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Tissue specific gene network

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https://www.readbyqxmd.com/read/27899510/identification-and-in-silico-modeling-of-enhancers-reveals-new-features-of-the-cardiac-differentiation-network
#1
Denis Seyres, Yad Ghavi-Helm, Guillaume Junion, Ouarda Taghli-Lamallem, Céline Guichard, Laurence Röder, Charles Girardot, Eileen E M Furlong, Laurent Perrin
Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27898171/hormesis-cellular-stress-response-and-neuroinflammation-in-schizophrenia-early-onset-versus-late-onset-state
#2
REVIEW
Vittorio Calabrese, James Giordano, Rosalia Crupi, Rosanna Di Paola, Martino Ruggieri, Rio Bianchini, Maria Laura Ontario, Salvatore Cuzzocrea, Edward J Calabrese
Abnormal redox homeostasis and oxidative stress have been proposed to play a role in the etiology of several neuropsychiatric spectrum disorders. Emerging interest has recently focused on markers of oxidative stress and neuroinflammation in schizophrenic spectrum disorders, at least in particular subgroups of patients. Altered expression of genes related to oxidative stress, oxidative damage to DNA, protein and lipids, as well as reduced glutathione levels in central and peripheral tissues could act synergistically, and contribute to the course of the disease...
November 29, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27871336/zfas1-a-long-noncoding-rna-associated-with-ribosomes-in-breast-cancer-cells
#3
Herah Hansji, Euphemia Y Leung, Bruce C Baguley, Graeme J Finlay, David Cameron-Smith, Vandre C Figueiredo, Marjan E Askarian-Amiri
BACKGROUND: Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development...
November 21, 2016: Biology Direct
https://www.readbyqxmd.com/read/27867075/sexually-dimorphic-traits-in-the-silkworm-bombyx-mori-are-regulated-by-doublesex
#4
Jun Xu, Shuai Zhan, Shuqing Chen, Baosheng Zeng, Zhiqian Li, Anthony A James, Anjiang Tan, Yongping Huang
The DM domain genes, doublesex (dsx) in insects, or their structural homologs, male abnormal 3 (mab-3) in nematodes and Dmrt1 (doublesex and mab-3-related transcription factor 1) in mammals, are downstream regulators of the sex determination pathway that control sexually dimorphic development. Despite the functional importance of dsx and its potential applications in sterile insect technologies (SITs), the mechanisms by which it controls sexually dimorphic traits and the subsequent developmental gene networks in insects are poorly understood...
November 17, 2016: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27865785/dnmt1-dnmt3a-and-dnmt3b-cooperate-in-photoreceptor-and-outer-plexiform-layer-development-in-the-mammalian-retina
#5
Ratnesh K Singh, Ramya K Mallela, Abigail Hayes, Nicholas R Dunham, Morgan E Hedden, Raymond A Enke, Robert N Fariss, Hal Sternberg, Michael D West, Igor O Nasonkin
Characterizing the role of epigenetic regulation in the mammalian retina is critical for understanding fundamental mechanisms of retinal development and disease. DNA methylation, an epigenetic modifier of genomic DNA, plays an important role in modulating networks of tissue and cell-specific gene expression. However, the impact of DNA methylation during retinal development and homeostasis of retinal neurons remains unclear. Here, we have created a tissue-specific DNA methyltransferase (Dnmt) triple mutant mouse in an effort to characterize the impact of DNA methylation in retinal development and homeostasis...
November 16, 2016: Experimental Eye Research
https://www.readbyqxmd.com/read/27864353/identification-of-clinically-predictive-metagenes-that-encode-components-of-a-network-coupling-cell-shape-to-transcription-by-image-omics
#6
Heba Z Sailem, Chris Bakal
The associations between clinical phenotypes (tumour grade, survival), and cell phenotypes, such as shape, signalling activity, and gene expression, are the basis for cancer pathology; but the mechanisms explaining these relationships are not always clear. The generation of large datasets containing information regarding cell phenotypes, and clinical data, provides an opportunity to describe these mechanisms. Here we develop an image-omics approach to integrate quantitative cell imaging data, gene expression, and protein-protein interaction data to systematically describe a 'shape-gene network' that couples specific aspects of breast cancer cell shape to signalling and transcriptional events...
