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https://www.readbyqxmd.com/read/28902868/discovery-of-numerous-novel-small-genes-in-the-intergenic-regions-of-the-escherichia-coli-o157-h7-sakai-genome
#1
Sarah M Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value...
2017: PloS One
https://www.readbyqxmd.com/read/28894972/gene-regulation-of-mammalian-long-non-coding-rna
#2
REVIEW
Heeyoun Bunch
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported...
September 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28887637/epigenetic-regulation-in-cell-senescence
#3
REVIEW
Li-Qin Cheng, Zhu-Qin Zhang, Hou-Zao Chen, De-Pei Liu
Cell senescence, which is an irreversible state of cell proliferative arrest, has emerged as a potentially important contributor to tissue dysfunction and organismal ageing. Cell senescence is triggered by a variety of senescence stressors, which affect gene expression and multiple signalling pathways that give rise to various senescence phenotypes. Epigenetic mechanisms, as critical regulators of chromosomal architecture and gene expression, have added an extra dimension to the molecular mechanisms of cell senescence...
September 8, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28884413/knockdown-of-long-non-coding-rna-prostate-cancer-associated-ncrna-transcript-1-inhibits-multidrug-resistance-and-c-myc-dependent-aggressiveness-in-colorectal-cancer-caco-2-and-ht-29-cells
#4
Lei Qiao, Xiangyu Liu, Yichao Tang, Zheng Zhao, Jilong Zhang, Huayan Liu
The long non-coding RNA (lncRNA) prostate cancer-associated ncRNA transcript 1 (PCAT-1) has been shown to promote prostate cancer cell proliferation through c-Myc and is associated with the poor prognosis of CRC patients. In the current study, it was hypothesized that the effect of PCAT-1 on the aggressiveness of CRC cells was dependent on the function of c-Myc. Human CRC cell lines Caco-2 and HT-29 were transfected with specific PCAT-1 shRNAs, and cell migration, invasiveness, and resistance to 5-fluorouracil were measured...
September 7, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28882222/role-of-the-trna-derived-small-rnas-in-cancer-new-potential-biomarkers-and-target-for-therapy
#5
Veronica Balatti, Yuri Pekarsky, Carlo M Croce
Noncoding RNAs are untranslated RNA molecules that can be divided into two main types: infrastructural, including transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), and regulatory, including long ncRNAs (lncRNAs) and small ncRNAs (sRNA). Among small ncRNA, the role of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) in cancer is well documented. Recently, other small ncRNAs have been described. In particular, tRNA-derived small RNAs (tsRNA) have been found to be frequently dysregulated in cancer. Since tsRNAs can be considered unique sequences and are able to bind both Argonaute proteins (like miRNAs) and Piwi proteins (like piRNAs), their dysregulation could play a critical role in cancer by interfering with gene expression regulation at different levels...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28874118/a-mirna-catalogue-and-ncrna-annotation-of-the-short-living-fish-nothobranchius-furzeri
#6
Mario Baumgart, Emanuel Barth, Aurora Savino, Marco Groth, Philipp Koch, Andreas Petzold, Ivan Arisi, Matthias Platzer, Manja Marz, Alessandro Cellerino
BACKGROUND: The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression. RESULTS: Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species...
September 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28863214/regulation-of-noncoding-transcriptome-in-developing-photoreceptors-by-rod-differentiation-factor-nrl
#7
Lina Zelinger, Gökhan Karakülah, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J Brooks, Anand Swaroop
Purpose: Transcriptome analysis by next generation sequencing allows qualitative and quantitative profiling of expression patterns associated with development and disease. However, most transcribed sequences do not encode proteins, and little is known about the functional relevance of noncoding (nc) transcriptome in neuronal subtypes. The goal of this study was to perform a comprehensive analysis of long noncoding (lncRNAs) and antisense (asRNAs) RNAs expressed in mouse retinal photoreceptors...
