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Tissue specific gene network

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https://www.readbyqxmd.com/read/28633640/biological-mechanisms-discriminating-growth-rate-and-adult-body-weight-phenotypes-in-two-chinese-indigenous-chicken-breeds
#1
Tengfei Dou, Sumei Zhao, Hua Rong, Dahai Gu, Qihua Li, Ying Huang, Zhiqiang Xu, Xiaohui Chu, Linli Tao, Lixian Liu, Changrong Ge, Marinus F W Te Pas, Junjing Jia
BACKGROUND: Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed...
June 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28633295/long-cold-exposure-induces-transcriptional-and-biochemical-remodelling-of-xylem-secondary-cell-wall-in-eucalyptus
#2
Raphael Ployet, Marçal Soler, Victor Carocha, Nathalie Ladouce, Ana Alves, José-Carlos Rodrigues, Luc Harvengt, Christiane Marque, Chantal Teulières, Jacqueline Grima-Pettenati, Fabien Mounet
Although eucalypts are the most planted hardwood trees worldwide, the majority of them are frost sensitive. The recent creation of frost-tolerant hybrids such as Eucalyptus gundal plants (E. gunnii × E. dalrympleana hybrids), now enables the development of industrial plantations in northern countries. Our objective was to evaluate the impact of cold on the wood structure and composition of these hybrids, and on the biosynthetic and regulatory processes controlling their secondary cell-wall (SCW) formation...
June 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28630873/an-integrative-developmental-genomics-and-systems-biology-approach-to-identify-an-in-vivo-sox-trio-mediated-gene-regulatory-network-in-murine-embryos
#3
Wenqing Jean Lee, Sumantra Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V Sivakamasundari, Hsiao Yun Chan, Prasanna R Kolatkar, Shyam Prabhakar, Thomas Lufkin
Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems biology approach offers to complement the reductionist methodology of current developmental biology and provide a more comprehensive and integrated view of the interrelationships of complex regulatory networks that occur during organogenesis...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28625053/annotation-of-the-domestic-pig-genome-by-quantitative-proteogenomics
#4
Harald Marx, Hannes Hahne, Susanne E Ulbrich, Angelika Schnieke, Oswald Rottmann, Dimitrij Frishman, Bernhard Kuster
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step towards the comprehensive understanding of porcine biology, evolution and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 to 39 days after gestation...
June 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28624497/new-paradigms-for-the-hedgehog-signaling-network-in-mammary-gland-development-and-breast-cancer
#5
REVIEW
Teresa Monkkonen, Michael T Lewis
The Hedgehog signaling network regulates organogenesis, cell fate, proliferation, survival, and stem cell self-renewal in many mammalian tissues. Aberrant activation of the Hedgehog signaling network is present in ~25% of all cancers, including breast. Altered expression of Hedgehog network genes in the mammary gland can elicit phenotypes at many stages of development. However, synthesizing a cohesive mechanistic model of signaling at different stages of development has been difficult. Emerging data suggest that this difficulty is due, in part, to non-canonical and tissue compartment-specific (i...
June 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28620889/levels-of-microrna-heterogeneity-in-cancer-biology
#6
REVIEW
Nina Petrovic, Sercan Ergün, Esma R Isenovic
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression, involved in the silencing of messenger RNA (mRNA) translation. The importance of miRNA signatures in disease screening, prognosis, and progression of different tumor types and subtypes is increasing. miRNA expression levels change depending on numerous factors. In this review, we are describing the circumstances under which miRNA levels can change, these are named 'levels' of heterogeneity of miRNAs. miRNAs can have oncogenic, tumor suppressive, or both roles depending on tumor type and target mRNA whose translation they silence...
June 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28619727/rna-seq-implicates-deregulation-of-the-immune-system-in-the-pathogenesis-of-diverticulitis
#7
Kathleen M Schieffer, Christine S Choi, Scott Emrich, Leonard Harris, Sue Deiling, Dipti M Karamchandani, Anna Salzberg, Yuka I Kawasawa, Gregory S Yochum, Walter A Koltun
Individuals with diverticula or outpouchings of the colonic mucosa and submucosa through the colonic wall have diverticulosis, which is usually asymptomatic. In 10-25% of individuals, the diverticula become inflamed, resulting in diverticulitis. Very little is known about the pathophysiology or gene regulatory pathways involved in the development of diverticulitis. To identify these pathways, we deep sequenced RNAs isolated from full-thickness sections of sigmoid colon from diverticulitis patients and control individuals...
