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Gene regulatory networks

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https://www.readbyqxmd.com/read/29679401/translational-regulation-of-ribosomal-protein-s15-drives-characteristic-patterns-of-protein-mrna-epistasis
#1
Saurav Mallik, Sudipto Basu, Suman Hait, Sudip Kundu
Do coding and regulatory segments of a gene co-evolve with each-other? Seeking answers to this question, here we analyze the case of Escherichia coli ribosomal protein S15, that represses its own translation by specifically binding its messenger RNA (rpsO mRNA) and stabilizing a pseudoknot structure at the upstream untranslated region, thus trapping the ribosome into an incomplete translation initiation complex. In the absence of S15, ribosomal protein S1 recognizes rpsO and promotes translation by melting this very pseudoknot...
April 21, 2018: Proteins
https://www.readbyqxmd.com/read/29678906/rnai-screening-identifies-a-mechanosensitive-rock-jak2-stat3-network-central-to-myofibroblast-activation
#2
Raymond S Oh, Andrew J Haak, Karry M J Smith, Giovanni Ligresti, Kyoung Moo Choi, Tiao Xie, Shaohua Wang, Paula R Walters, Michael A Thompson, Michelle R Freeman, Logan J Manlove, Vivian M Chu, Carol Feghali-Bostwick, Anja C Roden, Jürgen Schymeinsky, Christina M Pabelick, Y S Prakash, Robert Vassallo, Daniel J Tschumperlin
Myofibroblasts play key roles in wound healing and pathologic fibrosis. Here we undertook an RNAi screen to characterize myofibroblast regulatory genes, using a high-content imaging approach to quantify alpha-smooth muscle actin stress fibers in cultured human fibroblasts. Screen hits were validated on physiological compliance hydrogels, and selected hits tested in primary fibroblasts from patients with idiopathic pulmonary fibrosis. Our RNAi screen led to the identification of STAT3 as an essential mediator of myofibroblast activation and function...
April 20, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29678830/regulation-of-cell-to-cell-communication-and-cell-wall-integrity-by-a-network-of-map-kinase-pathways-and-transcription-factors-in-neurospora-crassa
#3
Monika S Fischer, Vincent W Wu, Ji E Lee, Ronan C O'Malley, N Louise Glass
Maintenance of cell integrity and cell-to-cell communication are fundamental biological processes. Filamentous fungi, such as Neurospora crassa , depend on communication to locate compatible cells, coordinate cell fusion, and establish a robust hyphal network. Two MAP-Kinase pathways are essential for communication and cell fusion in N. crassa ; the Cell Wall Integrity/MAK-1 pathway and the MAK-2 (signal response) pathway. Previous studies have demonstrated several points of cross talk between the MAK-1 and MAK-2 pathways, which is likely necessary for coordinating chemotropic growth toward an extracellular signal, and then mediating cell fusion...
April 20, 2018: Genetics
https://www.readbyqxmd.com/read/29676772/functional-roles-of-eriocalyxin-b-in-zebrafish-revealed-by-transcriptome-analysis
#4
Xunian Zhou, Cyanne Ye Cao, Angel Tsz-Yau Wan, Grace Gar-Lee Yue, Frankie Hin-Fai Kwok, Kwok-Pui Fung, Handong Sun, Clara Bik-San Lau, Pema-Tenzin Puno, Stephen Kwok-Wing Tsui
BACKGROUND: Eriocalyxin B (EriB) is a natural ent-kaurane diterpenoid obtained from Isodon eriocalyx var. laxiflora (family Lamiaceae), which has multiple biological activities (e.g. anti-tumor and anti-inflammatory) via the alteration of gene expression and signaling transduction. Recently, RNA sequencing (RNA-seq) has been developed as a dynamic transcriptome approach to analyze the transcriptional profile and in addition use such gene expression profiles to identify novel candidate genes in a zebrafish model...
