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Gene regulatory network

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https://www.readbyqxmd.com/read/28350855/diversification-of-spatiotemporal-expression-and-copy-number-variation-of-the-echinoid-hbox12-pmar1-micro1-multigene-family
#1
Vincenzo Cavalieri, Fabiana Geraci, Giovanni Spinelli
Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P...
2017: PloS One
https://www.readbyqxmd.com/read/28350462/automated-design-framework-for-synthetic-biology-exploiting-pareto-optimality
#2
Irene Otero-Muras, Julio R Banga
In this work we consider Pareto optimality for automated design in synthetic biology. We present a generalized framework based on a mixed-integer dynamic optimization formulation that, given design specifications, allows the computation of Pareto optimal sets of designs, i.e. the set of best trade-offs for the metrics of interest. We show how this framework can be used for (i) forward design, i.e., fnding the Pareto optimal set of synthetic designs for implementation, and (ii) reverse design i.e. analyzing and inferring motifs and/or design principles of gene regulatory networks from the Pareto set of optimal circuits...
March 28, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28346469/computational-identifying-and-characterizing-circular-rnas-and-their-associated-genes-in-hepatocellular-carcinoma
#3
Yan Li, Yongcheng Dong, Ziyan Huang, Qifan Kuang, Yiming Wu, Yizhou Li, Menglong Li
Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT...
2017: PloS One
https://www.readbyqxmd.com/read/28344638/the-feasibility-of-genome-scale-biological-network-inference-using-graphics-processing-units
#4
Raghuram Thiagarajan, Amir Alavi, Jagdeep T Podichetty, Jason N Bazil, Daniel A Beard
Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network interactions include statistical inference-based approaches and methods to identify dynamical systems models that are capable of fitting multivariate data. Availability of large data sets and so-called 'big data' applications in biology present great opportunities as well as major challenges for systems identification/reverse engineering applications...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28342977/the-role-of-mir-2%C3%A2-13%C3%A2-71-cluster-in-resistance-to-deltamethrin-in-culex-pipiens-pallens
#5
Qin Guo, Yun Huang, Feifei Zou, Bingqian Liu, Mengmeng Tian, Wenyun Ye, Juxin Guo, Xueli Sun, Dan Zhou, Yan Sun, Lei Ma, Bo Shen, Changliang Zhu
Excessive and continuous application of deltamethrin has resulted in the development of deltamethrin resistance among mosquitoes, which becomes a major obstacle for mosquito control. In a previous study, differentially expressed miRNAs between deltamethrin-susceptible (DS) strain and deltamethrin-resistant (DR) strain using illumina sequencing in Culex pipiens pallens were identified. In this study, we applied RNAi and the Centers for Disease Control and Prevention (CDC) bottle bioassay to investigate the relationship between miR-2∼13∼71 cluster (miR-2, miR-13 and miR-71) and deltamethrin resistance...
March 22, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28342111/ckb1-is-involved-in-abscisic-acid-and-gibberellic-acid-signaling-to-regulate-stress-responses-in-arabidopsis-thaliana
#6
Congying Yuan, Jianping Ai, Hongping Chang, Wenjun Xiao, Lu Liu, Cheng Zhang, Zhuang He, Ji Huang, Jinyan Li, Xinhong Guo
Casein kinase II (CK2), an evolutionarily well-conserved Ser/Thr kinase, plays critical roles in all higher organisms including plants. CKB1 is a regulatory subunit beta of CK2. In this study, homozygous T-DNA mutants (ckb1-1 and ckb1-2) and over-expression plants (35S:CKB1-1, 35S:CKB1-2) of Arabidopsis thaliana were studied to understand the role of CKB1 in abiotic stress and gibberellic acid (GA) signaling. Histochemical staining showed that although CKB1 was expressed in all organs, it had a relatively higher expression in conducting tissues...
March 24, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28341552/identification-of-a-molecular-signaling-gene-gene-regulatory-network-between-gwas-susceptibility-genes-adtrp-and-mia3-tango1-for-coronary-artery-disease
#7
Chunyan Luo, Fan Wang, Xiang Ren, Tie Ke, Chengqi Xu, Bo Tang, Subo Qin, Yufeng Yao, Qiuyun Chen, Qing Kenneth Wang
Coronary artery disease (CAD) is the leading cause of death worldwide. GWAS have identified >50 genomic loci for CAD, including ADTRP and MIA3/TANGO1. However, it is important to determine whether the GWAS genes form a molecular network. In this study, we have uncovered a novel molecular network between ADTRP and MIA3/TANGO1 for the pathogenesis of CAD. We showed that knockdown of ADTRP expression markedly down-regulated expression of MIA3/TANGO1. Mechanistically, ADTRP positively regulates expression of PIK3R3 encoding the regulatory subunit 3 of PI3K, which leads to activation of AKT, resulting in up-regulation of MIA3/TANGO1...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28341363/a-gene-regulatory-program-controlling-early-xenopus-mesendoderm-formation-network-conservation-and-motifs
#8
REVIEW
Rebekah M Charney, Kitt D Paraiso, Ira L Blitz, Ken W Y Cho
Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied intensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN)...
March 21, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28341132/stochastic-modeling-and-numerical-simulation-of-gene-regulatory-networks-with-protein-bursting
#9
Manuel Pájaro, Antonio A Alonso, Irene Otero-Muras, C Vázquez
Gene expression is inherently stochastic. Advanced single-cell microscopy techniques together with mathematical models for single gene expression led to important insights in elucidating the sources of intrinsic noise in prokaryotic and eukaryotic cells. In addition to the finite size effects due to low copy numbers, translational bursting is a dominant source of stochasticity in cell scenarios involving few short lived mRNA transcripts with high translational efficiency (as is typically the case for prokaryotes), causing protein synthesis to occur in random bursts...
