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Tissue specific gene network

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https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#1
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28429252/analysis-of-global-gene-expression-profiles-during-the-flowering-initiation-process-of-lilium%C3%A2-%C3%A3-%C3%A2-formolongi
#2
Yu-Fan Li, Ming-Fang Zhang, Meng Zhang, Gui-Xia Jia
The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70...
April 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28427347/comparative-transcriptomics-of-mountain-pine-beetle-pheromone-biosynthetic-tissues-and-functional-analysis-of-cyp6de3
#3
J A Nadeau, J Petereit, R L Tillett, K Jung, M Fotoohi, M MacLean, S Young, K Schlauch, G J Blomquist, C Tittiger
BACKGROUND: The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a highly destructive pest of pine forests in western North America. During flight to a new host tree and initiation of feeding, mountain pine beetles release aggregation pheromones. The biosynthetic pathways of these pheromones are sex-specific and localized in the midgut and fat body, but the enzymes involved have not all been identified or characterized. RESULTS: We used a comparative RNA-Seq analysis between fed and unfed male and female MPB midguts and fat bodies to identify candidate genes involved in pheromone biosynthesis...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28415684/the-long-noncoding-rna-linc-ned125-controls-the-expression-of-medulloblastoma-driver-genes-by-microrna-sponge-activity
#4
Pietro Laneve, Agnese Po, Annarita Favia, Ivano Legnini, Vincenzo Alfano, Jessica Rea, Valerio Di Carlo, Valeria Bevilacqua, Evelina Miele, Angela Mastronuzzi, Andrea Carai, Franco Locatelli, Irene Bozzoni, Elisabetta Ferretti, Elisa Caffarelli
Long noncoding RNAs (lncRNAs) are major regulators of physiological and disease-related gene expression, particularly in the central nervous system. Dysregulated lncRNA expression has been documented in several human cancers, and their tissue-specificity makes them attractive candidates as diagnostic/prognostic biomarkers and/or therapeutic agents. Here we show that linc-NeD125, which we previously characterized as a neuronal-induced lncRNA, is significantly overexpressed in Group 4 medulloblastomas (G4 MBs), the largest and least well characterized molecular MB subgroup...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415601/regulatory-network-of-gata3-in-pediatric-acute-lymphoblastic-leukemia
#5
Qianqian Hou, Fei Liao, Shouyue Zhang, Duyu Zhang, Yan Zhang, Xueyan Zhou, Xuyang Xia, Yuanxin Ye, Hanshuo Yang, Zhaozhi Li, Leiming Wang, Xi Wang, Zhigui Ma, Yiping Zhu, Liang Ouyang, Yuelan Wang, Hui Zhang, Li Yang, Heng Xu, Yang Shu
GATA3 polymorphisms were reported to be significantly associated with susceptibility of pediatric B-lineage acute lymphoblastic leukemia (ALL), by impacting on GATA3 expression. We noticed that ALL-related GATA3 polymorphism located around in the tissue-specific enhancer, and significantly associated with GATA3 expression. Although the regulatory network of GATA3 has been well reported in T cells, the functional status of GATA3 is poorly understood in B-ALL. We thus conducted genome-wide gene expression association analyses to reveal expression associated genes and pathways in nine independent B-ALL patient cohorts...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414270/human-biallelic-mfn2-mutations-induce-mitochondrial-dysfunction-upper-body-adipose-hyperplasia-and-suppression-of-leptin-expression
#6
Nuno M Rocha, David A Bulger, Andrea Frontini, Hannah Titheradge, Sigrid Bjerge Gribsholt, Rachel Knox, Matthew Page, Julie Harris, Felicity Payne, Claire Adams, Alison Sleigh, John Crawford, Anette Prior Gjesing, Jette Bork-Jensen, Oluf Pedersen, Inês Barroso, Torben Hansen, Helen Cox, Mary Reilly, Alex Rossor, Rebecca J Brown, Simeon I Taylor, Duncan McHale, Martin Armstrong, Elif A Oral, Vladimir Saudek, Stephen I O'Rahilly, Eamonn R Maher, Bjørn Richelsen, David B Savage, Robert K Semple
MFN2 encodes mitofusin 2, a membrane-bound mediator of mitochondrial membrane fusion and inter-organelle communication. MFN2 mutations cause axonal neuropathy, with associated lipodystrophy only occasionally noted, however homozygosity for the p.Arg707Trp mutation was recently associated with upper body adipose overgrowth. We describe similar massive adipose overgrowth with suppressed leptin expression in four further patients with biallelic MFN2 mutations and at least one p.Arg707Trp allele. Overgrown tissue was composed of normal-sized, UCP1-negative unilocular adipocytes, with mitochondrial network fragmentation, disorganised cristae, and increased autophagosomes...