November 18, 2016: Genome Research
https://www.readbyqxmd.com/read/27863388/comprehensive-analysis-of-aberrantly-expressed-profiles-of-lncrnas-and-mirnas-with-associated-cerna-network-in-muscle-invasive-bladder-cancer
#7
Hanbo Wang, Leilei Niu, Shaobo Jiang, Jing Zhai, Ping Wang, Feng Kong, Xunbo Jin
Although initially thought to be transcriptional noise, long noncoding RNAs (lncRNAs) are gaining increased attention in human cancers as its diversity function. At present, lncRNAs are regarded as the main part of competing endogenous RNA (ceRNA) network due to its regulation on protein-coding gene expression by acting as miRNA sponges. However, functional roles of lncRNA-mediated ceRNAs in muscle-invasive bladder cancer remain unclear. To clarify relevant potential mechanisms, here we comprehensively compared the expression profiles of mRNAs, lncRNAs and miRNAs between 322 muscle-invasive bladder cancer tissues and 19 non-tumor bladder tissues, based on the Cancer Genome Atlas (TCGA)...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27861625/computational-identification-of-tissue-specific-splicing-regulatory-elements-in-human-genes-from-rna-seq-data
#8
Eman Badr, Mahmoud ElHefnawi, Lenwood S Heath
Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs...
2016: PloS One
https://www.readbyqxmd.com/read/27852218/rna-seq-based-transcriptomic-map-reveals-new-insights-into-mouse-salivary-gland-development-and-maturation
#9
Christian Gluck, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose-Anne Romano
BACKGROUND: Mouse models have served a valuable role in deciphering various facets of Salivary Gland (SG) biology, from normal developmental programs to diseased states. To facilitate such studies, gene expression profiling maps have been generated for various stages of SG organogenesis. However these prior studies fall short of capturing the transcriptional complexity due to the limited scope of gene-centric microarray-based technology. Compared to microarray, RNA-sequencing (RNA-seq) offers unbiased detection of novel transcripts, broader dynamic range and high specificity and sensitivity for detection of genes, transcripts, and differential gene expression...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27851958/alternative-splicing-of-four-trafficking-genes-regulates-myofiber-structure-and-skeletal-muscle-physiology
#10
Jimena Giudice, James A Loehr, George G Rodney, Thomas A Cooper
During development, transcriptional and post-transcriptional networks are coordinately regulated to drive organ maturation. Alternative splicing contributes by producing temporal-specific protein isoforms. We previously found that genes undergoing splicing transitions during mouse postnatal heart development are enriched for vesicular trafficking and membrane dynamics functions. Here, we show that adult trafficking isoforms are also expressed in adult skeletal muscle and hypothesize that striated muscle utilizes alternative splicing to generate specific isoforms required for function of adult tissue...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27846841/integrative-transcriptome-network-analysis-of-ipsc-derived-neurons-from-schizophrenia-and-schizoaffective-disorder-patients-with-22q11-2-deletion
#11
Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R Puliafito, Stephanie R Gilbert, Deyou Zheng, Herbert M Lachman
BACKGROUND: Individuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in the deleted region have been implicated in the development of SZ, e.g., PRODH and DGCR8. However, the mechanistic connection between these genes and the neuropsychiatric phenotype remains unclear. To elucidate the molecular consequences of 22q11.2 deletion in early neural development, we carried out RNA-seq analysis to investigate gene expression in early differentiating human neurons derived from induced pluripotent stem cells (iPSCs) of 22q11...
November 15, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27846716/-mechanisms-of-protein-homeostasis-regulation-in-cancer-development
#12
F Trčka, P Müller, B Vojtěšek
BACKGROUND: The proteome of eukaryotic cells represents a complex system. Its components are exposed to various intrinsic and extrinsic stresses. Therefore, the function of the cellular proteome is dependent on the existence of compensatory mechanisms balancing the inner protein homeostasis - proteostasis. These mechanisms involve the network of molecular chaperones and transcriptional program regulating their expression. The process of cancerogenesis is accompanied by significant changes in the intracellular milieu of cancer cells - temperature, pH, availability of nutrients...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/27835598/snhg8-is-identified-as-a-key-regulator-of-epstein-barr-virus-ebv-associated-gastric-cancer-by-an-integrative-analysis-of-lncrna-and-mrna-expression
#13
Tao Huang, Yan Ji, Dan Hu, Baozheng Chen, Hejun Zhang, Chao Li, Gang Chen, Xingguang Luo, Xiong-Wei Zheng, Xiandong Lin
The Epstein-Barr virus (EBV) is associated with a variety of cancers, including gastric cancer, which has one of the highest mortality rates of all human cancers. Long non-coding RNAs (lncRNAs) have been suggested to have important causal roles in gastric cancer. However, the interaction between lncRNAs and EBV has not yet been studied. To this end, we sequenced 11,311 lncRNAs and 144,826 protein-coding transcripts from four types of tissue: one non-EBV-infected gastric carcinoma (EBVnGC) and its adjacent normal tissue, and one EBV-associated gastric carcinoma (EBVaGC) and its adjacent normal tissue...
