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https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#1
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28089543/optimal-regulatory-circuit-topologies-for-fold-change-detection
#2
Miri Adler, Pablo Szekely, Avi Mayo, Uri Alon
Evolution repeatedly converges on only a few regulatory circuit designs that achieve a given function. This simplicity helps us understand biological networks. However, why so few circuits are rediscovered by evolution is unclear. We address this question for the case of fold-change detection (FCD): a response to relative changes of input rather than absolute changes. Two types of FCD circuits recur in biological systems-the incoherent feedforward and non-linear integral-feedback loops. We performed an analytical screen of all three-node circuits in a class comprising ∼500,000 topologies...
January 10, 2017: Cell Systems
https://www.readbyqxmd.com/read/28087837/off-target-effects-of-neuroleptics-and-antidepressants-on-saccharomyces-cerevisiae
#3
M Caldara, S Graziano, M Gullì, S Cadonici, Nelson Marmiroli
Over the past years, the use of antidepressants and neuroleptics has steadily increased. Although incredibly useful to treat disorders like depression, schizophrenia, epilepsy, or mental retardation, these drugs display many side effects. Toxicogenomic studies aim to limit this problem by trying to identify cellular targets and off-targets of medical compounds. The baker yeast Saccharomyces cerevisiae has been shown to be a key player in this approach, as it represents an incredible toolbox for the dissection of complex biological processes...
January 13, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28087634/genome-wide-identification-of-regulatory-elements-in-sertoli-cells
#4
Danielle M Maatouk, Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E Crawford, Uwe Ohler, Blanche Capel
A current goal of molecular biology is to identify transcriptional networks regulating cell differentiation. However, identifying functional gene regulatory elements has been challenging in the context of developing tissues where material is limited and cell types are mixed. To identify regulatory sites during sex determination, we subjected Sertoli cells from mouse fetal testes to DNaseI-seq and ChIP-seq for H3K27ac. DNaseI-seq identified putative regulatory sites around Sertoli- and pregranulosa-enriched genes; however, active enhancers marked by H3K27ac were enriched proximal only to Sertoli-enriched genes...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#5
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081052/identification-of-key-transcription-factors-associated-with-lung-squamous-cell-carcinoma
#6
Feng Zhang, Xia Chen, Ke Wei, Daoming Liu, Xiaodong Xu, Xing Zhang, Hong Shi
BACKGROUND Lung squamous cell carcinoma (lung SCC) is a common type of lung cancer, but its mechanism of pathogenesis is unclear. The aim of this study was to identify key transcription factors in lung SCC and elucidate its mechanism. MATERIAL AND METHODS Six published microarray datasets of lung SCC were downloaded from Gene Expression Omnibus (GEO) for integrated bioinformatics analysis. Significance analysis of microarrays was used to identify differentially expressed genes (DEGs) between lung SCC and normal controls...
January 12, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28077403/gene-co-expression-analysis-for-functional-classification-and-gene-disease-predictions
#7
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28072866/the-regulatory-roles-of-microrna-in-effects-of-2-2-4-4-tetrabromodiphenyl-ether-bde47-on-the-transcriptome-of-zebrafish-larvae
#8
Jing Zhao, Ting Xu, Daqiang Yin, Bo Zhang, Jianfeng Bai
The developmental neurotoxicity caused by environmental pollutants has received great concern; however, there were still barely known about the underlying toxic mechanisms, especially the influence of varieties of regulatory factors such as microRNA (miRNA). A representative flame retardant, 2,2',4,4'-tetrabromodiphenyl ether (BDE47), was found to disrupt zebrafish development in visual perception and bone formation in previous study, thus here we investigated its effects on miRNA expression profiling of 6 days post fertilization (dpf) zebrafish larvae by deep sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28071676/transcriptome-analysis-of-neo-tetraploid-rice-reveals-specific-differential-gene-expressions-associated-with-fertility-and-heterosis
#9
Haibin Guo, Jean Nestor Mendrikahy, Lei Xie, Junfeng Deng, Zijun Lu, Jinwen Wu, Xiang Li, Muhammad Qasim Shahid, Xiangdong Liu
Polyploid rice hybrids have a powerful biological and yield potential that may become a new way for rice breeding; however, low fertility is major hindrance in commercial utilization. Here, we developed a neo-tetraploid rice that could overcome the sterility of autotetraploid rice and produce high heterosis. Transcriptome analysis of F1 hybrid developed by crossing neo-tetraploid with autotetraploid rice displayed 807, 663 and 866 differentially expressed genes that uniquely associated with F1 and specific to (DEGFu-sp) anther, ovary and leaf, respectively...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068481/micrornas-and-periodontal-homeostasis
#10
X Luan, X Zhou, J Trombetta-eSilva, M Francis, A K Gaharwar, P Atsawasuwan, T G H Diekwisch
MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28067773/a-systems-biological-view-of-life-and-death-decision-with-respect-to-endoplasmic-reticulum-stress-the-role-of-perk-pathway
#11
Margita Márton, Anita Kurucz, Beáta Lizák, Éva Margittai, Gábor Bánhegyi, Orsolya Kapuy
Accumulation of misfolded/unfolded proteins in the endoplasmic reticulum (ER) leads to the activation of three branches (Protein kinase (RNA)-like endoplasmic reticulum kinase [PERK], Inositol requiring protein 1 [IRE-1] and Activating trascription factor 6 [ATF6], respectively) of unfolded protein response (UPR). The primary role of UPR is to try to drive back the system to the former or a new homeostatic state by self-eating dependent autophagy, while excessive level of ER stress results in apoptotic cell death...