April 17, 2017: ELife
https://www.readbyqxmd.com/read/28409344/tissue-specific-functions-of-p53-during-kidney-development
#7
Zubaida Saifudeen
p53 is best identified as a tumor suppressor for its transcriptional control of genes involved in cell cycle progression and apoptosis. Beyond its irrefutable involvement in restraining unchecked cell proliferation, research over the past several years has indicated a requirement for p53 function in sustaining normal development. Here I summarize the role of p53 in embryonic development, with a focus on knowledge gained from p53 loss and overexpression during kidney development. In contrast to its classical role in suppressing proliferative pathways, p53 positively regulates nephron progenitor cell (NPC) renewal...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/28408751/mmp9-integrates-multiple-immunoregulatory-pathways-that-discriminate-high-suppressive-activity-of-human-mesenchymal-stem-cells
#8
Carolina Lavini-Ramos, Hernandez Moura Silva, Alessandra Soares-Schanoski, Sandra Maria Monteiro, Ludmila Rodrigues Pinto Ferreira, Ana Paula Pacanaro, Samirah Gomes, Janaína Batista, Kellen Faé, Jorge Kalil, Verônica Coelho
The mechanisms underlying mesenchymal stem cells' (MSC) suppressive potency are largely unknown. We here show that highly suppressive human adipose tissue-derived MSC (AdMSC) display and induce a differential immunologic profile, upon ongoing AdMSC suppressive activity, promoting: (i) early correlated inhibition of IFN-γ and TNF-α production, along IL-10 increase, (ii) CD73(+)Foxp3(+)Treg subset expansion, and (iii) specific correlations between gene expression increases, such as: MMP9 correlated with CCL22, TNF, FASL, RUNX3, and SEMAD4 in AdMSC and, in T cells, MMP9 upregulation correlated with CCR4, IL4 and TBX21, among others, whereas MMP2 correlated with BCL2 and LRRC31...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28402863/biotagging-of-specific-cell-populations-in-zebrafish-reveals-gene-regulatory-logic-encoded-in-the-nuclear-transcriptome
#9
Le A Trinh, Vanessa Chong-Morrison, Daria Gavriouchkina, Tatiana Hochgreb-Hägele, Upeka Senanayake, Scott E Fraser, Tatjana Sauka-Spengler
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels...
April 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28396678/identification-of-circular-rnas-in-kiwifruit-and-their-species-specific-response-to-bacterial-canker-pathogen-invasion
#10
Zupeng Wang, Yifei Liu, Dawei Li, Li Li, Qiong Zhang, Shuaibin Wang, Hongwen Huang
Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genus Actinidia under different situations using ribosomal RNA (rRNA) depleted RNA-Seq data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28390980/semi-synthetic-sapogenin-exerts-neuroprotective-effects-by-skewing-the-brain-ischemia-reperfusion-transcriptome-towards-inflammatory-resolution
#11
Laura García-Pupo, Jeney Ramírez Sánchez, Dariusz Ratman, Claudina Pérez-Novo, Ken Declerck, Karolien De Bosscher, Marios Nektarios Markakis, Gerrit Beemster, Armando Zaldo, Yanier Nuñez Figueredo, René Delgado Hernández, Wim Vanden Berghe
Stroke represents one of the first causes of mortality and morbidity worldwide. We evaluated the therapeutic potential of a novel semi-synthetic spirosteroid sapogenin derivative "S15" in a transient middle cerebral artery occlusion (tMCAO) focal ischemia model in rat. S15-treated rats had significantly reduced infarct volumes and improved neurological functions at 24 h post-reperfusion, compared with ischemia. Corresponding gene expression changes in brain were characterized by mRNA sequencing and qPCR approaches...
