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https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#1
Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Repoila Francis, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis...
July 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723760/bioinformatics-analysis-to-identify-the-critical-genes-micrornas-and-long-noncoding-rnas-in-melanoma
#2
Qian Zhang, Yang Wang, Jiulong Liang, Yaguang Tian, Yu Zhang, Kai Tao
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28723574/proteomic-analysis-of-the-human-tankyrase-protein-interaction-network-reveals-its-role-in-pexophagy
#3
Xu Li, Han Han, Mao-Tian Zhou, Bing Yang, Albert Paul Ta, Nan Li, Junjie Chen, Wenqi Wang
Tankyrase 1 (TNKS) and tankyrase 2 (TNKS2) belong to the poly(ADP-ribose) polymerase family of proteins, which use nicotinamide adenine dinucleotide to modify substrate proteins with ADP-ribose modifications. Emerging evidence has revealed the pathological relevance of TNKS and TNKS2, and identified these two enzymes as potential drug targets. However, the cellular functions and regulatory mechanisms of TNKS/2 are still largely unknown. Through a proteomic analysis, we defined the protein-protein interaction network for human TNKS/2 and revealed more than 100 high-confidence interacting proteins with numerous biological functions in this network...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28723411/the-risks-of-biomarker-based-epidemiology-associations-of-circulating-calcium-levels-with-age-mortality-and-frailty-vary-substantially-across-populations
#4
REVIEW
Alan A Cohen, Véronique Legault, Georg Fuellen, Tamàs Fülöp, Linda P Fried, Luigi Ferrucci
Recent studies have shown contradictory associations between calcium levels and health outcomes. We suspected these conflicting results were the consequence of more general issues with how biomarkers are analyzed in epidemiological studies, particularly in the context of aging. To demonstrate the risks of typical analyses, we used three longitudinal aging cohort studies and their demographic subsets to analyze how calcium levels change with age and predict risk of mortality and frailty. We show that calcium levels either increase or decrease with age depending on the population, and positively or negatively predict frailty depending on the population; both age and frailty results showed substantial heterogeneity...
July 16, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/28721939/two-faces-of-competition-target-mediated-reverse-signalling-in-microrna-and-mitogen-activated-protein-kinase-regulatory-networks
#5
REVIEW
Yongjin Jang, Min A Kim, Yoosik Kim
Biomolecular regulatory networks are organised around hubs, which can interact with a large number of targets. These targets compete with each other for access to their common hubs, but whether the effect of this competition would be significant in magnitude and in function is not clear. In this review, the authors discuss recent in vivo studies that analysed the system level retroactive effects induced by target competition in microRNA and mitogen-activated protein kinase regulatory networks. The results of these studies suggest that downstream targets can regulate the overall state of their upstream regulators, and thus cannot be ignored in analysing biomolecular networks...
August 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28720653/three-dimensional-structural-analysis-reveals-a-cdk5-mediated-kinase-cascade-regulating-hepatic-biliary-network-branching-in-zebrafish
#6
Manali Dimri, Cassandra Bilogan, Lain X Pierce, Gregory Naegele, Amit Vasanji, Isabel Gibson, Allyson McClendon, Kevin Tae, Takuya F Sakaguchi
The intrahepatic biliary network is a highly branched three-dimensional network lined by biliary epithelial cells, but how its branching patterns are precisely established is not clear. We designed a new computer-based algorithm that quantitatively computes the structural differences of the three-dimensional networks. Utilizing the algorithm, we showed that inhibition of Cyclin-dependent kinase 5 (Cdk5) led to reduced branching in the intrahepatic biliary network in zebrafish. Further, we identified a previously unappreciated downstream kinase cascade regulated by Cdk5...
July 15, 2017: Development
https://www.readbyqxmd.com/read/28720652/a-framework-for-understanding-the-roles-of-mirnas-in-animal-development
#7
REVIEW
Chiara Alberti, Luisa Cochella
MicroRNAs (miRNAs) contribute to the progressive changes in gene expression that occur during development. The combined loss of all miRNAs results in embryonic lethality in all animals analyzed, illustrating the crucial role that miRNAs play collectively. However, although the loss of some individual miRNAs also results in severe developmental defects, the roles of many other miRNAs have been challenging to uncover. This has been mostly attributed to their proposed function as tuners of gene expression or providers of robustness...