September 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28855739/noncoding-rnas-in-neurodegeneration
#8
REVIEW
Evgenia Salta, Bart De Strooper
The emerging complexity of the transcriptional landscape poses great challenges to our conventional preconceptions of how the genome regulates brain function and dysfunction. Non-protein-coding RNAs (ncRNAs) confer a high level of intricate and dynamic regulation of various molecular processes in the CNS and they have been implicated in neurodevelopment and brain ageing, as well as in synapse function and cognitive performance, in both health and disease. ncRNA-mediated processes may be involved in various aspects of the pathogenesis of neurodegenerative disorders...
October 2017: Nature Reviews. Neuroscience
https://www.readbyqxmd.com/read/28840253/interaction-and-cross-talk-between-non-coding-rnas
#9
REVIEW
Soichiro Yamamura, Mitsuho Imai-Sumida, Yuichiro Tanaka, Rajvir Dahiya
Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors...
August 24, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28830358/unitas-the-universal-tool-for-annotation-of-small-rnas
#10
Daniel Gebert, Charlotte Hewel, David Rosenkranz
BACKGROUND: Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs...
August 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28819097/the-non-coding-rna-bc1-regulates-experience-dependent-structural-plasticity-and-learning
#11
Victor Briz, Leonardo Restivo, Emanuela Pasciuto, Konrad Juczewski, Valentina Mercaldo, Adrian C Lo, Pieter Baatsen, Natalia V Gounko, Antonella Borreca, Tiziana Girardi, Rossella Luca, Julie Nys, Rogier B Poorthuis, Huibert D Mansvelder, Gilberto Fisone, Martine Ammassari-Teule, Lutgarde Arckens, Patrik Krieger, Rhiannon Meredith, Claudia Bagni
The brain cytoplasmic (BC1) RNA is a non-coding RNA (ncRNA) involved in neuronal translational control. Absence of BC1 is associated with altered glutamatergic transmission and maladaptive behavior. Here, we show that pyramidal neurons in the barrel cortex of BC1 knock out (KO) mice display larger excitatory postsynaptic currents and increased spontaneous activity in vivo. Furthermore, BC1 KO mice have enlarged spine heads and postsynaptic densities and increased synaptic levels of glutamate receptors and PSD-95...
August 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28818903/draft-genome-sequence-of-staphylococcus-aureus-s681-a-tetracycline-sensitive-livestock-associated-methicillin-resistant-clonal-complex-398-strain
#12
Marc J A Stevens, Roger Stephan, Sophia Johler
We present the draft genome sequence of an atypical tetracycline-susceptible livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) strain. It contains 2,817,340 bp and 2,858 coding sequences, including 6 rRNA operons, 56 tRNAs, and 4 noncoding RNA (ncRNA) genes. The strain harbors a tet(M) gene, but 15 point mutations in amino acids are present that likely impair the functionality of TetM.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28816061/redox-regulation-and-noncoding-rnas
#13
Matthias S Leisegang, Katrin Schröder, Ralf P Brandes
SIGNIFICANCE: RNA is a heterogeneous class of molecules with the minority being protein coding. Noncoding RNAs (ncRNAs) are involved in translation and epigenetic control mechanisms of gene expression. Recent Advances: In recent years, the number of identified ncRNAs has dramatically increased and it is now clear that ncRNAs provide a complex layer of differential gene expression control. CRITICAL ISSUES: NcRNAs exhibit interplay with redox regulation. Redox regulation alters the expression of ncRNAs; conversely, ncRNAs alter the expression of generator and effector systems of redox regulation in a complex manner, which will be the focus of this review article...
