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https://www.readbyqxmd.com/read/29455671/oncogenic-fusion-proteins-adopt-the-insulin-like-growth-factor-signaling-pathway
#1
REVIEW
Haim Werner, Shilhav Meisel-Sharon, Ilan Bruchim
The insulin-like growth factor-1 receptor (IGF1R) has been identified as a potent anti-apoptotic, pro-survival tyrosine kinase-containing receptor. Overexpression of the IGF1R gene constitutes a typical feature of most human cancers. Consistent with these biological roles, cells expressing high levels of IGF1R are expected not to die, a quintessential feature of cancer cells. Tumor specific chromosomal translocations that disrupt the architecture of transcription factors are a common theme in carcinogenesis...
February 19, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29455584/hepes-activates-a-mit-tfe-dependent-lysosomal-autophagic-gene-network-in-cultured-cells-a-call-for-caution
#2
Marc J Tol, Martijn J C van der Lienden, Tanit L Gabriel, Jacob J Hagen, Saskia Scheij, Tineke Veenendaal, Judith Klumperman, Wilma E Donker-Koopman, Arthur J Verhoeven, Hermen Overkleeft, Johannes M Aerts, Carmen A Argmann, Marco van Eijk
In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of "master lysosomal regulators". Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated...
February 17, 2018: Autophagy
https://www.readbyqxmd.com/read/29455385/transcriptome-analysis-of-wild-type-and-afss-deletion-mutant-strains-identifies-synergistic-transcriptional-regulator-of-afss-for-a-high-antibiotic-producing-strain-of-streptomyces-coelicolor-a3-2
#3
Min Woo Kim, Bo-Rahm Lee, SungYong You, Eun-Jung Kim, Ji-Nu Kim, Eunjung Song, Yung-Hun Yang, Daehee Hwang, Byung-Gee Kim
Most secondary metabolism in Actinobacteria is controlled by multi-layered, gene-regulatory networks. These regulatory mechanisms are not easily identified due to their complexity. As a result, when a strong transcriptional regulator (TR) governs activation of biosynthetic pathways of target antibiotics such as actinorhodin (ACT), additional enhancement of the biosynthesis is difficult in combination with other TRs. To find out any "synergistic transcriptional regulators (sTRs)" that show an additive effect on the major, often strong, transcriptional regulator (mTR), here, we performed a clustering analysis using the transcriptome datasets of an mTR deletion mutant and wild-type strain...
February 17, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29453388/identifying-noncoding-risk-variants-using-disease-relevant-gene-regulatory-networks
#4
Long Gao, Yasin Uzun, Peng Gao, Bing He, Xiaoke Ma, Jiahui Wang, Shizhong Han, Kai Tan
Identifying noncoding risk variants remains a challenging task. Because noncoding variants exert their effects in the context of a gene regulatory network (GRN), we hypothesize that explicit use of disease-relevant GRNs can significantly improve the inference accuracy of noncoding risk variants. We describe Annotation of Regulatory Variants using Integrated Networks (ARVIN), a general computational framework for predicting causal noncoding variants. It employs a set of novel regulatory network-based features, combined with sequence-based features to infer noncoding risk variants...
February 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29453387/structural-determinants-of-the-sine-b2-element-embedded-in-the-long-non-coding-rna-activator-of-translation-as-uchl1
#5
Peter Podbevšek, Francesca Fasolo, Carlotta Bon, Laura Cimatti, Sabine Reißer, Piero Carninci, Giovanni Bussi, Silvia Zucchelli, Janez Plavec, Stefano Gustincich
Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453355/co-expression-network-analysis-and-cis-regulatory-element-enrichment-determine-putative-functions-and-regulatory-mechanisms-of-grapevine-atl-e3-ubiquitin-ligases
#6
Darren C J Wong, Pietro Ariani, Simone Castellarin, Annalisa Polverari, Elodie Vandelle
Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453091/identification-of-mirnas-and-their-targets-in-maize-in-response-to-sugarcane-mosaic-virus-infection
#7
Zihao Xia, Zhenxing Zhao, Mingjun Li, Ling Chen, Zhiyuan Jiao, Yuanhua Wu, Tao Zhou, Weichang Yu, Zaifeng Fan
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play essential regulatory roles in plant development and environmental stress responses. Maize (Zea mays L.) is a global economically important food and forage crop. To date, a number of maize miRNAs have been identified as being involved in plant development and stress responses. However, the miRNA-mediated gene regulatory networks responsive to virus infections in maize remain largely unknown. In this study, the profiles of small RNAs in buffer- and Sugarcane mosaic virus (SCMV)-inoculated maize plants were obtained by high-throughput sequencing, respectively...
