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Gene regulatory network

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https://www.readbyqxmd.com/read/28733657/a-gene-network-regulated-by-fgf-signalling-during-ear-development
#1
Maryam Anwar, Monica Tambalo, Ramya Ranganathan, Timothy Grocott, Andrea Streit
During development cell commitment is regulated by inductive signals that are tightly controlled in time and space. In response, cells activate specific programmes, but the transcriptional circuits that maintain cell identity in a changing signalling environment are often poorly understood. Specification of inner ear progenitors is initiated by FGF signalling. Here, we establish the genetic hierarchy downstream of FGF by systematic analysis of many ear factors combined with a network inference approach. We show that FGF rapidly activates a small circuit of transcription factors forming positive feedback loops to stabilise otic progenitor identity...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733488/identification-of-optimal-strategies-for-state-transition-of-complex-biological-networks
#2
REVIEW
Meichen Yuan, Weirong Hong, Pu Li
Complex biological networks typically contain numerous parameters, and determining feasible strategies for state transition by parameter perturbation is not a trivial task. In the present study, based on dynamical and structural analyses of the biological network, we optimized strategies for controlling variables in a two-node gene regulatory network and a T-cell large granular lymphocyte signaling network associated with blood cancer by using an efficient dynamic optimization method. Optimization revealed the critical value for each decision variable to steer the system from an undesired state into a desired attractor...
July 21, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28733463/tlr4-and-c5ar-crosstalk-in-dendritic-cells-induces-a-core-regulatory-network-of-rsk2-pi3k%C3%AE-sgk1-and-foxo-transcription-factors
#3
Anouk Zaal, Benjamin Nota, Kat S Moore, Miranda Dieker, S Marieke van Ham, Anja Ten Brinke
Crosstalk between complement component 5a receptors (C5aRs) and TLRs in dendritic cells (DCs) occurs upon pathogen invasion; however, studies on C5aR and TLR crosstalk mainly focused on the modulating effect of C5a on TLR-induced cytokine production. To elucidate the breadth of C5aR and TLR4 crosstalk, the effect of simultaneous treatment with C5a and LPS was investigated in human monocyte-derived DCs (moDCs) 2 h after stimulation using whole transcriptome sequencing analysis. Although the effect of C5a on hallmark genes defining TLR4-induced DC maturation was limited at this time point, RNA sequencing analysis revealed a great variety of novel C5a targets, of which many interfere with TLR4-mediated immune activation...
July 21, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28733351/multi-cellular-transcriptional-analysis-of-mammalian-heart-regeneration
#4
Gregory A Quaife-Ryan, Choon Boon Sim, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Mirana Ramialison, Assam El-Osta, James E Hudson, Enzo R Porrello
Background -The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time...
July 21, 2017: Circulation
https://www.readbyqxmd.com/read/28733120/employing-decomposable-partially-observable-markov-decision-processes-to-control-gene-regulatory-networks
#5
Utku Erdogdu, Faruk Polat, Reda Alhajj
OBJECTIVE: Formulate the induction and control of gene regulatory networks (GRNs) from gene expression data using Partially Observable Markov Decision Processes (POMDPs). METHODS AND MATERIAL: Different approaches exist to model GRNs; they are mostly simulated as mathematical models that represent relationships between genes. Actually, it has been realized that biological functions at the cellular level are controlled by genes; thus, by controlling the behavior of genes, it is possible to regulate these biological functions...
July 18, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28732206/a-utx-mll4-p300-transcriptional-regulatory-network-coordinately-shapes-active-enhancer-landscapes-for-eliciting-transcription
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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