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Gene regulatory network

Yuanyuan Zhou, Xia Zheng, Jiaojiao Lu, Wei Chen, Xu Li, Le Zhao
BACKGROUND/AIMS: The Warburg effect is one of the main energy metabolism features supporting cancer cell growth. 20(S)-Rg3 exerts anti-tumor effect on ovarian cancer partly by inhibiting the Warburg effect. microRNAs are important regulators of the Warburg effect. However, the microRNA regulatory network mediating the anti-Warburg effect of 20(S)-Rg3 was largely unknown. METHODS: microRNA deep sequencing was performed to identify the 20(S)-Rg3-influenced microRNAs in SKOV3 ovarian cancer cells...
March 16, 2018: Cellular Physiology and Biochemistry
Keunsub Lee, Kan Wang
During the last decade, small noncoding RNAs (ncRNAs) have emerged as essential post-transcriptional regulators in bacteria. Nearly all important physiological and stress responses are modulated by ncRNA regulators, such as riboswitches, trans-acting small RNAs (sRNAs), and cis-antisense RNAs. Recently, three RNA-seq studies identified a total of 1534 candidate ncRNAs from Agrobacterium tumefaciens, a pathogen and biotechnology tool for plants. Only a few ncRNAs have been functionally characterized in A. tumefaciens, and some of them appear to be involved in virulence...
March 20, 2018: Current Topics in Microbiology and Immunology
Shirin Moradifard, Moslem Hoseinbeyki, Shahla Mohammad Ganji, Zarrin Minuchehr
Understanding the molecular mechanisms underlying Alzheimer's disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways...
March 19, 2018: Scientific Reports
Peng Xu, Junhua Wang, Bo Sun, Zhongdang Xiao
Investigating the potential biological function of differential changed genes through integrating multiple omics data including miRNA and mRNA expression profiles, is always hot topic. However, how to evaluate the repression effect on target genes integrating miRNA and mRNA expression profiles are not fully solved. In this study, we provide an analyzing method by integrating both miRNAs and mRNAs expression data simultaneously. Difference analysis was adopted based on the repression score, then significantly repressed mRNAs were screened out by DEGseq...
March 16, 2018: Gene
Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buness, Ewa Janosz, Natalia Lopez-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimir Benes, Martin Hemberg, Christophe Lancrin
Recent advances in single-cell transcriptomics techniques have opened the door to the study of gene regulatory networks (GRNs) at the single-cell level. Here, we studied the GRNs controlling the emergence of hematopoietic stem and progenitor cells from mouse embryonic endothelium using a combination of single-cell transcriptome assays. We found that a heptad of transcription factors (Runx1, Gata2, Tal1, Fli1, Lyl1, Erg and Lmo2) is specifically co-expressed in an intermediate population expressing both endothelial and hematopoietic markers...
March 20, 2018: ELife
Jayanna N Banavath, Thammineni Chakradhar, Varakumar Pandit, Sravani Konduru, Krishna K Guduru, Chandra S Akila, Sudhakar Podha, Chandra O R Puli
Peanut is an important oilseed and food legume cultivated as a rain-fed crop in semi-arid tropics. Drought and high salinity are the major abiotic stresses limiting the peanut productivity in this region. Development of drought and salt tolerant peanut varieties with improved yield potential using biotechnological approach is highly desirable to improve the peanut productivity in marginal geographies. As abiotic stress tolerance and yield represent complex traits, engineering of regulatory genes to produce abiotic stress-resilient transgenic crops appears to be a viable approach...
2018: Frontiers in Chemistry
Joke Terryn, Tine Tricot, Madhavsai Gajjar, Catherine Verfaillie
Pluripotent stem cells have the property of long-term self-renewal and the potential to give rise to descendants of the three germ layers and hence all mature cells in the human body. Therefore, they hold the promise of offering insight not only into human development but also for human disease modeling and regenerative medicine. However, the generation of mature differentiated cells that closely resemble their in vivo counterparts remains challenging. Recent advances in single-cell transcriptomics and computational modeling of gene regulatory networks are revealing a better understanding of lineage commitment and are driving modern genome editing approaches...
2018: F1000Research
Xiaofu Wang, Bin Hao, Changbao Xu, Xinghua Zhao, Changwei Liu, Xiaohan Chu, Yuan Lv, Yongli Zhao, Shengwei Zhang, Pengsen Wang, Youzhi Wang
Background: Renal carcinoma is a common urologic tumor, and there is no ideal tumor marker for clinical diagnosis except for imaging diagnosis. This study aims to screen the serum tumor markers closely related with the benign and malignant of renal carcinoma out and chart out the regulatory network that involves renal carcinoma-related genes. Methods: Based on 96 pathologically diagnosed renal cancer patients, factors strongly linked to renal carcinoma character were selected using Fisher discriminant analysis...
December 2017: Saudi Journal of Biological Sciences
Yibin Hao, Jianhua Zhang, Guoyong Shan, Ning Zhang, Wenwen Jin, Kejun Nan
Objective: to establish regulatory network of colorectal cancer involving p42.3 protein and to provide theoretical evidence for deep functional exploration of p42.3 protein in the onset and development of colorectal cancer. Methods: with protein similarity algorithm, reference protein set of p42.3 cell apoptosis was built according to structural features of p42.3. GO and KEGG databases were used to establish regulatory network of tumor cell apoptosis involving p42.3; meanwhile, the largest possible working pathway that involves p42...