April 5, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28389669/exploring-functions-of-long-noncoding-rnas-across-multiple-cancers-through-co-expression-network
#12
Suqing Li, Bin Li, Yuanting Zheng, Menglong Li, Leming Shi, Xuemei Pu
In contrast to protein-coding genes, long-noncoding RNAs (lncRNAs) are much less well understood, despite increasing evidence indicating a wide range of their biological functions, and possible roles in various cancers. Based on public RNA-seq datasets of four solid cancer types, we here utilize Weighted Correlation Network Analysis (WGCNA) to propose a strategy for exploring the functions of lncRNAs altered in more than two cancer types, which we call onco-lncRNAs. Results indicate that cancer-expressed lncRNAs show high tissue specificity and are weakly expressed, more so than protein-coding genes...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28388878/medium-term-water-deficit-elicits-distinct-transcriptome-responses-in-eucalyptus-species-of-contrasting-environmental-origin
#13
Antanas V Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
BACKGROUND: Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E...
April 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28388590/integrated-expression-profiles-analysis-reveals-novel-predictive-biomarker-in-pancreatic-ductal-adenocarcinoma
#14
Hongzhe Li, Xinjing Wang, Yuan Fang, Zhen Huo, Xiongxiong Lu, Xi Zhan, Xiaxin Deng, Chenghong Peng, Baiyong Shen
Pancreatic ductal adenocarcinoma (PDAC) is the most lethal human malignant tumor, with a dismal 5-year survival rate of less than 5%. The lack of specific symptoms at early tumor stages and the paucity of biomarkers contribute to the poor diagnosis of pancreatic ductal adenocarcinoma. To improve prognosis, a screening biomarker for early diagnosis of pancreatic cancer is in urgent need. We searched the databases of expression profiling by array on GEO, aiming at comparing gene expression profile of matched pairs of pancreatic tumor and adjacent non-tumor tissues, and we screen out 4 suitable series of gene expression microarray data ("GSE15471", "GSE18670", "GSE28735" and "GSE58561")...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28385952/dieldrin-augments-mtor-signaling-and-inhibits-lysosomal-acidification-in-the-adult-zebrafish-heart-danio-rerio
#15
Logan Slade, Andrew Cowie, Chris J Martynuik, Petra C Kienesberger, Thomas Pulinilkunnil
Dieldrin is a legacy organochlorine pesticide that is persistent in the environment, despite being discontinued from use in North America since the 1970s. Some epidemiological studies suggest that exposure to dieldrin is associated with increased risks of neurodegenerative disease and breast cancer by inducing inflammatory responses in tissues as well as oxidative stress. However, the direct effects of organochlorine pesticides on the heart have not been adequately addressed to date given that these chemicals are detectable in human serum and are environmentally persistent, thus individuals may show latent adverse effects in the cardiovasculature system due to chronic, low dose exposure over time...
April 6, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28380363/polycomb-and-hox-genes-control-jnk-induced-remodeling-of-the-segment-boundary-during-drosophila-morphogenesis
#16
Solange Roumengous, Raphaël Rousset, Stéphane Noselli
In segmented tissues, anterior and posterior compartments represent independent morphogenetic domains, which are made of distinct lineages separated by boundaries. During dorsal closure of the Drosophila embryo, specific "mixer cells" (MCs) are reprogrammed in a JNK-dependent manner to express the posterior determinant engrailed (en) and cross the segment boundary. Here, we show that JNK signaling induces de novo expression of en in the MCs through repression of Polycomb (Pc) and release of the en locus from the silencing PcG bodies...
