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no-coding RNA

Martina Faraldi, Marta Gomarasca, Giuseppe Banfi, Giovanni Lombardi
Circulating molecules that are released into the circulation in response to specific stimuli are considered potential biomarkers for physiological or pathological processes. Their effective usefulness as biomarkers resides in their stability and high availability in all the biological fluids, combined with the limited invasiveness of intervention. Among the circulating molecules, miRNAs represent a novel class of biomarkers as they possess all the required characteristics such as sensitivity, predictivity, specificity, robustness, translatability, and noninvasiveness...
2018: Advances in Clinical Chemistry
Vivien A C Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G Schupp, Matthew C Canver, Takahiro Maeda, Luca Pinello, Daniel E Bauer
CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets, we develop CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genomes, transcripts, and protein coordinates and structures. No currently available tool has similar functionality. The ensuing genotype-phenotype linear and three-dimensional maps raise hypotheses about structure-function relationships at discrete protein regions...
October 19, 2018: Genome Biology
Anna Adamus, Petra Müller, Bente Nissen, Annika Kasten, Stefan Timm, Hermann Bauwe, Guido Seitz, Nadja Engel
Since it is known that cancer cells exhibit a preference for increased glycine consumption, the respective glycine metabolizing enzymes are in focus of many research projects. However, no cancer associated studies are available for the Glycine Cleavage System Protein H (GCSH) to date. Our initial analysis revealed a GCSH-overexpression of the protein-coding transcript variant 1 (Tv1) in breast cancer cells and tissue. Furthermore, a shorter (391 bp) transcript variant (Tv*) was amplified with an increased expression in healthy breast cells and a decreased expression in breast cancer samples...
October 18, 2018: Scientific Reports
Xiang Lin, QingXiang Gao, LiYan Zhu, GuiXuan Zhou, ShiWei Ni, Hao Han, ZhiCao Yue
Long noncoding RNAs (lncRNAs) are non-protein coding transcripts that are involved in a broad range of biological processes. Here, we examined the functional roles of lncRNAs in feather regeneration. RNA-seq profiling of the regenerating feather blastema revealed that the Wnt signaling is among the most active pathways during feather regeneration, with the Wnt ligands and their inhibitors showing distinct expression patterns. Co-expression analysis identified hundreds of lncRNAs with similar expression patterns to either the Wnt ligands (the Lwnt group) or their downstream target genes (the Twnt group)...
October 16, 2018: Development
Olivia J Conway, Minerva M Carrasquillo, Xue Wang, Jenny M Bredenberg, Joseph S Reddy, Samantha L Strickland, Curtis S Younkin, Jeremy D Burgess, Mariet Allen, Sarah J Lincoln, Thuy Nguyen, Kimberly G Malphrus, Alexandra I Soto, Ronald L Walton, Bradley F Boeve, Ronald C Petersen, John A Lucas, Tanis J Ferman, William P Cheshire, Jay A van Gerpen, Ryan J Uitti, Zbigniew K Wszolek, Owen A Ross, Dennis W Dickson, Neill R Graff-Radford, Nilüfer Ertekin-Taner
BACKGROUND: Rare coding variants ABI3_rs616338-T and PLCG2_rs72824905-G were identified as risk or protective factors, respectively, for Alzheimer's disease (AD). METHODS: We tested the association of these variants with five neurodegenerative diseases in Caucasian case-control cohorts: 2742 AD, 231 progressive supranuclear palsy (PSP), 838 Parkinson's disease (PD), 306 dementia with Lewy bodies (DLB) and 150 multiple system atrophy (MSA) vs. 3351 controls; and in an African-American AD case-control cohort (181 AD, 331 controls)...
October 11, 2018: Molecular Neurodegeneration
Laurence Tessier, Olivier Côté, Dorothee Bienzle
Background: Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods: RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total)...
