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Gene regulatory networks

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https://www.readbyqxmd.com/read/28732206/a-utx-mll4-p300-transcriptional-regulatory-network-coordinately-shapes-active-enhancer-landscapes-for-eliciting-transcription
#1
Shu-Ping Wang, Zhanyun Tang, Chun-Wei Chen, Miho Shimada, Richard P Koche, Lan-Hsin Wang, Tomoyoshi Nakadai, Alan Chramiec, Andrei V Krivtsov, Scott A Armstrong, Robert G Roeder
Enhancer activation is a critical step for gene activation. Here we report an epigenetic crosstalk at enhancers between the UTX (H3K27 demethylase)-MLL4 (H3K4 methyltransferase) complex and the histone acetyltransferase p300. We demonstrate that UTX, in a demethylase activity-independent manner, facilitates conversion of inactive enhancers in embryonic stem cells to an active (H3K4me1(+)/H3K27ac(+)) state by recruiting and coupling the enzymatic functions of MLL4 and p300. Loss of UTX leads to attenuated enhancer activity, characterized by reduced levels of H3K4me1 and H3K27ac as well as impaired transcription...
July 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#2
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28731857/cytomcs-a-multiple-maximum-common-subgraph-detection-tool-for-cytoscape
#3
Simon J Larsen, Jan Baumbach
Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#4
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28729650/large-scale-analysis-of-drug-side-effects-via-complex-regulatory-modules-composed-of-micrornas-transcription-factors-and-gene-sets
#5
Xiaodong Jia, Qing Jin, Xiangqiong Liu, Xiusen Bian, Yunfeng Wang, Lei Liu, Hongzhe Ma, Fujian Tan, Mingliang Gu, Xiujie Chen
Identifying the occurrence mechanism of drug-induced side effects (SEs) is critical for design of drug target and new drug development. The expression of genes in biological processes is regulated by transcription factors(TFs) and/or microRNAs. Most of previous studies were focused on a single level of gene or gene sets, while studies about regulatory relationships of TFs, miRNAs and biological processes are very rare. Discovering the complex regulating relations among TFs, gene sets and miRNAs will be helpful for researchers to get a more comprehensive understanding about the mechanism of side reaction...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729527/comparative-transcriptome-analysis-of-the-floral-transition-in-rosa-chinensis-old-blush-and-r-odorata-var-gigantea
#6
Xuelian Guo, Chao Yu, Le Luo, Huihua Wan, Yushu Li, Jia Wang, Tangren Cheng, Huitang Pan, Qixiang Zhang
The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis 'Old Blush', which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727558/understanding-robust-adaptation-dynamics-of-gene-regulatory-network
#7
Xiao-Na Huang, Hai-Peng Ren
Robust adaptation is a critical attribute for gene regulatory network (GRN), understanding the relationship between adaptation and the GRN topology, and corresponding parameters is a challenging issue. The work in this paper includes: first, seven constraint multiobjective optimization algorithms are used to find sufficient solutions to get more reliable statistic rules. Meanwhile, the algorithms are compared to facilitate the future algorithm selection; second, a fuzzy c-mean algorithm is used to analyze solutions and to classify the solutions into different groups; third, the histogram analysis for all satisfactory solutions shows the preferred parameter range, i...
July 18, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28727484/construction-and-analysis-of-circular-rna-molecular-regulatory-networks-in-liver-cancer
#8
Shuangchun Ren, Zhuoyuan Xin, Yinyan Xu, Jianting Xu, Guoqing Wang
Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we employed a systems biology approach to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network...
July 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28727145/transcriptional-control-of-photosynthetic-capacity-conservation-and-divergence-from-arabidopsis-to-rice
#9
REVIEW
Peng Wang, Ross-William Hendron, Steven Kelly
1 I. 1 II. 2 III. 5 IV. 10 12 References 12 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression...
July 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28724903/co-expression-network-analysis-of-toxin-antitoxin-loci-in-mycobacterium-tuberculosis-reveals-key-modulators-of-cellular-stress
#10
Amita Gupta, Balaji Venkataraman, Madavan Vasudevan, Kiran Gopinath Bankar
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724751/tomo-seq-identifies-sox9-as-a-key-regulator-of-cardiac-fibrosis-during-ischemic-injury
#11
Grégory P A Lacraz, Jan Philipp Junker, Monika M Gladka, Bas Molenaar, Koen T Scholman, Marta Vigil-Garcia, Danielle Versteeg, Hesther de Ruiter, Marit W Vermunt, Menno P Creyghton, Manon M H Huibers, Nicolaas de Jonge, Alexander van Oudenaarden, Eva van Rooij
Background -Cardiac ischemic injury induces a pathological remodeling response, which can ultimately lead to heart failure. Detailed mechanistic insights into molecular signaling pathways relevant for different aspects of cardiac remodeling will support the identification of novel therapeutic targets. Methods -While genome-wide transcriptome analysis on diseased tissues has greatly advanced our understanding of the regulatory networks that drive pathological changes in the heart, this approach has been disadvantaged by the fact that the signals are derived from tissue homogenates...
July 19, 2017: Circulation
https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#12
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
#13
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/28720652/a-framework-for-understanding-the-roles-of-mirnas-in-animal-development
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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