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Tissue specific gene network

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https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#1
Haoyang Zeng, David K Gifford
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331574/microrna-and-thyroid-hormone-signaling-in-cardiac-and-skeletal-muscle
#2
REVIEW
Duo Zhang, Yan Li, Shengnan Liu, Yu-Cheng Wang, Feifan Guo, Qiwei Zhai, Jingjing Jiang, Hao Ying
Thyroid hormone (TH) signaling plays critical roles in the differentiation, growth, metabolism, and physiological function of all organs or tissues, including heart and skeletal muscle. Due to the significant progress in our understanding of the molecular mechanisms that underlie TH action, it's widely accepted that TH signaling is regulated at multiple levels. A growing number of discoveries suggest that microRNAs (miRNAs) act as fine-tune regulators of gene expression and adds sophisticated regulatory tiers to signaling pathways...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28330499/a-novel-multi-network-approach-reveals-tissue-specific-cellular-modulators-of-fibrosis-in-systemic-sclerosis
#3
Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy B Christmann, Harrison W Farber, Robert A Lafyatis, Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J Matthew Mahoney, Michael L Whitfield
BACKGROUND: Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. METHODS: We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues...
March 23, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#4
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28319331/morphogen-interpretation-concentration-time-competence-and-signaling-dynamics
#5
REVIEW
Andreas Sagner, James Briscoe
Tissue patterning during animal development is orchestrated by a handful of inductive signals. Most of these developmental cues act as morphogens, meaning they are locally produced secreted molecules that act at a distance to govern tissue patterning. The iterative use of the same signaling molecules in different developmental contexts demands that signal interpretation occurs in a highly context-dependent manner. Hence the interpretation of signal depends on the specific competence of the receiving cells. Moreover, it has become clear that the differential interpretation of morphogens depends not only on the level of signaling but also the signaling dynamics, particularly the duration of signaling...
March 20, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28319090/a-single-copy-sleeping-beauty-transposon-mutagenesis-screen-identifies-new-pten-cooperating-tumor-suppressor-genes
#6
Jorge de la Rosa, Julia Weber, Mathias Josef Friedrich, Yilong Li, Lena Rad, Hannes Ponstingl, Qi Liang, Sandra Bernaldo de Quirós, Imran Noorani, Emmanouil Metzakopian, Alexander Strong, Meng Amy Li, Aurora Astudillo, María Teresa Fernández-García, María Soledad Fernández-García, Gary J Hoffman, Rocío Fuente, George S Vassiliou, Roland Rad, Carlos López-Otín, Allan Bradley, Juan Cadiñanos
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor suppressors. Toward this aim, we coupled mobilization of a single-copy inactivating Sleeping Beauty transposon to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared data sets of known and candidate genes involved in cancer...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28317894/swim-a-computational-tool-to-unveiling-crucial-nodes-in-complex-biological-networks
#7
Paola Paci, Teresa Colombo, Giulia Fiscon, Aymone Gurtner, Giulio Pavesi, Lorenzo Farina
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302318/regional-differences-of-tibial-and-femoral-cartilage-in-the-chondrocyte-gene-expression-immunhistochemistry-and-composite-in-different-stages-of-osteoarthritis
#8
A Lahm, D Dabravolski, H Spank, H Merk, J Esser, R Kasch
The function of articular cartilage as an avascular tissue is mainly served by collagen type II and proteoglycan molecules. Within this matrix homeostasis between production and breakdown of the matrix is exceptionally sensitive. The current study was conducted to identify regional differences in specific alterations in cartilage composition during the osteoarthritic process of the human knee joint. Therefor the changes in the expression of the key molecules of the extracellular matrix were measured in dependence of the anatomical side (femoral vs tibial) and associated with immunohistochemistry and quantitative measurement...
February 24, 2017: Tissue & Cell
https://www.readbyqxmd.com/read/28295365/comparative-transcriptome-analysis-of-isogenic-cell-line-models-and-primary-cancers-links-cic-loss-to-activation-of-the-mapk-signalling-cascade
#9
Veronique G LeBlanc, Marlo Firme, Jungeun Song, Susanna Y Chan, Min Hye Lee, Stephen Yip, Suganthi Chittaranjan, Marco A Marra
CIC encodes a transcriptional repressor whose disrupted activity appears to be involved in several cancer types, including Type I low-grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results to analyses of transcriptome data from TCGA for Type I LGGs and STADs...
March 15, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28283057/super-enhancer-mediated-rna-processing-revealed-by-integrative-microrna-network-analysis
#10
Hiroshi I Suzuki, Richard A Young, Phillip A Sharp
Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28279183/circles-reshaping-the-rna-world-from-waste-to-treasure
#11
REVIEW
Jing Liu, Tian Liu, Xiaman Wang, Aili He
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions...
March 9, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28272987/opposing-functions-of-h2bk120-ubiquitylation-and-h3k79-methylation-in-the-regulation-of-pluripotency-by-the-paf1-complex
#12
Alexandros Strikoudis, Charalampos Lazaris, Panagiotis Ntziachristos, Aristotelis Tsirigos, Iannis Aifantis
Maintenance of stem cell plasticity is determined by the ability to balance opposing forces that control gene expression. Regulation of transcriptional networks, signaling cues and chromatin-modifying mechanisms constitute crucial determinants of tissue equilibrium. Histone modifications can affect chromatin compaction, therefore co-transcriptional events that influence their deposition determine the propensities towards quiescence, self-renewal, or cell specification. The Paf1 complex (Paf1C) is a critical regulator of RNA PolII elongation that controls gene expression and deposition of histone modifications, however few studies have focused on its role affecting stem cell fate decisions...