2018: PeerJ
Irene Lacal, Rossella Ventura
Parents' stressful experiences can influence an offspring's vulnerability to many pathological conditions, including psychopathologies, and their effects may even endure for several generations. Nevertheless, the cause of this phenomenon has not been determined, and only recently have scientists turned to epigenetics to answer this question. There is extensive literature on epigenetics, but no consensus exists with regard to how and what can (and must) be considered to study and define epigenetics processes and their inheritance...
2018: Frontiers in Molecular Neuroscience
Ruixia Zhu, Xu Liu, Zhiyi He
Objectives Long non-coding RNAs (lncRNAs) have been identified as key regulators in the development of atherosclerosis, which is a major cause of ischemic stroke. However, to date, there are no reports on the association between lncRNA gene variation and the risk of ischemic stroke. Therefore, we assessed the association between H19 and MALAT1 gene polymorphisms and susceptibility to ischemic stroke in a northern Chinese Han population. Methods In our study, we genotyped four genetic variations in lncRNA-H19 and -MALAT1 (rs217727, rs2251375, rs619586, and rs3200401) in a case-control study of 567 ischemic stroke patients and 552 control subjects...
October 10, 2018: Molecular Brain
Emma Briggs, Graham Hamilton, Kathryn Crouch, Craig Lapsley, Richard McCulloch
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs...
October 10, 2018: Nucleic Acids Research
Jiechen Wang, Chen Ji, Qi Li, Yong Zhou, Yongrui Wu
BACKGROUND: PLATZ proteins are a novel class of plant-specific zinc-dependent DNA-binding proteins that are classified as transcription factors (TFs). However, their common biochemical features and functions are poorly understood. RESULT: Here, we identified and cloned 17 PLATZ genes in the maize (Zea mays) genome. All ZmPLATZs were located in nuclei, consistent with their predicted role as TFs. However, none of ZmPLATZs was found to have intrinsic activation properties in yeast...
October 5, 2018: BMC Plant Biology
Bin Xu, Ya Zhu, Yu Tang, Zhenyong Zhang, Qiaxian Wen
BACKGROUND Growing evidence indicates that a non-coding RNA named miR-34b/c plays crucial roles in carcinogenesis, and its common polymorphism, pri-miR-34b/c rs4938723, also participates in this process and is associated with cancer susceptibility. However, this association was previously undefined and ambiguous. Therefore, we carried out an updated analysis to evaluate this relationship between rs4938723 polymorphism and cancer susceptibility. MATERIAL AND METHODS PubMed, EMbase, Web of Science and Chinese language (WanFang, CNKI and VIP) databases were searched for relevant studies until Sep 10, 2018...
October 4, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
César Aguilar, Gabriel Martínez-Batallar, Noemí Flores, Fabián Moreno-Avitia, Sergio Encarnación, Adelfo Escalante, Francisco Bolívar
The previous deletion of the cytoplasmic components of the phosphotransferase system (PTS) in Escherichia coli JM101 resulted in the PTS- derivative strain PB11 with severely impaired growth capability in glucose as the sole carbon source. Previous adaptive laboratory evolution (ALE) experiment led to select a fast-growing strain named PB12 from PB11. Comparative genome analysis of PB12 showed a chromosomal deletion, which result in the loss of several genes including rppH which codes for the RNA pyrophosphohydrolase RppH, involved in the preparation of hundreds of mRNAs for further degradation by RNase E...
October 3, 2018: Applied Microbiology and Biotechnology
Mohamed Salem, Rafet Al-Tobasei, Ali Ali, Daniela Lourenco, Guangtu Gao, Yniv Palti, Brett Kenney, Timothy D Leeds
Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. This study has two-fold objectives, first to develop, and validate a 50K transcribed gene SNP-chip using RNA-Seq data. To achieve this objective, two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD)...
