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Gene regulatory network

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https://www.readbyqxmd.com/read/28805544/rna-silencing-in-plant-symbiotic-bacteria-insights-from-a-protein-centric-view
#1
José I Jiménez-Zurdo, Marta Robledo
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28803234/rna-sequencing-and-bioinformatics-analysis-implicate-the-regulatory-role-of-a-long-noncoding-rna-mrna-network-in-hepatic-stellate-cell-activation
#2
Can-Jie Guo, Xiao Xiao, Li Sheng, Lili Chen, Wei Zhong, Hai Li, Jing Hua, Xiong Ma
BACKGROUND/AIMS: To analyze the long noncoding (lncRNA)-mRNA expression network and potential roles in rat hepatic stellate cells (HSCs) during activation. METHODS: LncRNA expression was analyzed in quiescent and culture-activated HSCs by RNA sequencing, and differentially expressed lncRNAs verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) were subjected to bioinformatics analysis. In vivo analyses of differential lncRNA-mRNA expression were performed on a rat model of liver fibrosis...
August 11, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28802251/microrna-720-regulates-e-cadherin-%C3%AE-e-catenin-complex-and-promotes-renal-cell-carcinoma
#3
Nadeem S Bhat, Melissa Colden, Altaf A Dar, Sharanjot Saini, Prerna Arora, Varahram Shahryari, Soichiro Yamamura, Yuichiro Tanaka, Taku Kato, Shahana Majid, Rajvir Dahiya
MicroRNAs are implicated in regulating cancer progression and metastasis. Here we show that miR-720 is positively associated with renal cell carcinoma (RCC). Elevated levels of miR-720 were observed in a panel of RCC cell lines and clinical tissues compared to non-malignant cell line and normal samples. Loss of miR-720 function inhibited proliferation, migration and invasion and induced apoptosis in RCC cell lines in vitro and repressed tumor growth in xenograft mouse model. Conversely, gain of miR-720 function in non-malignant HK-2 cells induced pro-cancerous characteristics...
August 11, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28801229/immunomodulation-a-definitive-role-of-microrna-142
#4
REVIEW
Salil Sharma
Majority of microRNAs are evolutionarily conserved in vertebrates. This is suggestive of their similar roles in regulation of gene networks. In addition to their conserved mature sequences and regulatory roles, a few microRNAs show very cell or tissue specific expression. These microRNAs are highly enriched in some cell types or organs. One such microRNA is microRNA-142 (miR-142). The classical stem-loop structure of miR142 encodes for two species of mature microRNAs; miR142-5p and miR142-3p. MiR-142 is abundant in cells of hematopoietic origin, and therefore, aptly plays a role in lineage differentiation of hematopoietic cells...
August 9, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28800327/analytical-strategy-to-prioritize-alzheimer-s-disease-candidate-genes-in-gene-regulatory-networks-using-public-expression-data
#5
Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Alzheimer's disease (AD) progressively destroys cognitive abilities in the aging population with tremendous effects on memory. Despite recent progress in understanding the underlying mechanisms, high drug attrition rates have put a question mark behind our knowledge about its etiology. Re-evaluation of past studies could help us to elucidate molecular-level details of this disease. Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates...
August 8, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28800289/viral-master-circuits-from-discovery-to-new-therapy-targets
#6
Anand Pai, Leor S Weinberger
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates)...
August 11, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28799693/the-small-rna-real-a-novel-regulatory-element-embedded-in-the-pseudomonas-aeruginosa-quorum-sensing-networks
#7
Sara Carloni, Raffaella Macchi, Sara Sattin, Silvia Ferrara, Giovanni Bertoni
The small RNA ReaL of the opportunistic pathogen Pseudomonas aeruginosa has been characterized. Our results indicate that ReaL contributes to P. aeruginosa virulence. In the Galleria mellonella infection model, reaL gene deletion resulted in decreased virulence, while ReaL overexpression resulted in a hyper-virulent phenotype. We also demonstrate that ReaL is embedded in the P. aeruginosa quorum sensing (QS) with the role of linking las to pqs systems. We show that ReaL is negatively regulated by the las regulator LasR and impacts positively the synthesis of the pqs quinolone signal PQS by a positive post-transcriptional effect on the pqsC gene...