April 20, 2018: Molecular omics
https://www.readbyqxmd.com/read/29675796/construction-of-transcriptional-regulatory-network-of-alzheimer-s-disease-based-on-panda-algorithm
#5
Jieyuan Ding, Wei Kong, Xiaoyang Mou, Shuaiqun Wang
The focus of modern biomedical research concentrates on molecular level regulatory mechanisms and how the normal and abnormal phenotypes of tissue functional are affected by regulatory mechanisms. Most of the research on regulatory mechanism starts from the reconstruction of gene regulation network. At present, a large number of reconstruction methods construct the network using a single data set. These methods of inferring and predicting the relationship between the target gene and the transcription factor (TF) can be used to identify individual interactions between genes, while there is not much research on the interaction of many functional-related genes...
April 19, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29675029/aaein3-mediates-the-downregulation-of-artemisinin-biosynthesis-by-ethylene-signaling-through-promoting-leaf-senescence-in-artemisia-annua
#6
Yueli Tang, Ling Li, Tingxiang Yan, Xueqing Fu, Pu Shi, Qian Shen, Xiaofen Sun, Kexuan Tang
Artemisinin is an important drug for malaria treatment, which is exclusively produced in Artemisia annua . It's important to dissect the regulatory mechanism of artemisinin biosynthesis by diverse plant hormones and transcription factors. Our study shows ethylene, a plant hormone which accelerates flower and leaf senescence and fruit ripening, suppressed the expression of genes encoding three key enzymes ADS, DBR2, CYP71AV1, and a positive regulator AaORA involved in artemisinin biosynthesis. Then we isolated the gene encoding ETHYLENE-INSENSITIVE3 (EIN3), a key transcription factor in ethylene signaling pathway, by screening the transcriptome and genome database from Artemisia annua , named AaEIN3 ...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29674689/comparative-transcriptome-analysis-to-investigate-the-potential-role-of-mirnas-in-milk-protein-fat-quality
#7
Xuehui Wang, Li Zhang, Jing Jin, Anting Xia, Chunmei Wang, Yingjun Cui, Bo Qu, Qingzhang Li, Chunyan Sheng
miRNAs play an important role in the processes of cell differentiation, biological development, and physiology. Here we investigated the molecular mechanisms regulating milk secretion and quality in dairy cows via transcriptome analyses of mammary gland tissues from dairy cows during the high-protein/high-fat, low-protein/low-fat or dry periods. To characterize the important roles of miRNAs and mRNAs in milk quality and to elucidate their regulatory networks in relation to milk secretion and quality, an integrated analysis was performed...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29673687/the-brassinosteroid-regulated-transcription-factors-bzr1-bes1-function-as-a-coordinator-in-multisignal-regulated-plant-growth
#8
REVIEW
Qian-Feng Li, Jun Lu, Jia-Wen Yu, Chang-Quan Zhang, Jun-Xian He, Qiao-Quan Liu
BZR1 and BES1 are key transcription factors of brassinosteroid (BR) signaling and represent the integration node of numerous signaling cascades. Their direct target genes have been identified, and BZR1/BES1-DNA interactions have been experimentally verified. Importantly, BZR1/BES1 also integrate different growth and development events via direct protein-protein interactions. For instance, DELLAs, PIFs, ARF6, and PKL, all directly interact with BZR1/BES1, forming a BZR1/BES1-centered regulatory network to coordinate cell elongation...
April 16, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29672926/insights-into-the-etiology-associated-gene-regulatory-networks-in-hepatocellular-carcinoma-from-the-cancer-genome-atlas
#9
Veerabrahma Pratap Seshachalam, Karthik Sekar, Kam M Hui
BACKGROUND AND AIM: Hepatitis B virus, hepatitis C virus, alcoholic consumption and non-alcoholic fatty liver are the major known risk factors for Hepatocellular carcinoma (HCC). There have been very few studies comparing the underlying biological mechanisms associated with the different etiologies of HCC. In this study, we hypothesized the existence of different regulatory networks associated with different liver disease etiologies involved in hepatocarcinogenesis. METHODS: Using upstream regulatory analysis tool in ingenuity pathway analysis software, URs were predicted using differential expressed genes for HCC to facilitate the interrogation of global gene regulation...
