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Gene regulatory networks

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https://www.readbyqxmd.com/read/29040739/papaya-cpein3a-and-cpnac2-cooperatively-regulate-carotenoid-biosynthesis-related-genes-cppds2-4-cplcy-e-and-cpchy-b-during-fruit-ripening
#1
Chang-Chun Fu, Yan-Chao Han, Jian-Fei Kuang, Jian-Ye Chen, Wang-Jin Lu
Papaya is an important tropical fruit with a rich source of carotenoids. The ripening of papaya is a physiological and metabolic process with remarkable changes including carotenoids accumulation, which depends primarily on the action of ethylene. Ethylene response is mediated by a transcriptional cascade involving the transcription factor families of EIN3/EILs and ERFs. Although ERF members have been reported to control carotenoids production in Arabidopsis and tomato, whether EIN3/EILs are also involved in carotenoid biosynthesis during fruit ripening remains unclear...
October 12, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#2
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040382/generalized-correlation-measure-using-count-statistics-for-gene-expression-data-with-ordered-samples
#3
Y X Rachel Wang, Ke Liu, Elizabeth Theusch, Jerome I Rotter, Marisa W Medina, Michael S Waterman, Haiyan Huang
Motivation: Capturing association patterns in gene expression levels under different conditions or time points is important for inferring gene regulatory interactions. In practice, temporal changes in gene expression may result in complex association patterns that require more sophisticated detection methods than simple correlation measures. For instance, the effect of regulation may lead to time-lagged associations and interactions local to a subset of samples. Furthermore, expression profiles of interest may not be aligned or directly comparable (e...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040362/prediction-of-protein-protein-interactions-between-fungus-magnaporthe-grisea-and-rice-oryza-sativa-l
#4
Shiwei Ma, Qi Song, Huan Tao, Andrew Harrison, Shaobo Wang, Wei Liu, Shoukai Lin, Ziding Zhang, Yufang Ai, Huaqin He
Rice blast disease caused by the fungus Magnaporthe grisea (M. grisea) is one of the most serious diseases for the cultivated rice Oryza sativa (O. sativa). A key factor causing rice blast disease and defense might be protein-protein interactions (PPIs) between rice and fungus. In this research, we have developed a computational pipeline to predict PPIs between blast fungus and rice. After cross-prediction by interolog-based and domain-based method, we achieved 532 potential PPIs between 27 fungus proteins and 236 rice proteins...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29036684/yeastract-an-upgraded-database-for-the-analysis-of-transcription-regulatory-networks-in-saccharomyces-cerevisiae
#5
Miguel C Teixeira, Pedro T Monteiro, Margarida Palma, Catarina Costa, Cláudia P Godinho, Pedro Pais, Mafalda Cavalheiro, Miguel Antunes, Alexandre Lemos, Tiago Pedreira, Isabel Sá-Correia
The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT-www.yeastract.com) information system has been, for 11 years, a key tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in Saccharomyces cerevisiae. Since its last update in June 2017, YEASTRACT includes approximately 163000 regulatory associations between transcription factors (TF) and target genes in S. cerevisiae, based on more than 1600 bibliographic references; it also includes 247 specific DNA binding consensus recognized by 113 TFs...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036633/rna-sequencing-of-brassica-napus-reveals-cellular-redox-control-of-sclerotinia-infection
#6
Ian J Girard, Chaobo Tong, Michael G Becker, Xingyu Mao, Junyan Huang, Teresa de Kievit, W G Dilantha Fernando, Shengyi Liu, Mark F Belmonte
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathogen interactions at the molecular level, we have yet to fully understand the biological processes and underlying gene regulatory networks responsible for determining disease outcomes. Using global RNA sequencing, we profiled gene activity at the first point of infection on the leaf surface 24 hours after pathogen exposure in susceptible (B...
September 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036516/a-two-stage-approach-of-gene-network-analysis-for-high-dimensional-heterogeneous-data
#7
Sangin Lee, Faming Liang, Ling Cai, Guanghua Xiao
Gaussian graphical models have been widely used to construct gene regulatory networks from gene expression data. Most existing methods for Gaussian graphical models are designed to model homogeneous data, assuming a single Gaussian distribution. In practice, however, data may consist of gene expression studies with unknown confounding factors, such as study cohort, microarray platforms, experimental batches, which produce heterogeneous data, and hence lead to false positive edges or low detection power in resulting network, due to those unknown factors...