March 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#10
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28340173/f-box-protein-fbx92-affects-leaf-size-in-arabidopsis-thaliana
#11
Joke Baute, Stefanie Polyn, Jolien De Block, Jonas Blomme, Mieke Van Lijsebettens, Dirk Inzé
F-box proteins are part of one of the largest families of regulatory proteins that play important roles in protein degradation. In plants, F-box proteins are functionally very diverse, and only a small subset has been characterized in detail. Here, we identified a novel F-box protein FBX92 as a repressor of leaf growth in Arabidopsis. Overexpression of AtFBX92 resulted in plants with smaller leaves than wild type, whereas plants with reduced levels of AtFBX92 showed in contrast increased leaf growth by stimulating cell proliferation...
March 14, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28339085/integrated-analysis-of-mrna-and-mirna-expression-profiles-in-pancreatic-ductal-adenocarcinoma
#12
Hongwei Sun, Liang Zhao, Kehua Pan, Zhao Zhang, Mengtao Zhou, Guoquan Cao
In the present study, to investigate the potential molecular mechanism of pancreatic ductal adenocarcinoma (PDAC), mRNA and miRNA expression profiles were integrated for systematic analysis. Results showed that a total of 76 common differentially expressed genes (DEGs) were identified from 2 mRNA expression profiles that contained 39 tumor and 15 normal samples. Notably, the tumor and normal samples were able to be clearly classified into 4 groups based on the DEGs. mRNA‑miRNA regulation network analysis indicated that 22 out of the 76 DEGs including MUC4, RRM2 and CCL2 are regulated by 5 reported miRNAs...
March 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#13
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
March 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338822/gene-expression-atlas-of-pigeonpea-and-its-application-to-gain-insights-into-genes-associated-with-pollen-fertility-implicated-in-seed-formation
#14
Lekha T Pazhamala, Shilp Purohit, Rachit K Saxena, Vanika Garg, L Krishnamurthy, Jerome Verdier, Rajeev K Varshney
Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To link the genome sequence information with agronomic traits resulting from specific developmental processes, a Cajanus cajan gene expression atlas (CcGEA) was developed using the Asha genotype. Thirty tissues/organs representing developmental stages from germination to senescence were used to generate 590.84 million paired-end RNA-Seq data. The CcGEA revealed a compendium of 28 793 genes with differential, specific, spatio-temporal and constitutive expression during various stages of development in different tissues...
February 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28337802/the-snf1-activating-kinase-sak1-is-a-key-regulator-of-metabolic-adaptation-and-in-vivo-fitness-of-candida-albicans
#15
Bernardo Ramírez-Zavala, Austin Mottola, Julia Haubenreißer, Sabrina Schneider, Stefanie Allert, Sascha Brunke, Knut Ohlsen, Bernhard Hube, Joachim Morschhäuser
The metabolic flexibility of the opportunistic fungal pathogen Candida albicans is important for colonisation and infection of different host niches. Complex regulatory networks, in which protein kinases play central roles, link metabolism and other virulence-associated traits, such as filamentous growth and stress resistance, and thereby control commensalism and pathogenicity. By screening a protein kinase deletion mutant library that was generated in the present work using an improved SAT1 flipper cassette, we found that the previously uncharacterised kinase Sak1 is a key upstream activator of the protein kinase Snf1, a highly conserved regulator of nutrient stress responses that is essential for viability in C...
March 23, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28337174/regulation-of-mammalian-physiology-by-interconnected-circadian-and-feeding-rhythms
#16
REVIEW
Florian Atger, Daniel Mauvoisin, Benjamin Weger, Cédric Gobet, Frédéric Gachon
Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a wide range of signals that differentially schedule physiology and gene expression in a tissue-specific manner. The peripheral clocks, such as those found in the liver, are particularly sensitive to rhythmic external cues like feeding behavior, which modulate the phase and amplitude of rhythmic gene expression...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28335719/enhanced-construction-of-gene-regulatory-networks-using-hub-gene-information
#17
Donghyeon Yu, Johan Lim, Xinlei Wang, Faming Liang, Guanghua Xiao
BACKGROUND: Gene regulatory networks reveal how genes work together to carry out their biological functions. Reconstructions of gene networks from gene expression data greatly facilitate our understanding of underlying biological mechanisms and provide new opportunities for biomarker and drug discoveries. In gene networks, a gene that has many interactions with other genes is called a hub gene, which usually plays an essential role in gene regulation and biological processes. In this study, we developed a method for reconstructing gene networks using a partial correlation-based approach that incorporates prior information about hub genes...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335718/rnav-2-0-a-visualization-tool-for-bacterial-srna-mediated-regulatory-networks-mining
#18
Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault
BACKGROUND: Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging with the lack of knowledge of the topological and biological constraints behind the formation of sRNA-mRNA duplexes. Even with the most sophisticated bioinformatics target prediction tools, the large proportion of false predictions may be prohibitive for further analyses...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335028/defining-the-5%C3%AE-and-3%C3%AE-landscape-of-the-drosophila-transcriptome-with-exo-seq-and-rnaseh-seq
#19
Shaked Afik, Osnat Bartok, Maxim N Artyomov, Alexander A Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5΄- and 3΄-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334889/the-primary-transcriptome-of-neisseria-meningitidis-and-its-interaction-with-the-rna-chaperone-hfq
#20
Nadja Heidrich, Saskia Bauriedl, Lars Barquist, Lei Li, Christoph Schoen, Jörg Vogel
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N...
March 17, 2017: Nucleic Acids Research
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