September 18, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28794025/retrovirus-based-virus-like-particle-immunogenicity-and-its-modulation-by-toll-like-receptor-activation
#14
Fabien Pitoiset, Thomas Vazquez, Beatrice Levacher, Djamel Nehar-Belaid, Nicolas Dérian, James Vigneron, David Klatzmann, Bertrand Bellier
Retrovirus-derived virus-like particles (VLPs) are particularly interesting vaccine platforms as they trigger efficient humoral and cellular immune responses and can be used to display heterologous antigens. In this study, we characterized the intrinsic immunogenicity of VLPs and investigated their possible adjuvantization by incorporation of toll-like receptor (TLR) ligands. We designed a non-coding single-stranded RNA (ncRNA) that could be encapsidated by VLPs and induce TLR7/8-signaling. We found that VLPs efficiently induce in vitro dendritic cell activation, which can be improved by ncRNA encapsidation (ncRNAVLPs)...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28777303/novel-biomarkers-in-the-diagnosis-of-chronic-kidney-disease-and-the-prediction-of-its-outcome
#15
REVIEW
Jacek Rysz, Anna Gluba-Brzózka, Beata Franczyk, Zbigniew Jabłonowski, Aleksandra Ciałkowska-Rysz
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value...
August 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28765094/non-coding-rnas-as-a-new-dawn-in-tumor-diagnosis
#16
REVIEW
Anna Grimaldi, Mayra Rachele Zarone, Carlo Irace, Silvia Zappavigna, Angela Lombardi, Hiromichi Kawasaki, Michele Caraglia, Gabriella Misso
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern...
July 29, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28762653/single-cell-transcriptomics-of-noncoding-rnas-and-their-cell-specificity
#17
REVIEW
Katerina A B Gawronski, Junhyong Kim
Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability...
August 1, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28760736/targeting-long-non-coding-rna-dancr-inhibits-triple-negative-breast-cancer-progression
#18
Sha Sha, Dongya Yuan, Yuejun Liu, Baosan Han, Nanbert Zhong
Triple negative breast cancer (TNBC) is non-responsive to conventional anti-hormonal and Her2-targeted therapies, making it necessary to identify new molecular targets for therapy. Long non-coding RNA anti-differentiation ncRNA (lncRNA DANCR) was identified participating in carcinogenesis of hepatocellular carcinoma, but its expression and potential role in TNBC progression is still unclear. In the present study, our results showed that DANCR expression was increased in TNBC tissues compared with the adjacent normal tissues using quantitative real-time PCR (qRT-PCR) in 63 TNBC specimens...
September 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28757239/beyond-mrna-the-role-of-non-coding-rnas-in-normal-and-aberrant-hematopoiesis
#19
REVIEW
Mark C Wilkes, Claire E Repellin, Kathleen M Sakamoto
The role of non-coding Ribonucleic Acids (ncRNAs) in biology is currently an area of intense focus. Hematopoiesis requires rapidly changing regulatory molecules to guide appropriate differentiation and ncRNA are well suited for this. It is not surprising that virtually all aspects of hematopoiesis have roles for ncRNAs assigned to them and doubtlessly much more await characterization. Stem cell maintenance, lymphoid, myeloid and erythroid differentiation are all regulated by various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and various transposable elements within the genome...
July 25, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28751461/novel-aberrations-uncovered-in-barrett-s-esophagus-and-esophageal-adenocarcinoma-using-whole-transcriptome-sequencing
#20
Jesper Maag, Oliver M Fisher, Angelique J Levert-Mignon, Dominik C Kaczorowski, Melissa L Thomas, Damian Hussey, David Watson, Antony Wettstein, Yuri V Bobryshev, Melanie Edwards, Marcel E Dinger, Reginald V Lord
Esophageal adenocarcinoma (EAC) has one of the fastest increases in incidence of any cancer, along with poor five-year survival rates. Barrett's esophagus (BE) is the main risk factor for EAC, however the mechanisms driving EAC development remain poorly understood. Here, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on premalignant and malignant Barrett's tissues to better understand this disease. Machine-learning and network analysis methods were applied to discover novel driver genes for EAC development...
July 27, 2017: Molecular Cancer Research: MCR
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