July 18, 2017: Biostatistics
https://www.readbyqxmd.com/read/29036481/identification-of-the-direct-regulon-of-ntca-during-early-acclimation-to-nitrogen-starvation-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#8
Joaquín Giner-Lamia, Rocío Robles-Rengel, Miguel A Hernández-Prieto, M Isabel Muro-Pastor, Francisco J Florencio, Matthias E Futschik
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036198/the-homeodomain-interacting-protein-kinase-hpk-1-preserves-protein-homeostasis-and-longevity-through-master-regulatory-control-of-the-hsf-1-chaperone-network-and-torc1-restricted-autophagy-in-caenorhabditis-elegans
#9
Ritika Das, Justine A Melo, Manjunatha Thondamal, Elizabeth A Morton, Adam B Cornwell, Beresford Crick, Joung Heon Kim, Elliot W Swartz, Todd Lamitina, Peter M Douglas, Andrew V Samuelson
An extensive proteostatic network comprised of molecular chaperones and protein clearance mechanisms functions collectively to preserve the integrity and resiliency of the proteome. The efficacy of this network deteriorates during aging, coinciding with many clinical manifestations, including protein aggregation diseases of the nervous system. A decline in proteostasis can be delayed through the activation of cytoprotective transcriptional responses, which are sensitive to environmental stress and internal metabolic and physiological cues...
October 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29034968/genetics-and-evolution-of-mixta-genes-regulating-cotton-lint-fiber-development
#10
Huaitong Wu, Yue Tian, Qun Wan, Lei Fang, Xueying Guan, Jiedan Chen, Yan Hu, Wenxue Ye, Hua Zhang, Wangzhen Guo, Xiaoya Chen, Tianzhen Zhang
Cotton, with cellulose-enriched mature fibers, is the largest source of natural textiles. Through a map-based cloning strategy, we isolated an industrially important lint fiber development gene (Li3 ) that encodes an MYB-MIXTA-like transcription factor (MML) on chromosome D12 (GhMML4_D12). Virus-induced gene silencing or decreasing the expression of the GhMML4_D12 gene in n2 NSM plants resulted in a significant reduction in epidermal cell prominence and lint fiber production. GhMML4_D12 is arranged in tandem with GhMML3, another MIXTA gene responsible for fuzz fiber development...
October 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/29034245/handshakes-and-fights-the-regulatory-interplay-of-rna-binding-proteins
#11
REVIEW
Erik Dassi
What drives the flow of signals controlling the outcome of post-transcriptional regulation of gene expression? This regulatory layer, presiding to processes ranging from splicing to mRNA stability and localization, is a key determinant of protein levels and thus cell phenotypes. RNA-binding proteins (RBPs) form a remarkable army of post-transcriptional regulators, strong of more than 1,500 genes implementing this expression fine-tuning plan and implicated in both cell physiology and pathology. RBPs can bind and control a wide array of RNA targets...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29033978/integrative-analysis-of-transcription-factor-combinatorial-interactions-using-a-bayesian-tensor-factorization-approach
#12
Yusen Ye, Lin Gao, Shihua Zhang
Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29033902/analyzing-the-complex-regulatory-landscape-of-hfq-an-integrative-multi-omics-approach
#13
Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V Galmozzi, Günter Kramer, Jacob G Malone
The ability of bacteria to respond to environmental change is based on the ability to coordinate, redirect and fine-tune their genetic repertoire as and when required. While we can learn a great deal from reductive analysis of individual pathways and global approaches to gene regulation, a deeper understanding of these complex signaling networks requires the simultaneous consideration of several regulatory layers at the genome scale. To highlight the power of this approach we analyzed the Hfq transcriptional/translational regulatory network in the model bacterium Pseudomonas fluorescens...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29032836/the-impact-of-interferon-regulatory-factors-to-macrophage-differentiation-and-polarization-into-m1-and-m2
#14
REVIEW
Dimitry A Chistiakov, Veronika A Myasoedova, Victor V Revin, Alexander N Orekhov, Yuri V Bobryshev
The mononuclear phagocytes control the body homeostasis through the involvement in resolving tissue injury and further wound healing. Indeed, local tissue microenvironmental changes can significantly influence the functional behavior of monocytes and macrophages. Such microenvironmental changes for example occur in an atherosclerotic plaque during all progression stages. In response to exogenous stimuli, macrophages show a great phenotypic plasticity and heterogeneity. Exposure of monocytes to inflammatory or anti-inflammatory conditions also induces predominant differentiation to proinflammatory (M1) or anti-inflammatory (M2) macrophage subsets and phenotype switch between macrophage subsets...