April 19, 2018: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/29672343/polygenic-risk-score-for-schizophrenia-is-not-strongly-associated-with-the-expression-of-specific-genes-or-gene-sets
#10
David Curtis
BACKGROUND: The polygenic risk score (PRS) is derived from single nucleotide polymorphisms (SNPs) including those that are genome-wide significant and also including a large number of others more weakly associated with schizophrenia. Such variants are widely dispersed, though concentrated near genes expressed in the brain, and it has been proposed that these SNP associations result from impacts on cell regulatory networks that ultimately affect the expression or function of a modest number of 'core' genes...
April 18, 2018: Psychiatric Genetics
https://www.readbyqxmd.com/read/29672174/th9-cells-probable-players-in-ulcerative-colitis-pathogenesis
#11
Mojtaba Shohan, Shokrollah Elahi, Hedayatollah Shirzad, Mahmoud Rafieian-Kopaei, Nader Bagheri, Emad Soltani
T lymphocytes represent an important part of adaptive immune system undertaking different functions to regulate immune responses. CD4+ T cells are the most important activator cells in inflammatory conditions. Depending on the type of induced cells and inflamed sites, expression and activity of different subtypes of helper T cells are changed. Recent studies have confirmed the existence of a new subset of helper T lymphocytes called Th9. Naive T cells can differentiate into Th9 subtypes if they are exposed simultaneously by interleukin (IL) 4 and transforming growth factor β and also secondary activation of a complicated network of transcription factors such as interferon regulatory factor 4 (IRF4) and Smads which are essential for adequate induction of this phenotype...
April 19, 2018: International Reviews of Immunology
https://www.readbyqxmd.com/read/29670360/integrated-bioinformatic-analysis-unveils-significant-genes-and-pathways-in-the-pathogenesis-of-supratentorial-primitive-neuroectodermal-tumor
#12
Guang-Yu Wang, Ling Li, Bo Liu, Xiao Han, Chun-Hua Wang, Ji-Wen Wang
Purpose: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET). Materials and methods: Gene expression profile of GSE14295 was downloaded from publicly available Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out in primary sPNET samples compared with normal fetal and adult brain reference samples (sPNET vs fetal brain and sPNET vs adult brain)...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29670281/identification-of-the-tumour-transition-states-occurring-during-emt
#13
Ievgenia Pastushenko, Audrey Brisebarre, Alejandro Sifrim, Marco Fioramonti, Tatiana Revenco, Soufiane Boumahdi, Alexandra Van Keymeulen, Daniel Brown, Virginie Moers, Sophie Lemaire, Sarah De Clercq, Esmeralda Minguijón, Cédric Balsat, Youri Sokolow, Christine Dubois, Florian De Cock, Samuel Scozzaro, Federico Sopena, Angel Lanas, Nicky D'Haene, Isabelle Salmon, Jean-Christophe Marine, Thierry Voet, Panagiota A Sotiropoulou, Cédric Blanpain
In cancer, the epithelial-to-mesenchymal transition (EMT) is associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However, there is no direct in vivo evidence for this idea. Here we screen a large panel of cell surface markers in skin and mammary primary tumours, and identify the existence of multiple tumour subpopulations associated with different EMT stages: from epithelial to completely mesenchymal states, passing through intermediate hybrid states...