April 4, 2017: Cell Reports
https://www.readbyqxmd.com/read/28380293/network-analysis-reveals-similar-transcriptomic-responses-to-intrinsic-properties-of-carbon-nanomaterials-in-vitro-and-in-vivo
#17
Pia Kinaret, Veer Marwah, Vittorio Fortino, Marit Ilves, Henrik Wolff, Lasse Ruokolainen, Petri Auvinen, Kai Savolainen, Harri Alenius, Dario Greco
Understanding the complex molecular alterations related to engineered nanomaterial (ENM) exposure is essential for carrying out toxicity assessment. Current experimental paradigms rely both on in vitro and in vivo exposure setups that often are difficult to compare, resulting in questioning the real efficacy of cell models to mimic more complex exposure scenarios at the organism level. Here we have systematically investigated transcriptomic responses of THP-1 macrophage cell line and lung tissues of mice, after exposure to several Carbon nanomaterials (CNM)...
April 5, 2017: ACS Nano
https://www.readbyqxmd.com/read/28379402/slp-2-interacts-with-parkin-in-mitochondria-and-prevents-mitochondrial-dysfunction-in-parkin-deficient-human-ipsc-derived-neurons-and-drosophila
#18
Alessandra Zanon, Sreehari Kalvakuri, Aleksandar Rakovic, Luisa Foco, Marianna Guida, Christine Schwienbacher, Alice Serafin, Franziska Rudolph, Michaela Trilck, Anne Grünewald, Nancy Stanslowsky, Florian Wegner, Valentina Giorgio, Alexandros A Lavdas, Rolf Bodmer, Peter P Pramstaller, Christine Klein, Andrew A Hicks, Irene Pichler, Philip Seibler
Mutations in the Parkin gene (PARK2) have been linked to a recessive form of Parkinson's disease (PD) characterized by the loss of dopaminergic neurons in the substantia nigra. Deficiencies of mitochondrial respiratory chain complex I activity have been observed in the substantia nigra of PD patients, and loss of Parkin results in the reduction of complex I activity shown in various cell and animal models. Using co-immunoprecipitation and proximity ligation assays on endogenous proteins, we demonstrate that Parkin interacts with mitochondrial Stomatin-like protein 2 (SLP-2), which also binds the mitochondrial lipid cardiolipin and functions in the assembly of respiratory chain proteins...
April 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28373358/neurofilaments-and-neurofilament-proteins-in-health-and-disease
#19
REVIEW
Aidong Yuan, Mala V Rao, Veeranna, Ralph A Nixon
SUMMARYNeurofilaments (NFs) are unique among tissue-specific classes of intermediate filaments (IFs) in being heteropolymers composed of four subunits (NF-L [neurofilament light]; NF-M [neurofilament middle]; NF-H [neurofilament heavy]; and α-internexin or peripherin), each having different domain structures and functions. Here, we review how NFs provide structural support for the highly asymmetric geometries of neurons and, especially, for the marked radial expansion of myelinated axons crucial for effective nerve conduction velocity...
April 3, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28373298/mob1-mediated-phospho-recognition-in-the-core-mammalian-hippo-pathway
#20
Amber L Couzens, Shawn Xiong, James Dr Knight, Daniel Y Mao, Sebastian Guettler, Sarah Picaud, Igor Kurinov, Panagis Filippakopoulos, Frank Sicheri, Anne-Claude Gingras
The Hippo tumor suppressor pathway regulates organ size and tissue homoeostasis in response to diverse signaling inputs. The core of the pathway consists of a short kinase cascade: MST1 and MST2 phosphorylate and activate LATS1 and LATS2, which in turn phosphorylate and inactivate key transcriptional co-activators, YAP1 and TAZ (gene WWTR1). The MOB1 adapter protein regulates both phosphorylation reactions firstly by concurrently binding to the upstream MST and downstream LATS kinases to enable the trans phosphorylation reaction, and secondly by allosterically activating the catalytic function of LATS1 and LATS2 to directly stimulate phosphorylation of YAP and TAZ...
April 3, 2017: Molecular & Cellular Proteomics: MCP
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