January 31, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29453041/microrna-signature-of-regulatory-t-cells-in-health-and-autoimmunity
#8
REVIEW
Mehdi Soltanzadeh-Yamchi, Mehdi Shahbazi, Saeed Aslani, Mousa Mohammadnia-Afrouzi
MicroRNAs (miRNAs) are small RNA molecules with regulatory functions on the expression of genes through binding directly to target messenger RNA (mRNA) transcripts, eventuating in gene expression suppression via translational hindrance and/or target mRNA cleavage. These molecules have been established to participate in numerous critical cellular settings, including differentiation, development, and function of immune cells. As an important suppressor cell of immune system, regulatory T cells (Tregs) are important in modulating the immune homeostasis as well as tolerance to self-antigens...
February 13, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29452643/combinatorial-crispr-cas9-metabolic-screens-reveal-critical-redox-control-points-dependent-on-the-keap1-nrf2-regulatory-axis
#9
Dongxin Zhao, Mehmet G Badur, Jens Luebeck, Jose H Magaña, Amanda Birmingham, Roman Sasik, Christopher S Ahn, Trey Ideker, Christian M Metallo, Prashant Mali
The metabolic pathways fueling tumor growth have been well characterized, but the specific impact of transforming events on network topology and enzyme essentiality remains poorly understood. To this end, we performed combinatorial CRISPR-Cas9 screens on a set of 51 carbohydrate metabolism genes that represent glycolysis and the pentose phosphate pathway (PPP). This high-throughput methodology enabled systems-level interrogation of metabolic gene dispensability, interactions, and compensation across multiple cell types...
February 15, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29451874/a-stochastic-and-dynamical-view-of-pluripotency-in-mouse-embryonic-stem-cells
#10
Yen Ting Lin, Peter G Hufton, Esther J Lee, Davit A Potoyan
Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks. The rapid growth of single-cell sequencing data has greatly stimulated applications of statistical and machine learning methods for inferring topologies of pluripotency regulating genetic networks. The inferred network topologies, however, often only encode Boolean information while remaining silent about the roles of dynamics and molecular stochasticity inherent in gene expression...
February 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29451210/intravenous-morphine-self-administration-alters-accumbal-microrna-profiles-in-the-mouse-brain
#11
Juhwan Kim, Heh-In Im, Changjong Moon
A significant amount of evidence indicates that microRNAs (miRNAs) play an important role in drug addiction. The nucleus accumbens (NAc) is a critical part of the brain's reward circuit and is involved in a variety of psychiatric disorders, including depression, anxiety, and drug addiction. However, few studies have examined the expression of miRNAs and their functional roles in the NAc under conditions of morphine addiction. In this study, mice were intravenously infused with morphine (0.01, 0.03, 0.3, 1 and 3 mg/kg/infusion) and showed inverted U-shaped response...
January 2018: Neural Regeneration Research
https://www.readbyqxmd.com/read/29449773/potential-breast-anticancer-drug-targets-revealed-by-differential-gene-regulatory-network-analysis-and-molecular-docking-neoadjuvant-docetaxel-drug-as-a-case-study
#12
Adel Aloraini, Karim M ElSawy
Understanding gene-gene interaction and its causal relationship to protein-protein interaction is a viable route for understanding drug action at the genetic level, which is largely hindered by inability to robustly map gene regulatory networks. Here, we use biological prior knowledge of family-to-family gene interactions available in the KEGG database to reveal individual gene-to-gene interaction networks that underlie the gene expression profiles of 2 cell line data sets, sensitive and resistive to neoadjuvant docetaxel breast anticancer drug...
2018: Cancer Informatics
https://www.readbyqxmd.com/read/29449088/temperature-modulates-tissue-specification-program-to-control-fruit-dehiscence-in-brassicaceae
#13
Xin-Ran Li, Joyita Deb, S Vinod Kumar, Lars Østergaard
Plants respond to diurnal and seasonal changes in temperature by reprogramming vital developmental pathways. Understanding the molecular mechanisms that define environmental modulation of plant growth and reproduction is critical in the context of climate change that threatens crop yield worldwide. Here, we report that elevated temperature accelerates fruit dehiscence in members of the Brassicaceae family including the model plant Arabidopsis thaliana and important crop species. Arabidopsis fruit development is controlled by a network of interacting regulatory genes...