November 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27833659/identification-of-activated-enhancers-and-linked-transcription-factors-in-breast-prostate-and-kidney-tumors-by-tracing-enhancer-networks-using-epigenetic-traits
#14
Suhn Kyong Rhie, Yu Guo, Yu Gyoung Tak, Lijing Yao, Hui Shen, Gerhard A Coetzee, Peter W Laird, Peggy J Farnham
BACKGROUND: Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27833589/systemic-approach-to-virulence-gene-network-analysis-for-gaining-new-insight-into-cryptococcal-virulence
#15
Antoni N Malachowski, Mohamed Yosri, Goun Park, Yong-Sun Bahn, Yongqun He, Michal A Olszewski
Cryptococcus neoformans is pathogenic yeast, responsible for highly lethal infections in compromised patients around the globe. C. neoformans typically initiates infections in mammalian lung tissue and subsequently disseminates to the central nervous system where it causes significant pathologies. Virulence genes of C. neoformans are being characterized at an increasing rate, however, we are far from a comprehensive understanding of their roles and genetic interactions. Some of these reported virulence genes are scattered throughout different databases, while others are not yet included...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27831464/a-network-of-epigenetic-modifiers-and-dna-repair-genes-controls-tissue-specific-copy-number-alteration-preference
#16
Dina Cramer, Luis Serrano, Martin H Schaefer
Copy number alterations (CNAs) in cancer patients show a large variability in their number, length and position, but the sources of this variability are not known. CNA number and length are linked to patient survival, suggesting clinical relevance. We have identified genes that tend to be mutated in samples that have few or many CNAs, which we term CONIM genes (COpy Number Instability Modulators). CONIM proteins cluster into a densely connected subnetwork of physical interactions and many of them are epigenetic modifiers...
November 10, 2016: ELife
https://www.readbyqxmd.com/read/27829360/disease-gene-prioritization-by-integrating-tissue-specific-molecular-networks-using-a-robust-multi-network-model
#17
Jingchao Ni, Mehmet Koyuturk, Hanghang Tong, Jonathan Haines, Rong Xu, Xiang Zhang
BACKGROUND: Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity network and molecular networks such as protein interaction or gene co-expression networks. Although successful, a common limitation of the existing methods is that they assume all diseases share the same molecular network and a single generic molecular network is used to predict candidate genes for all diseases...
November 10, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27828940/different-tissue-phagocytes-sample-apoptotic-cells-to-direct-distinct-homeostasis-programs
#18
Ryan J Cummings, Gaetan Barbet, Gerold Bongers, Boris M Hartmann, Kyle Gettler, Luciana Muniz, Glaucia C Furtado, Judy Cho, Sergio A Lira, J Magarian Blander
Recognition and removal of apoptotic cells by professional phagocytes, including dendritic cells and macrophages, preserves immune self-tolerance and prevents chronic inflammation and autoimmune pathologies. The diverse array of phagocytes that reside within different tissues, combined with the necessarily prompt nature of apoptotic cell clearance, makes it difficult to study this process in situ. The full spectrum of functions executed by tissue-resident phagocytes in response to homeostatic apoptosis, therefore, remains unclear...
November 9, 2016: Nature
https://www.readbyqxmd.com/read/27825118/amplification-of-muc1-in-prostate-cancer-metastasis-and-crpc-development
#19
Nicholas Wong, Pierre Major, Anil Kapoor, Fengxiang Wei, Judy Yan, Tariq Aziz, Mingxing Zheng, Dulitha Jayasekera, Jean-Claude Cutz, Mathilda Jing Chow, Damu Tang
Evidence supports the upregulation of MUC1 in prostate cancer (PC). However, this has not been thoroughly investigated. We report here an association of MUC1 upregulation with PC metastasis and the development of castration resistant PC (CRPC). MUC1 expression was specifically increased in DU145 cell-derived PC stem-like cells (PCSLCs) in comparison to their non-PCSLCs counterparts. While immunohistochemistry staining of 34 primary PCs revealed variability in MUC1 expression, Nanostring technology demonstrated elevated MUC1 mRNA levels in 4 of 7 PCs compared to their normal matched tissues...
November 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27822416/hydroxyl-hif2-alpha-is-potential-therapeutic-target-for-renal-cell-carcinomas
#20
Takahiro Isono, Tokuhiro Chano, Tetsuya Yoshida, Susumu Kageyama, Akihiro Kawauchi, Masafumi Suzaki, Takeshi Yuasa
Dormant cancer cells are deprivation-resistant, and cause a number of problems for therapeutic approaches for cancers. Renal cell carcinomas (RCCs) include deprivation-resistant cells that are resistant to various treatments. In this study, the specific characteristics of deprivation-resistant cells were transcriptionally identified by next generation sequencing. The hypoxia-inducible factors (HIF) transcription factor network was significantly enhanced in deprivation-resistant RCCs compared to the sensitive RCCs...
2016: American Journal of Cancer Research
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