July 15, 2017: Development
https://www.readbyqxmd.com/read/28720596/elongator-regulates-hypocotyl-growth-in-darkness-and-during-photomorphogenesis
#8
Magdalena Woloszynska, Olimpia Gagliardi, Filip Vandenbussche, Steven De Groeve, Luis Alonso Baez, Pia Neyt, Sabine Le Gall, Jorge Fung, Paloma Mas, Dominique Van Der Straeten, Mieke Van Lijsebettens
Elongator promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response, sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, i.e. downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors...
July 18, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28719625/differences-of-immune-disorders-between-alzheimer-s-disease-and-breast-cancer-based-on-transcriptional-regulation
#9
Wei Kong, Xiaoyang Mou, Jin Deng, Benteng Di, Ruxing Zhong, Shuaiqun Wang, Yang Yang, Weiming Zeng
Although chronic inflammation and immune disorders are of great importance to the pathogenesis of both dementia and cancer, the pathophysiological mechanisms are not clearly understood. In recent years, growing epidemiological evidence and meta-analysis data suggest an inverse association between Alzheimer's disease (AD), which is the most common form of dementia, and cancer. It has been revealed that some common genes and biological processes play opposite roles in AD and cancer; however, the biological immune mechanism for the inverse association is not clearly defined...
2017: PloS One
https://www.readbyqxmd.com/read/28718798/co-expression-network-and-pathway-analyses-reveal-important-modules-of-mirnas-regulating-milk-yield-and-component-traits
#10
Duy N Do, Pier-Luc Dudemaine, Ran Li, Eveline M Ibeagha-Awemu
Co-expression network analyses provide insights into the molecular interactions underlying complex traits and diseases. In this study, co-expression network analysis was performed to detect expression patterns (modules or clusters) of microRNAs (miRNAs) during lactation, and to identify miRNA regulatory mechanisms for milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) via miRNA target gene enrichment analysis. miRNA expression (713 miRNAs), and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28718380/the-burden-of-genetic-and-epigenetic-traits-in-prematurity
#11
Bruna Ribeiro de Andrade Ramos, Márcia Guimarães da Silva
Despite decades of investigations and accumulated scientific knowledge, preterm birth (PTB) remains a significant burden worldwide. Several mechanisms have been proposed to explain this condition, and a number of risk factors from infectious to behavioral and genetic/epigenetic factors influence this outcome. The heritability of PTB is estimated to be 17% to 36%, which demonstrates that genetic predisposition plays a key role in PTB. Structural DNA modifications without changes in the DNA sequence and post-transcriptional regulation also have an impact on gene expression and thus influence pregnancy outcomes...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28717649/circular-rna-profiling-and-bioinformatic-modeling-identify-its-regulatory-role-in-hepatic-steatosis
#12
Xing-Ya Guo, Chong-Xin He, Yu-Qin Wang, Chao Sun, Guang-Ming Li, Qing Su, Qin Pan, Jian-Gao Fan
Circular RNAs (circRNAs) exhibit a wide range of physiological and pathological activities. To uncover their role in hepatic steatosis, we investigated the expression profile of circRNAs in HepG2-based hepatic steatosis induced by high-fat stimulation. Differentially expressed circRNAs were subjected to validation using QPCR and functional analyses using principal component analysis, hierarchical clustering, target prediction, gene ontology (GO), and pathway annotation, respectively. Bioinformatic integration established the circRNA-miRNA-mRNA regulatory network so as to identify the mechanisms underlying circRNAs' metabolic effect...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28717181/discovery-of-novel-human-gene-regulatory-modules-from-gene-co-expression-and-promoter-motif-analysis
#13
Shisong Ma, Michael Snyder, Savithramma P Dinesh-Kumar
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716938/dynamic-responses-of-the-adrenal-steroidogenic-regulatory-network
#14
Francesca Spiga, Eder Zavala, Jamie J Walker, Zidong Zhao, John R Terry, Stafford L Lightman
The hypothalamic-pituitary-adrenal axis is a dynamic system regulating glucocorticoid hormone synthesis in the adrenal glands. Many key factors within the adrenal steroidogenic pathway have been identified and studied, but little is known about how these factors function collectively as a dynamic network of interacting components. To investigate this, we developed a mathematical model of the adrenal steroidogenic regulatory network that accounts for key regulatory processes occurring at different timescales...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28716889/cytokines-transcription-factors-and-the-initiation-of-t-cell-development
#15
Hiroyuki Hosokawa, Ellen V Rothenberg
Multipotent blood progenitor cells migrate into the thymus and initiate the T-cell differentiation program. T-cell progenitor cells gradually acquire T-cell characteristics while shedding their multipotentiality for alternative fates. This process is supported by extracellular signaling molecules, including Notch ligands and cytokines, provided by the thymic microenvironment. T-cell development is associated with dynamic change of gene regulatory networks of transcription factors, which interact with these environmental signals...