August 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28799567/identification-of-breast-cancer-mechanism-based-on-weighted-gene-coexpression-network-analysis
#8
X Guo, H Xiao, S Guo, L Dong, J Chen
Our gene expression-profiling analysis aimed to explain the mechanism of breast cancer development by identifying key pathways and constructing networks of related transcription factors (TFs) and microRNAs (miRNAs) in breast cancer tissues. Gene expression profiles of normal and breast cancer tissues were downloaded to identify differentially expressed genes (DEGs). Coexpression modules were explored using weighted gene coexpression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to discover the enriched functionally associated gene groups and define pathways in breast cancer, respectively...
August 11, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28799488/environment-and-neurodegenerative-diseases-an-update-on-mirna-role
#9
Margherita Ferrante, Gea Oliveri Conti
INTRODUCTION: The importance of neurodegenerative diseases on the management of public health is growing and the real role of the environment and miRNA in their occurrence is still unclear. miRNA can affect significantly the regulatory network. The complex variety and gene-regulatory capacity of miRNAs is particularly valuable in the brain, being a very complex organ with a functional specialization of neurons highly adaptable to environmental stimuli. In particular a miRNAs role is demonstrated in neurological diseases as the effect to toxic and mutagenic substances exposure by the environment...
August 11, 2017: MicroRNA
https://www.readbyqxmd.com/read/28798667/the-foxp2-driven-network-in-developmental-disorders-and-neurodegeneration
#10
Franz Oswald, Patricia Klöble, André Ruland, David Rosenkranz, Bastian Hinz, Falk Butter, Sanja Ramljak, Ulrich Zechner, Holger Herlyn
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28796489/rational-modular-rna-engineering-based-on-in-vivo-profiling-of-structural-accessibility
#11
Abigail N Leistra, Paul Amador, Aishwarya Buvanendiran, Alex Moon-Walker, Lydia M Contreras
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28796037/functional-prediction-of-mir-3144-5p-in-human-cardiac-myocytes-based-on-transcriptome-sequencing-and-bioinformatics
#12
Lei Ruan, Yi Yang, Yi Huang, Ling Ding, Cuntai Zhang, Xiaofen Wu
BACKGROUND: RAN guanine nucleotide release factor (RANGRF) encoding protein MOG1 plays an important role in cardiac arrhythmia, so we intended to investigate the regulatory miRNA of RANGRF and explore its potential regulatory mechanism in arrhythmogenesis. METHODS: Based on bioinformatic analysis, miR-3144-5p was predicted to be a regulatory miRNA of RANGRF, which were then validated through a dual-luciferase reporter plasmid assay. Subsequently, the expression level of miR-3144-5p in human cardiac myocytes (HCMs) was detected, followed by cell transfection with miR-3144-5p mimics...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28795861/lnc00673-errlr01-is-a-prognostic-indicator-of-overall-survival-in-breast-cancer
#13
Ubaidat Abdul-Rahman, Balázs Gyoörffy, Brian D Adams
LncRNAs are novel noncoding RNAs involved in the epigenetic regulation of gene expression by recruiting ribonucleoprotein complexes to specific genomic loci to initiate histone methylation and/or other chromatin modifications. LncRNAs themselves function as tumor suppressors or oncogenes, depending on the gene regulatory networks they govern. We identified lnc00673 (ERRLR01) as a marker of overall survival (OS) in breast cancer patients. Specifically, ERRLR01 levels were elevated in triple-negative breast cancer (TNBC) as compared to Luminal- A, Luminal-B, and HER2 breast cancer subtypes...
