, efficient targeted treatment for these wound disorders is still lacking, which is largely due to our limited understanding of the biological mechanisms underlying these diseases. Research driven around discovering new therapies for these complications is, therefore, an urgent need...
March 1, 2017: Advances in Wound Care
https://www.readbyqxmd.com/read/28279183/circles-reshaping-the-rna-world-from-waste-to-treasure
#11
REVIEW
Jing Liu, Tian Liu, Xiaman Wang, Aili He
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions...
March 9, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28274175/the-origins-and-evolutionary-history-of-human-non-coding-rna-regulatory-networks
#12
Masih Sherafatian, Seyed Javad Mowla
The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human...
February 1, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28270684/regulatory-feedback-from-nascent-rna-to-chromatin-and-transcription
#13
REVIEW
Lenka Skalska, Manuel Beltran-Nebot, Jernej Ule, Richard G Jenner
Transcription and chromatin function are regulated by proteins that bind to DNA, nucleosomes or RNA polymerase II, with specific non-coding RNAs (ncRNAs) functioning to modulate their recruitment or activity. Unlike ncRNAs, nascent pre-mRNA was considered to be primarily a passive player in these processes. In this Opinion article, we describe recently identified interactions between nascent pre-mRNAs and regulatory proteins, highlight commonalities between the functions of nascent pre-mRNA and nascent ncRNA, and propose that both types of RNA have an active role in transcription and chromatin regulation...
March 8, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28267419/expanding-the-repertoire-of-deadenylases
#14
Ilias Skeparnias, Dimitrios Αnastasakis, Athanasios-Nasir Shaukat, Katerina Grafanaki, Constantinos Stathopoulos
Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homologue PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development...
March 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28254434/bimodal-expression-of-yeast-gal-genes-is-controlled-by-a-long-non-coding-rna-and-a-bifunctional-galactokinase
#15
Ioannis Zacharioudakis, Dimitris Tzamarias
Bimodality in gene expression can generate phenotypic heterogeneity facilitating fitness and growth of isogenic cell populations in suboptimal environments. We investigated the mechanism by which, in conditions of limiting galactose, yeast cell populations activate GAL genes in a bimodal fashion with a cell fraction expressing GAL genes (ON), while the rest subpopulation is kept at the non-expressing (OFF) state. We show that a long non-coding RNA (GAL10-ncRNA) crossing the bidirectional GAL1-10 promoter, decreases the rate by which single cells commit transition to the ON state without affecting the rate of GAL transcription per se in ON cells...
February 27, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28245801/differentiation-of-ncrnas-from-small-mrnas-in-escherichia-coli-o157-h7-edl933-ehec-by-combined-rnaseq-and-riboseq-ryhb-encodes-the-regulatory-rna-ryhb-and-a-peptide-ryhp
#16
Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A Keim, Siegfried Scherer
BACKGROUND: While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. RESULTS: Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28231281/the-intron-in-centromeric-noncoding-rna-facilitates-rnai-mediated-formation-of-heterochromatin
#17
Masatoshi Mutazono, Misato Morita, Chihiro Tsukahara, Madoka Chinen, Shiori Nishioka, Tatsuhiro Yumikake, Kohei Dohke, Misuzu Sakamoto, Takashi Ideue, Jun-Ichi Nakayama, Kojiro Ishii, Tokio Tani
In fission yeast, the formation of centromeric heterochromatin is induced through the RNA interference (RNAi)-mediated pathway. Some pre-mRNA splicing mutants (prp) exhibit defective formation of centromeric heterochromatin, suggesting that splicing factors play roles in the formation of heterochromatin, or alternatively that the defect is caused by impaired splicing of pre-mRNAs encoding RNAi factors. Herein, we demonstrate that the splicing factor spPrp16p is enriched at the centromere, and associates with Cid12p (a factor in the RNAi pathway) and the intron-containing dg ncRNA...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28220611/non-coding-rnas-emerging-regulatory-factors-in-the-derivation-and-differentiation-of-mammalian-parthenogenetic-embryonic-stem-cells
#18
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
#19
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
#20
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
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