2018: Frontiers in Genetics
Sana Maher Aghbari, Shaimaa Omar Zayed, Olfat Gamil Shaker, Abdelrahman Ibrahim Abushouk
BACKGROUND: MicroRNA-27b (miR27b) is a small, non-coding RNA that is involved in physiological keratinocyte differentiation and pathological inflammatory processes. We performed this study to investigate the value of miR27b as a diagnostic marker for oral lichen planus (OLP) and the correlation between CD8 (cytotoxic T-cell marker) and miR27b tissue expression in OLP patients. METHODS: Forty participants (including 20 OLP patients and 20 controls) underwent oral biopsy...
October 1, 2018: Journal of Oral Pathology & Medicine
Jason P Tourigny, Moustafa M Saleh, Kenny Schumacher, Didier Devys, Gabriel E Zentner
Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNA (ncRNA) genes including those encoding small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA and mRNA expression relies on a set of common factors, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear...
October 1, 2018: Molecular and Cellular Biology
Shuguo Yang, Jingang Sun
It has been well established that long non‑coding RNAs (lncRNAs) are crucial mediators in a diverse range of diseases, including atherosclerosis. The present study aimed to examine the molecular mechanisms underlying the association between steroid receptor RNA activator (SRA) and atherosclerosis. Reverse transcription‑quantitative polymerase chain reaction analysis, western blot analysis and luciferase assays were performed to examine interactions among SRA, adipose triglyceride lipase (ATGL) and peroxisome proliferator‑activated receptor (PPARγ), and the effect of resveratrol (RSV) on the levels of SRA, ATGL and PPARγ...
September 20, 2018: Molecular Medicine Reports
Xiujun Li, Jiali Wang, Yuchen Pan, Yujun Xu, Dan Liu, Yayi Hou, Guangfeng Zhao
Further studies on the molecular mechanisms of mesenchymal stem cells in the maintenance of growth and function are essential for their clinical application. Growing evidence has shown that long non-coding RNAs (lncRNAs) play an important role in the regulation of mesenchymal stem cells. Recently, it is reported that highly upregulated in liver cancer (HULC), with another lncRNA MALAT-1, accelerated liver cancer stem cell growth. The regulating role of MALAT-1 in mesenchymal stem cells has been investigated...
September 30, 2018: Experimental Biology and Medicine
Shanmugapriya, Hisham Alkatib Huda, Soundararajan Vijayarathna, Chern Ein Oon, Yeng Chen, Jagat R Kanwar, Mei Li Ng, Sreenivasan Sasidharan
Circular RNAs characterize a class of widespread and diverse endogenous RNAs which are non-coding RNAs that are made by back-splicing events and have covalently closed loops with no polyadenylated tails. Various indications specify that circular RNAs (circRNAs) are plentiful in the human transcriptome. However, their participation in biological processes remains mostly undescribed. To date thousands of circRNAs have been revealed in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies specify that these transcripts control expression of protein-coding linear transcripts and thus encompass a key component of gene expression regulation...
2018: Advances in Experimental Medicine and Biology
Xinye Wang, Yantao Luo, Dongying Liu, Jiamei Wang, Shi Wei, Liang Zhao
Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province, China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete genome sequence information and genome annotation. The 7,374,589 bp long genome which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one chromosome and four plasmids...
2018: Standards in Genomic Sciences
Joseph A Kendra, Vivek M Advani, Bin Chen, Joseph W Briggs, Jinyi Zhu, Hannah J Bress, Sushrut M Pathy, Jonathan D Dinman
Climate change and human globalization have spurred the rapid spread of mosquito-borne diseases to naïve populations. One such emerging virus of public health concern is Chikungunya virus (CHIKV), a member of the Togaviridae family, genus alphavirus. CHIKV pathogenesis is predominately characterized by acute febrile symptoms and severe arthralgia, which can persist in the host long after viral clearance. CHIKV has also been implicated in cases of acute encephalomyelitis, and its vertical transmission has been reported...
September 21, 2018: Journal of Biological Chemistry
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