December 2017: Saudi Journal of Biological Sciences
Daniel Pensold, Geraldine Zimmer
The correct establishment of inhibitory circuits is crucial for cortical functionality and defects during the development of γ-aminobutyric acid-expressing cortical interneurons contribute to the pathophysiology of psychiatric disorders. A critical developmental step is the migration of cortical interneurons from their site of origin within the subpallium to the cerebral cortex, orchestrated by intrinsic and extrinsic signals. In addition to genetic networks, epigenetic mechanisms such as DNA methylation by DNA methyltransferases (DNMTs) are suggested to drive stage-specific gene expression underlying developmental processes...
2018: Journal of Experimental Neuroscience
Yong-Eun Kim, Chungoo Park, Kyoon Eon Kim, Kee K Kim
Alternative splicing is an essential process in eukaryotes, as it increases the complexity of gene expression by generating multiple proteins from a single pre-mRNA. However, information on the regulatory mechanisms for alternative splicing is lacking, because splicing occurs over a short period via the transient interactions of proteins within functional complexes of the spliceosome. Here, we investigated in detail the molecular mechanisms connecting alternative splicing with epigenetic mechanisms. We identified interactions between histone proteins and splicing factors such as Rbfox2, Rbfox3, and splicing factor proline and glutamine rich protein (SFPQ) by in vivo crosslinking and immunoprecipitation...
March 15, 2018: Biochemical and Biophysical Research Communications
Mousumi Sahu, Bibekanand Mallick
MicroRNAs (miRNAs) play crucial roles in pluripotency and differentiation of human Embryonic Stem Cells (hESCs). However, synergism among multiple miRNAs and their regulatory effects on stem cells are largely unknown. We investigated the synergistic regulations among miRNAs, which are differentially expressed in hESCs and fibroblasts (Fibs) to gain deeper insights into the regulatory mechanisms of miRNA-miRNA synergism in differentiation of hESCs into Fibs. In this study, we identified miRNA targets incorporating differential expression profiles of miRNAs and genes in hESCs-Fibs as well as miRNA targeting information followed by enrichment analysis...
March 14, 2018: International Journal of Biological Macromolecules
Chun-Fu Hong, Ying-Chen Chen, Wei-Chun Chen, Keng-Chang Tu, Meng-Hsiun Tsai, Yung-Kuan Chan, Shyr Shen Yu
A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers...
March 14, 2018: Journal of Biomedical Informatics
Jaana Rysä, Heikki Tokola, Heikki Ruskoaho
Mechanical forces are able to activate hypertrophic growth of cardiomyocytes in the overloaded myocardium. However, the transcriptional profiles triggered by mechanical stretch in cardiac myocytes are not fully understood. Here, we performed the first genome-wide time series study of gene expression changes in stretched cultured neonatal rat ventricular myocytes (NRVM)s, resulting in 205, 579, 737, 621, and 1542 differentially expressed (>2-fold, P < 0.05) genes in response to 1, 4, 12, 24, and 48 hours of cyclic mechanical stretch...
March 16, 2018: Scientific Reports
Anny Waloski Robert, Addeli Bez Batti Angulski, Lucia Spangenberg, Patrícia Shigunov, Isabela Tiemy Pereira, Paulo Sergio Loiacono Bettes, Hugo Naya, Alejandro Correa, Bruno Dallagiovanna, Marco Augusto Stimamiglio
Mesenchymal stem cells (MSCs) have been widely studied with regard to their potential use in cell therapy protocols and regenerative medicine. However, a better comprehension about the factors and molecular mechanisms driving cell differentiation is now mandatory to improve our chance to manipulate MSC behavior and to benefit future applications. In this work, we aimed to study gene regulatory networks at an early step of osteogenic differentiation. Therefore, we analyzed both the total mRNA and the mRNA fraction associated with polysomes on human adipose tissue-derived stem cells (hASCs) at 24 h of osteogenesis induction...
March 16, 2018: Scientific Reports
Amelia Weber Hall, Anna M Battenhouse, Haridha Shivram, Adam R Morris, Matthew C Cowperthwaite, Max Shpak, Vishwanath R Iyer
Glioblastoma multiforme (GBM) can be clustered by gene expression into four main subtypes associated with prognosis and survival, but enhancers and other gene regulatory elements have not yet been identified in primary tumors. Here, we profiled six histone modifications and CTCF binding as well as gene expression in primary gliomas, and identified chromatin states that define distinct regulatory elements across the tumor genome. Enhancers in mesenchymal and classical tumor subtypes drove gene expression associated with cell migration and invasion, while enhancers in proneural tumors controlled genes associated with a less aggressive phenotype in GBM...
March 16, 2018: Cancer Research
Sa Geng, Ayano Miyagi, James G Umen
Volvocine algae comprise a unique comparative model for investigating the evolution of distinct male and female sexes (oogamy) from an isogamous ancestral state with mating types. The mating-type or sex-determining gene MID encodes a putative RWP-RK family transcription factor, and orthologs of MID are present throughout the volvocine algal lineage in either the MT- or male mating locus of dioecious species. It was previously found that ectopic expression of isogamous Chlamydomonas reinhardtii MID ( CrMID ) in a C...
March 16, 2018: Development
Ovidiu Lipan, Cameron Ferwerda
The deterministic Hill function depends only on the average values of molecule numbers. To account for the fluctuations in the molecule numbers, the argument of the Hill function needs to contain the means, the standard deviations, and the correlations. Here we present a method that allows for stochastic Hill functions to be constructed from the dynamical evolution of stochastic biocircuits with specific topologies. These stochastic Hill functions are presented in a closed analytical form so that they can be easily incorporated in models for large genetic regulatory networks...
February 2018: Physical Review. E
Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Caleb J Bashor, James J Collins
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function...
March 16, 2018: Annual Review of Biophysics
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