August 10, 2017: Transcription
https://www.readbyqxmd.com/read/28794899/an-extended-model-for-culture-dependent-heterogenous-gene-expression-and-proliferation-dynamics-in-mouse-embryonic-stem-cells
#14
Simon Godwin, Daniel Ward, Elisa Pedone, Martin Homer, Alexander G Fletcher, Lucia Marucci
During development, pluripotency is a transient state describing a cell's ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell subpopulations...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28793339/modeling-mirna-mrna-interactions-that-cause-phenotypic-abnormality-in-breast-cancer-patients
#15
Sanghoon Lee, Xia Jiang
BACKGROUND: The dysregulation of microRNAs (miRNAs) alters expression level of pro-oncogenic or tumor suppressive mRNAs in breast cancer, and in the long run, causes multiple biological abnormalities. Identification of such interactions of miRNA-mRNA requires integrative analysis of miRNA-mRNA expression profile data. However, current approaches have limitations to consider the regulatory relationship between miRNAs and mRNAs and to implicate the relationship with phenotypic abnormality and cancer pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28793269/cell-type-specific-gene-programs-of-the-normal-human-nephron-define-kidney-cancer-subtypes
#16
David Lindgren, Pontus Eriksson, Krzysztof Krawczyk, Helén Nilsson, Jennifer Hansson, Srinivas Veerla, Jonas Sjölund, Mattias Höglund, Martin E Johansson, Håkan Axelson
Comprehensive transcriptome studies of cancers often rely on corresponding normal tissue samples to serve as a transcriptional reference. In this study, we performed in-depth analyses of normal kidney tissue transcriptomes from the TCGA and demonstrate that the histological variability in cellularity, inherent in the kidney architecture, lead to considerable transcriptional differences between samples. This should be considered when comparing expression profiles of normal and cancerous kidney tissues. We exploited these differences to define renal-cell-specific gene signatures and used these as a framework to analyze renal cell carcinoma (RCC) ontogeny...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28793267/epigenomic-landscapes-of-hesc-derived-neural-rosettes-modeling-neural-tube-formation-and-diseases
#17
Cristina Valensisi, Colin Andrus, Sam Buckberry, Naresh Doni Jayavelu, Riikka J Lund, Ryan Lister, R David Hawkins
We currently lack a comprehensive understanding of the mechanisms underlying neural tube formation and their contributions to neural tube defects (NTDs). Developing a model to study such a complex morphogenetic process, especially one that models human-specific aspects, is critical. Three-dimensional, human embryonic stem cell (hESC)-derived neural rosettes (NRs) provide a powerful resource for in vitro modeling of human neural tube formation. Epigenomic maps reveal enhancer elements unique to NRs relative to 2D systems...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28793250/mir-7-buffers-differentiation-in-the-developing-drosophila-visual-system
#18
Elizabeth E Caygill, Andrea H Brand
The 40,000 neurons of the medulla, the largest visual processing center of the Drosophila brain, derive from a sheet of neuroepithelial cells. During larval development, a wave of differentiation sweeps across the neuroepithelium, converting neuroepithelial cells into neuroblasts that sequentially express transcription factors specifying different neuronal cell fates. The switch from neuroepithelial cells to neuroblasts is controlled by a complex gene regulatory network and is marked by the expression of the proneural gene l'sc...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28792517/comparison-of-alternative-approaches-for-analysing-multi-level-rna-seq-data
#19
Irina Mohorianu, Amanda Bretman, Damian T Smith, Emily K Fowler, Tamas Dalmay, Tracey Chapman
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D...
2017: PloS One
https://www.readbyqxmd.com/read/28791388/bioinformatic-analysis-of-microrna-mrna-expression-profiles-of-bladder-tissue-induced-by-bladder-outlet-obstruction-in-a-rat-model
#20
Liu Jian Duan, Qi Feng Cao, Ding Xu, Hai Long Liu, Jun Qi
Various microRNAs (miRNAs) have previously been demonstrated to exhibit an association with the process of bladder remodeling, induced by bladder outlet obstruction (BOO). However, little is known about miRNA and gene expression profiles and the molecular mechanism underlying bladder pathophysiological alterations. The present study used bioinformatic analysis technology to examine the altered miRNA and mRNA expression profiles of bladder tissue in a rat model of BOO and validate the involved signaling pathways...
August 7, 2017: Molecular Medicine Reports
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