March 8, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28272493/effects-of-different-kinds-of-essentiality-on-sequence-evolution-of-human-testis-proteins
#13
Julia Schumacher, Hans Zischler, Holger Herlyn
We asked if essentiality for either fertility or viability differentially affects sequence evolution of human testis proteins. Based on murine knockout data, we classified a set of 965 proteins expressed in human seminiferous tubules into three categories: proteins essential for prepubertal survival ("lethality proteins"), associated with male sub- or infertility ("male sub-/infertility proteins"), and nonessential proteins. In our testis protein dataset, lethality genes evolved significantly slower than nonessential and male sub-/infertility genes, which is in line with other authors' findings...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28268898/a-large-scale-detailed-neuronal-model-of-electrical-stimulation-of-the-dentate-gyrus-and-perforant-path-as-a-platform-for-electrode-design-and-optimization
#14
Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger
Owing to the dramatic rise in treatment of neurological disorders with electrical micro-stimulation it has become apparent that the major technological limitation in deploying effective devices lies in the process of designing efficient, safe, and outcome specific electrode arrays. The time-consuming and low-fidelity nature of gathering test data using experimental means and the immense control and flexibility of computational models, has prompted us and others to build models of electrical stimulation of neural networks that can be simulated in a computer...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28266556/integrative-diffusion-weighted-imaging-and-radiogenomic-network-analysis-of-glioblastoma-multiforme
#15
Dieter Henrik Heiland, Carl Philipp Simon-Gabriel, Theo Demerath, Gerrit Haaker, Dietmar Pfeifer, Elias Kellner, Valerij G Kiselev, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
In the past, changes of the Apparent Diffusion Coefficient in glioblastoma multiforme have been shown to be related to specific genes and described as being associated with survival. The purpose of this study was to investigate diffusion imaging parameters in combination with genome-wide expression data in order to obtain a comprehensive characterisation of the transcriptomic changes indicated by diffusion imaging parameters. Diffusion-weighted imaging, molecular and clinical data were collected prospectively in 21 patients...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265057/auxin-response-cell-autonomously-controls-ground-tissue-initiation-in-the-early-arabidopsis-embryo
#16
Barbara K Möller, Colette A Ten Hove, Daoquan Xiang, Nerys Williams, Lorena González López, Saiko Yoshida, Margot Smit, Raju Datla, Dolf Weijers
Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28264977/constant-light-desynchronises-olfactory-versus-object-and-visuospatial-recognition-memory-performance
#17
Shu K E Tam, Sibah Hasan, Harry M C Choi, Laurence A Brown, Aarti Jagannath, Steven Hughes, Mark W Hankins, Russell G Foster, Vladyslav V Vyazovskiy, David M Bannerman, Stuart N Peirson
Circadian rhythms optimise physiology and behaviour to the varying demands of the 24-hour day. The master circadian clock is located in the suprachiasmatic nuclei (SCN) of the hypothalamus and it regulates circadian oscillators in tissues throughout the body to prevent internal desynchrony. Here we demonstrate for the first time that, under standard 12-h:12-h light--dark cycles (LD), object, visuospatial, and olfactory recognition performance in C57BL/6J mice is consistently better at midday relative to midnight...
March 6, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28262971/the-opportunity-of-precision-medicine-for-breast-cancer-with-context-sensitive-tumor-suppressor-maspin
#18
Margarida M Bernardo, Sijana H Dzinic, Maria J Matta, Ivory Dean, Lina Saker, Shijie Sheng
To improve the precision of molecular diagnosis and to develop and guide targeted therapies of breast cancer, it is essential to determine the mechanisms that underlie the specific tumor phenotypes. To this end, the application of a snapshot of gene expression profile for breast cancer diagnosis and prognosis is fundamentally challenged since the tissue-based data are derived from heterogonous cell types and are not likely to reflect the dynamics of context-dependent tumor progression and drug sensitivity. The intricate network of epithelial differentiation program can be concertedly controlled by tumor suppressor maspin, a homologue of clade B serine protease inhibitors (serpin), through its multifaceted molecular interactions in multiple subcellular localizations...
March 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28261234/phytophthora-megakarya-and-p-palmivora-causal-agents-of-black-pod-rot-induce-similar-plant-defense-responses-late-during-infection-of-susceptible-cacao-pods
#19
Shahin S Ali, Jonathan Shao, David J Lary, Mary D Strem, Lyndel W Meinhardt, Bryan A Bailey
Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) cause black pod rot of Theobroma cacao L. (cacao). Of these two clade 4 species, Pmeg is more virulent and is displacing Ppal in many cacao production areas in Africa. Symptoms and species specific sporangia production were compared when the two species were co-inoculated onto pod pieces in staggered 24 h time intervals. Pmeg sporangia were predominantly recovered from pod pieces with unwounded surfaces even when inoculated 24 h after Ppal. On wounded surfaces, sporangia of Ppal were predominantly recovered if the two species were simultaneously applied or Ppal was applied first but not if Pmeg was applied first...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28254881/the-cell-specificity-of-gene-expression-in-the-response-to-heat-stress-in-corals
#20
N Traylor-Knowles, N H Rose, S R Palumbi
Previous transcriptional studies in heat stressed corals have shown that many genes are responsive to generalized heat stress whereas the expression patterns of specific gene networks after heat stress show strong correlations with variation in bleaching outcomes. However, where these specific genes are expressed is unknown. Here we employed in situ hybridization to identify patterns of spatial gene expression of genes previously predicted to be involved in general stress response and bleaching. We found that Tumor Necrosis Factor Receptors (TNFRs), known to be strong responders to heat stress, were not expressed in gastrodermal symbiont-containing cells but were widely expressed in specific cells of the epidermal layer...
March 2, 2017: Journal of Experimental Biology
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