February 7, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29448158/despacito-the-slow-evolutionary-changes-in-plant-micrornas
#14
REVIEW
Patricia Baldrich, Aleksandra Beric, Blake C Meyers
MicroRNAs (miRNAs) are key regulators of gene expression. A handful of miRNAs are broadly conserved in land plants, while the majority are lineage specific; this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution...
February 12, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29447160/modeling-the-interactions-of-sense-and-antisense-period-transcripts-in-the-mammalian-circadian-clock-network
#15
Dorjsuren Battogtokh, Shihoko Kojima, John J Tyson
In recent years, it has become increasingly apparent that antisense transcription plays an important role in the regulation of gene expression. The circadian clock is no exception: an antisense transcript of the mammalian core-clock gene PERIOD2 (PER2), which we shall refer to as Per2AS RNA, oscillates with a circadian period and a nearly 12 h phase shift from the peak expression of Per2 mRNA. In this paper, we ask whether Per2AS plays a regulatory role in the mammalian circadian clock by studying in silico the potential effects of interactions between Per2 and Per2AS RNAs on circadian rhythms...
February 15, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29444945/interaction-of-human-cytomegalovirus-tegument-proteins-ppul35-and-ppul35a-with-sorting-nexin-5-regulates-glycoprotein-b-gpul55-localization
#16
Gregor Maschkowitz, Sabine Gärtner, Heike Hofmann-Winkler, Helmut Fickenscher, Michael Winkler
Human cytomegalovirus (HCMV) is a wide-spread human pathogen that causes asymptomatic infection in healthy individuals, but poses a serious threat to immunocompromised patients. During the late phase of HCMV infection, the viral capsid is transported to the cytoplasmic viral assembly center (cVAC) where it is enclosed by the tegument protein layer and the viral envelope. The cVAC consists of circularly arranged vesicles from the trans-Golgi and endosomal networks. The HCMV gene UL35 encodes ppUL35 and its shorter form ppUL35A...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29442330/roles-of-zic2-in-regulation-of-pluripotent-stem-cells
#17
Hisato Kondoh
Pioneered by the classical mouse embryonic stem cells (ESCs), various stem cell lines representing the peri- and postimplantation stages of embryogenesis have been established. To gain insight into the gene regulatory network operating in these cells, we first investigated epiblast stem cells (EpiSCs), performing ChIP-seq analysis for five major transcription factors (TFs) involved in epiblast regulation. The analysis indicated that SOX2-POU5F1 TF pairs highlighted in mouse ESCs are not the major players in other stem cells...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29441670/energy-drives-the-dynamic-localization-of-cyanobacterial-nitrogen-regulators-during-diurnal-cycles
#18
Javier Espinosa, José I Labella, Raquel Cantos, Asunción Contreras
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as integrators of signals of the nitrogen and carbon balance, PipX proteins are unique to cyanobacteria, where they provide a mechanistic link between PII signalling and the control of gene expression by the global nitrogen regulator NtcA...
February 14, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29441565/metabolomics-and-transcriptomics-profiles-reveal-the-dysregulation-of-the-tricarboxylic-acid-cycle-and-related-mechanisms-in-prostate-cancer
#19
Yaping Shao, Guozhu Ye, Shancheng Ren, Hai-Long Piao, Xinjie Zhao, Xin Lu, Fubo Wang, Ma Wang, Jia Li, Peiyuan Yin, Tian Xia, Chuanliang Xu, Jane J Yu, Yinghao Sun, Guowang Xu
Genetic alterations drive metabolic reprogramming to meet increased biosynthetic precursor and energy demands for cancer cell proliferation and survival in unfavorable environments. A systematic study of gene-metabolite regulatory networks and metabolic dysregulation should reveal the molecular mechanisms underlying prostate cancer (PCa) pathogenesis. Herein, we performed gas chromatography-mass spectrometry (GC-MS)-based metabolomics and RNA-seq analyses in prostate tumors and matched adjacent normal tissues (ANTs) to elucidate the molecular alterations and potential underlying regulatory mechanisms in PCa...
February 14, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29441447/transcriptional-mechanisms-of-secondary-fracture-healing
#20
REVIEW
Joseph L Roberts, David N Paglia, Hicham Drissi
PURPOSE OF REVIEW: Growing evidence supports the critical role of transcriptional mechanisms in promoting the spatial and temporal progression of bone healing. In this review, we evaluate and discuss new transcriptional and post-transcriptional regulatory mechanisms of secondary bone repair, along with emerging evidence for epigenetic regulation of fracture healing. RECENT FINDINGS: Using the candidate gene approach has identified new roles for several transcription factors in mediating the reactive, reparative, and remodeling phases of fracture repair...
February 13, 2018: Current Osteoporosis Reports
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