October 5, 2017: Immunobiology
https://www.readbyqxmd.com/read/29032608/microrna-profiling-reveals-dysregulated-micrornas-and-their-target-gene-regulatory-networks-in-cemento-ossifying-fibroma
#15
Thaís Dos Santos Fontes Pereira, João Artur Ricieri Brito, André Luiz Sena Guimarães, Carolina Cavaliéri Gomes, Júlio Cesar Tanos de Lacerda, Wagner Henriques de Castro, Roney Santos Coimbra, Marina Gonçalves Diniz, Ricardo Santiago Gomez
BACKGROUND: Cemento-ossifying fibroma (COF) is a benign fibro-osseous neoplasm of uncertain pathogenesis and its treatment results morbidity. MicroRNAs (miRNA) are small non-coding RNAs that regulate gene expression and may represent therapeutic targets. The purpose of the study was to generate a comprehensive miRNA profile of COF compared to normal bone. Additionally, the most relevant pathways and target genes of differentially expressed miRNA were investigated by in silico analysis...
October 15, 2017: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/29032146/microrna-single-polynucleotide-polymorphism-influences-on-microrna-biogenesis-and-mrna-target-specificity
#16
REVIEW
Jarosław Króliczewski, Aleksandra Sobolewska, Dawid Lejnowski, James F Collawn, Rafał Bartoszewski
microRNAs (miRNAs) are nowadays recognized as an essential component of gene regulatory networks. Furthermore, deregulation of miRNAs expression often contributes to human pathologies. Recently, a substantial number of single nucleotide polymorphism (SNPs) and rare mutations within pri-, pre- and mature miRNA sequences have been reported. These miRNA SNPs have often been associated with human disease. However, due to the complexity of miRNA biogenesis and the genome-wide functional effects of miRNAs, the determination of biological consequences of these miRNA SNPs remains challenging...
October 12, 2017: Gene
https://www.readbyqxmd.com/read/29031031/riceanthernet-a-gene-co-expression-network-for-identifying-anther-and-pollen-development-genes
#17
Hong Lin, Jing Yu, Simon Pearce, Dabing Zhang, Zoe Wilson
In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29030730/introduction-eric-davidson-and-the-molecular-biology-of-evolution-and-development
#18
EDITORIAL
Michel Morange, Ute Deichmann
Between November 30th and December 2nd, 2015, the Jacques Loeb Centre for the History and Philosophy of the Life Sciences at Ben-Gurion University of the Negev in Beer Sheva (Israel) held its Eighth International Workshop under the title "From Genome to Gene: Causality, Synthesis and Evolution". Eric Davidson, the founder of the concept of developmental Gene Regulatory Networks, had regularly attended the previous meetings, and his participation in this one was expected, but he suddenly passed away 3 months before...
October 13, 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/29030469/single-cell-gene-expression-analysis-reveals-regulators-of-distinct-cell-subpopulations-among-developing-human-neurons
#19
Jiaxu Wang, Piroon Jenjaroenpun, Akshay Bhinge, Vladimir Espinosa Angarica, Antonio Del Sol, Intawat Nookaew, Vladimir A Kuznetsov, Lawrence W Stanton
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators...
October 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29030344/cell-type-specific-chromatin-signatures-underline-regulatory-dna-elements-in-human-induced-pluripotent-stem-cells-and-somatic-cells
#20
Mingtao Zhao, Ning-Yi Shao, Shijun Hu, Ning Ma, Rajini Srinivasan, Fereshteh Jahanbani, Jaecheol Lee, Sophia L Zhang, Michael P Snyder, Joseph C Wu
Rationale: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is a mystery how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. Objective: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression...
October 13, 2017: Circulation Research
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