April 18, 2018: Nature
https://www.readbyqxmd.com/read/29669315/characterization-and-analysis-of-whole-transcriptome-of-giant-panda-spleens-implying-critical-roles-of-long-non-coding-rnas-in-immunity
#14
Rui Peng, Yuliang Liu, Zhigang Cai, Fujun Shen, Jiasong Chen, Rong Hou, Fangdong Zou
BACKGROUND/AIMS: Giant pandas, an endangered species, are a powerful symbol of species conservation. Giant pandas may suffer from a variety of diseases. Owing to their highly specialized diet of bamboo, giant pandas are thought to have a relatively weak ability to resist diseases. The spleen is the largest organ in the lymphatic system. However, there is little known about giant panda spleen at a molecular level. Thus, clarifying the regulatory mechanisms of spleen could help us further understand the immune system of the giant panda as well as its conservation...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29668013/drosophila-relics-hobo-and-hobo-mites-transposons-as-raw-material-for-new-regulatory-networks
#15
Elgion L S Loreto, Maríndia Deprá, José F Diesel, Yanina Panzera, Vera Lucia S Valente-Gaiesky
Hypermutable strains of Drosophila simulans have been studied for 20 years. Several mutants were isolated and characterized, some of which had phenotypes associated with alteration in development; for example, showing ectopic legs with eyes being expressed in place of antennae. The causal agent of this hypermutability is a non-autonomous hobo-related sequence (hoboVA). Around 100 mobilizable copies of this element are present in the D. simulans genome, and these are likely mobilized by the autonomous and canonical hobo element...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29666124/generation-of-a-double-binary-transgenic-zebrafish-model-to-study-myeloid-gene-regulation-in-response-to-oncogene-activation-in-melanocytes
#16
Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Vanessa Chong-Morrison, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka-Spengler
A complex network of inflammatory genes is closely linked to somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. Here, we describe the development of a double binary zebrafish model that enables regulatory programming of the myeloid cells as they respond to oncogene-activated melanocytes to be explored, focussing on the initial phase when cells become the precursors of cancer...
April 6, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29665782/a-direct-regulatory-link-between-microrna-137-and-shank2-implications-for-neuropsychiatric-disorders
#17
Ana de Sena Cortabitarte, Simone Berkel, Flavia-Bianca Cristian, Christine Fischer, Gudrun A Rappold
BACKGROUND: Mutations in the SHANK genes, which encode postsynaptic scaffolding proteins, have been linked to a spectrum of neurodevelopmental disorders. The SHANK genes and the schizophrenia-associated microRNA-137 show convergence on several levels, as they are both expressed at the synapse, influence neuronal development, and have a strong link to neurodevelopmental and neuropsychiatric disorders like intellectual disability, autism, and schizophrenia. This compiled evidence raised the question if the SHANKs might be targets of miR-137...
April 17, 2018: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/29665672/regulatory-network-of-arf-in-cancer-development
#18
Aram Ko, Su Yeon Han, Jaewhan Song
ARF is a tumor suppressor protein that has a pivotal role in the prevention of cancer development through regulating cell proliferation, senescence, and apoptosis. As a factor that induces senescence, the role of ARF as a tumor suppressor is closely linked to the p53-MDM2 axis, which is a key process that restrains tumor formation. Thus, many cancer cells either lack a functional ARF or p53, which enables them to evade cell oncogenic stress-mediated cycle arrest, senescence, or apoptosis. In particular, the ARF gene is a frequent target of genetic and epigenetic alterations including promoter hypermethylation or gene deletion...
April 18, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29665143/identification-of-potential-tumor-educated-platelets-rna-biomarkers-in-non-small-cell-lung-cancer-by-integrated-bioinformatical-analysis
#19
Linlin Xue, Li Xie, Xingguo Song, Xianrang Song
BACKGROUND: Platelets have emerged as key players in tumorigenesis and tumor progression. Tumor-educated platelet (TEP) RNA profile has the potential to diagnose non-small-cell lung cancer (NSCLC). The objective of this study was to identify potential TEP RNA biomarkers for the diagnosis of NSCLC and to explore the mechanisms in alternations of TEP RNA profile. METHODS: The RNA-seq datasets GSE68086 and GSE89843 were downloaded from Gene Expression Omnibus DataSets (GEO DataSets)...
April 17, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29664344/how-criticality-of-gene-regulatory-networks-affects-the-resulting-morphogenesis-under-genetic-perturbations
#20
Hyobin Kim, Hiroki Sayama
Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single-cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher level has not been fully explored. Here we aim at revealing a potential role of criticality of GRNs in morphogenesis, which is hard to uncover through the single-cell-level studies, especially from an evolutionary viewpoint. Our model simulated the growth of a cell population from a single seed cell...
April 17, 2018: Artificial Life
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