July 17, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28716713/n-myc-regulates-growth-and-fiber-cell-differentiation-in-lens-development
#16
Gabriel R Cavalheiro, Gabriel E Matos-Rodrigues, Yilin Zhao, Anielle L Gomes, Deepti Anand, Danilo Predes, Silmara de Lima, Jose G Abreu, Deyou Zheng, Salil A Lachke, Ales Cvekl, Rodrigo A P Martins
Myc proto-oncogenes regulate diverse cellular processes during development, but their roles during morphogenesis of specific tissues are not fully understood. We found that c-myc regulates cell proliferation in mouse lens development and previous genome-wide studies suggested functional roles for N-myc in developing lens. Here, we examined the role of N-myc in mouse lens development. Genetic inactivation of N-myc in the surface ectoderm or lens vesicle impaired eye and lens growth, while "late" inactivation in lens fibers had no effect...
July 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28716407/overexpression-of-lsi1-in-cold-sensitive-rice-mediates-transcriptional-regulatory-networks-and-enhances-resistance-to-chilling-stress
#17
Changxun Fang, Pengli Zhang, Xin Jian, Weisi Chen, Hongmei Lin, Yingzhe Li, Wenxiong Lin
Frequent cold spells in late spring can damage early rice seedlings. However, overexpression of the silicon-uptake gene Lsi1 (Lsi1-OX) in cold-sensitive rice (Oryza sativa L., accession: Dular) notably enhances its chilling resistance. In this study, we found that continual chilling led to chlorophyll and RNA degradation in wild-type Dular leaves, whereas leaves from a Lsi1-OX line exhibited no obvious changes. A comparison of the global mRNA expression between the two rice lines showed that genes encoding photosynthesis-antenna proteins were downregulated and those encoding the proteasome were upregulated in the wild-type organism...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28715336/combination-of-supervised-and-unsupervised-approaches-for-mirna-target-prediction
#18
Nafiseh Sedaghat, Mahmood Fathy, Mohammad Hossein Modarressi, Ali Shojaie
MicroRNAs (miRNAs) are short non-coding RNAs which target mRNAs by binding to them and regulating their expression. Involvement of miRNAs has been discovered in many diseases, so it is fruitful to investigate the miRNAs and their targets to develop new therapeutic ways by designing anti-miRNA oligonucleotides. There are various computational methods to predict the target genes, however, their precisions are not good enough. In this paper, we apply a two-step approach to refine the results of sequence-based prediction algorithms...
July 13, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28714865/microglia-in-prion-diseases
#19
Adriano Aguzzi, Caihong Zhu
Prion diseases are a group of progressive and fatal neurodegenerative disorders characterized by deposition of scrapie prion protein (PrPSc) in the CNS. This deposition is accompanied by neuronal loss, spongiform change, astrogliosis, and conspicuous microglial activation. Here, we argue that microglia play an overall neuroprotective role in prion pathogenesis. Several microglia-related molecules, such as Toll-like receptors (TLRs), the complement system, cytokines, chemokines, inflammatory regulators, and phagocytosis mediators, are involved in prion pathogenesis...
July 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28714412/regulation-mechanism-of-micrornas-in-non-small-cell-lung-cancer
#20
Feng-Yun Gong, Tao Bai, Ding-Yu Zhang, Chao-Lin Huang, Jing Lv, Jing-Li Wang, Xu-Dong Hu, Juan Wang, Wei Liu
MicroRNAs are small non-coding RNAs with regulatory biological activity, by modulating target genes on epigenetic, transcriptional, post-transciptional and translational levels. Hundreds of reports indicated that miRNAs play important roles in non-small cell lung cancer (NSCLC). Actually, microRNAs are both regulation targets and regulators targeting effector genes. This article reviewed multifaceted role of microRNAs associated to NSCLC, not only targeting to but also targeted by tumor related genes, to help us understand microRNAs related complex regulation networks...
July 14, 2017: Current Pharmaceutical Design
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