January 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28065897/trfba-an-algorithm-to-integrate-genome-scale-metabolic-and-transcriptional-regulatory-networks-with-incorporation-of-expression-data
#12
Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari
MOTIVATION: Integration of different biological networks and data-types has been a major challenge in systems biology. The present study introduces the transcriptional regulated flux balance analysis (TRFBA) algorithm that integrates transcriptional regulatory and metabolic models using a set of expression data for various perturbations. RESULTS: TRFBA considers the expression levels of genes as a new continuous variable and introduces two new linear constraints...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28060821/customized-regulation-of-diverse-stress-response-genes-by-the-multiple-antibiotic-resistance-activator-mara
#13
Nicholas A Rossi, Mary J Dunlop
Stress response networks frequently have a single upstream regulator that controls many downstream genes. However, the downstream targets are often diverse, therefore it remains unclear how their expression is specialized when under the command of a common regulator. To address this, we focused on a stress response network where the multiple antibiotic resistance activator MarA from Escherichia coli regulates diverse targets ranging from small RNAs to efflux pumps. Using single-cell experiments and computational modeling, we showed that each downstream gene studied has distinct activation, noise, and information transmission properties...
January 6, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28056558/mechanisms-and-strategies-of-plant-defense-against-botrytis-cinerea
#14
Synan AbuQamar, Khaled Moustafa, Lam-Son Phan Tran
Biotic factors affect plant immune responses and plant resistance to pathogen infections. Despite the considerable progress made over the past two decades in manipulating genes, proteins and their levels from diverse sources, no complete genetic tolerance to environmental stresses has been developed so far in any crops. Plant defense response to pathogens, including Botrytis cinerea, is a complex biological process involving various changes at the biochemical, molecular (i.e. transcriptional) and physiological levels...
January 5, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28052708/chaos-and-hyperchaos-in-simple-gene-network-with-negative-feedback-and-time-delays
#15
Tamara M Khlebodarova, Vladislav V Kogai, Stanislav I Fadeev, Vitaly A Likhoshvai
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos...
November 29, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28052084/linking-hematopoietic-differentiation-to-co-expressed-sets-of-pluripotency-associated-and-imprinted-genes-and-to-regulatory-microrna-transcription-factor-motifs
#16
Mohamed Hamed, Johannes Trumm, Christian Spaniol, Riccha Sethi, Mohammad R Irhimeh, Georg Fuellen, Martina Paulsen, Volkhard Helms
Maintenance of cell pluripotency, differentiation, and reprogramming are regulated by complex gene regulatory networks (GRNs) including monoallelically-expressed imprinted genes. Besides transcriptional control, epigenetic modifications and microRNAs contribute to cellular differentiation. As a model system for studying the capacity of cells to preserve their pluripotency state and the onset of differentiation and subsequent specialization, murine hematopoiesis was used and compared to embryonic stem cells (ESCs) as a control...
2017: PloS One
https://www.readbyqxmd.com/read/28050009/co-expression-analysis-of-blood-cell-genome-expression-to-preliminary-investigation-of-regulatory-mechanisms-in-uremia
#17
Liu Cheng, Wu Yonggui
BACKGROUND Uremia involves a series of clinical manifestations and is a common syndrome that occurs in nearly all end-stage kidney diseases. However, the exact genetic and/or molecular mechanisms that underlie uremia remain poorly understood. MATERIAL AND METHODS In this case-control study, we analyzed whole-genome microarray of 75 uremia patients and 20 healthy controls to investigate changes in gene expression and cellular mechanisms relevant to uremia. Gene co-expression network analysis was performed to construct co-expression networks using differentially expressed genes (DEGs) in uremia...
January 4, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28045465/methylomic-profiling-of-cortex-samples-from-completed-suicide-cases-implicates-a-role-for-psors1c3-in-major-depression-and-suicide
#18
T M Murphy, B Crawford, E L Dempster, E Hannon, J Burrage, G Turecki, Z Kaminsky, J Mill
Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25))...
January 3, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28045116/comparative-analysis-of-dna-methylome-and-transcriptome-of-skeletal-muscle-in-lean-obese-and-mini-type-pigs
#19
Yalan Yang, Guoming Liang, Guanglin Niu, Yuanyuan Zhang, Rong Zhou, Yanfang Wang, Yulian Mu, Zhonglin Tang, Kui Li
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28044434/quantitative-proteomics-reveals-eva1a-related-proteins-involved-in-neuronal-differentiation
#20
Lijun Zhong, Juntuo Zhou, Xi Chen, Jiao Liu, Zhen Liu, Yingyu Chen, Yun Bai
EVA1A is an autophagy-related protein, which plays an important role in embryonic neurogenesis. In this study, we found that loss of EVA1A could decrease neural differentiation in the brain of adult Eva1a(-/-) mice. To determine the mechanism underlying this phenotype, we performed label-free quantitative proteomics and bioinformatics analysis using the brains of Eva1a(-/-) and wild type mice. We identified 11 proteins that were up-regulated and 17 that were down-regulated in the brains of the knockout mice compared to the wild-type counterparts...
January 3, 2017: Proteomics
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