June 15, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28611571/exosomes-and-homeostatic-synaptic-plasticity-are-linked-to-each-other-and-to-huntington-s-parkinson-s-and-other-neurodegenerative-diseases-by-database-enabled-analyses-of-comprehensively-curated-datasets
#8
James K T Wang, Peter Langfelder, Steve Horvath, Michael J Palazzolo
Huntington's disease (HD) is a progressive and autosomal dominant neurodegeneration caused by CAG expansion in the huntingtin gene (HTT), but the pathophysiological mechanism of mutant HTT (mHTT) remains unclear. To study HD using systems biological methodologies on all published data, we undertook the first comprehensive curation of two key PubMed HD datasets: perturbation genes that impact mHTT-driven endpoints and therefore are putatively linked causally to pathogenic mechanisms, and the protein interactome of HTT that reflects its biology...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28608414/use-of-lecithin-to-control-fibre-morphology-in-electrospun-poly-%C3%AE%C2%B5-caprolactone-scaffolds-for-improved-tissue-engineering-applications
#9
Benjamin D M Coverdale, Julie E Gough, William W Sampson, Judith A Hoyland
We elucidate the effects of incorporating surfactants into electrospun poly (ε-caprolactone) (PCL) scaffolds on network homogeneity, cellular adherence and osteogenic differentiation. Lecithin was added with a range of concentrations to PCL solutions, which were electrospun to yield functionalised scaffolds. Addition of lecithin yielded a dose-dependent reduction in scaffold hydrophobicity, whilst reducing fibre width and hence increasing specific surface area. These changes in scaffold morphology were associated with increased cellular attachment of Saos-2 osteoblasts 3-hours post-seeding...
June 12, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28606124/remodeling-adipose-tissue-through-in-silico-modulation-of-fat-storage-for-the-prevention-of-type-2-diabetes
#10
Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof, Rafael J Najmanovich
BACKGROUND: Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is related to increased cardiometabolic risk leading to type 2 diabetes. Studying mechanisms underlying adipocyte hypertrophy could lead to the identification of potential targets for the treatment of these conditions. RESULTS: We present iTC1390adip, a highly curated metabolic network of the human adipocyte presenting various improvements over the previously published iAdipocytes1809...
June 12, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28599291/dna-methylation-signature-of-long-noncoding-rna-genes-during-human-pre-implantation-embryonic-development
#11
Jingyu Li, Wei Han, Xiaoli Shen, Shubiao Han, Hong Ye, Guoning Huang
DNA methylation have crucial roles in regulating the expression of developmental genes during mammalian pre-implantation embryonic development (PED). However, the DNA methylation dynamic pattern of long noncoding RNA (lncRNA) genes, one type of epigenetic regulators, in human PED have not yet been demonstrated. Here, we performed a comprehensive analysis of lncRNA genes in human PED based on public reduced representation bisulphite sequencing (RRBS) data. We observed that both lncRNA and protein-coding genes complete the major demethylation wave at the 2-cell stage, whereas the promoters of lncRNA genes show higher methylation level than protein-coding genes during PED...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28588595/the-role-of-shi-sty-srs-genes-in-organ-growth-and-carpel-development-is-conserved-in-the-distant-eudicot-species-arabidopsis-thaliana-and-nicotiana-benthamiana
#12
Africa Gomariz-Fernández, Verónica Sánchez-Gerschon, Chloé Fourquin, Cristina Ferrándiz
Carpels are a distinctive feature of angiosperms, the ovule-bearing female reproductive organs that endow them with multiple selective advantages likely linked to the evolutionary success of flowering plants. Gene regulatory networks directing the development of carpel specialized tissues and patterning have been proposed based on genetic and molecular studies carried out in Arabidopsis thaliana. However, studies on the conservation/diversification of the elements and the topology of this network are still scarce...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28588354/pax6-binds-to-promoter-sequence-elements-associated-with-immunological-surveillance-and-energy-homeostasis-in-brain-of-aging-mice
#13
Shashank Kumar Maurya, Rajnikant Mishra
BACKGROUND: Patients having mutations of Pax6 bear phenotypes that match age-associated neurological disorders. Mutations affect most cellular functions such as cell division, growth, differentiation, and cell death in brain, eyes, pituitary, pineal, and pancreas. The progressive reduction in the level of Pax6 during aging has also been observed. However, information about downstream targets of Pax6 in brain is unclear. Therefore, it is presumed that age-dependent alterations of Pax6 may also affect cascades of promoter sequence recognition in brain during aging...
May 2017: Annals of Neurosciences
https://www.readbyqxmd.com/read/28588073/brd4-brd2-isoform-switching-coordinates-pluripotent-exit-and-smad2-dependent-lineage-specification
#14
Rosalia Fernandez-Alonso, Lindsay Davidson, Jens Hukelmann, Michael Zengerle, Alan R Prescott, Angus Lamond, Alessio Ciulli, Gopal P Sapkota, Greg M Findlay
Pluripotent stem cells (PSCs) hold great clinical potential, as they possess the capacity to differentiate into fully specialised tissues such as pancreas, liver, neurons and cardiac muscle. However, the molecular mechanisms that coordinate pluripotent exit with lineage specification remain poorly understood. To address this question, we perform a small molecule screen to systematically identify novel regulators of the Smad2 signalling network, a key determinant of PSC fate. We reveal an essential function for BET family bromodomain proteins in Smad2 activation, distinct from the role of Brd4 in pluripotency maintenance...
June 6, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28584125/drosophila-pax6-promotes-development-of-the-entire-eye-antennal-disc-thereby-ensuring-proper-adult-head-formation
#15
Jinjin Zhu, Sneha Palliyil, Chen Ran, Justin P Kumar
Paired box 6 (Pax6) is considered to be the master control gene for eye development in all seeing animals studied so far. In vertebrates, it is required not only for lens/retina formation but also for the development of the CNS, olfactory system, and pancreas. Although Pax6 plays important roles in cell differentiation, proliferation, and patterning during the development of these systems, the underlying mechanism remains poorly understood. In the fruit fly, Drosophila melanogaster, Pax6 also functions in a range of tissues, including the eye and brain...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28583088/uncovering-the-transcriptomic-and-epigenomic-landscape-of-nicotinic-receptor-genes-in-non-neuronal-tissues
#16
Bo Zhang, Pamela Madden, Junchen Gu, Xiaoyun Xing, Savita Sankar, Jennifer Flynn, Kristen Kroll, Ting Wang
BACKGROUND: Nicotinic acetylcholine receptors (nAChRs) play an important role in cellular physiology and human nicotine dependence, and are closely associated with many human diseases including cancer. For example, previous studies suggest that nAChRs can re-wire gene regulatory networks in lung cancer cell lines. However, the tissue specificity of nAChRs genes and their regulation remain unexplored. RESULT: In this study, we integrated data from multiple large genomic consortiums, including ENCODE, Roadmap Epigenomics, GTEx, and FANTOM, to define the transcriptomic and epigenomic landscape of all nicotinic receptor genes across many different human tissues and cell types...
June 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28580277/expression-and-functional-assessment-of-candidate-type-2-diabetes-susceptibility-genes-identify-four-new-genes-contributing-to-human-insulin-secretion
#17
Fatou K Ndiaye, Ana Ortalli, Mickaël Canouil, Marlène Huyvaert, Clara Salazar-Cardozo, Cécile Lecoeur, Marie Verbanck, Valérie Pawlowski, Raphaël Boutry, Emmanuelle Durand, Iandry Rabearivelo, Olivier Sand, Lorella Marselli, Julie Kerr-Conte, Vikash Chandra, Raphaël Scharfmann, Odile Poulain-Godefroy, Piero Marchetti, François Pattou, Amar Abderrahmani, Philippe Froguel, Amélie Bonnefond
OBJECTIVES: Genome-wide association studies (GWAS) have identified >100 loci independently contributing to type 2 diabetes (T2D) risk. However, translational implications for precision medicine and for the development of novel treatments have been disappointing, due to poor knowledge of how these loci impact T2D pathophysiology. Here, we aimed to measure the expression of genes located nearby T2D associated signals and to assess their effect on insulin secretion from pancreatic beta cells...
June 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28575147/tissue-specific-network-based-genome-wide-study-of-amygdala-imaging-phenotypes-to-identify-functional-interaction-modules
#18
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Casey S Greene, Jason H Moore, Andrew J Saykin, Li Shen
Motivation: Network-based genome-wide association studies (GWAS) aim to identify functional modules from biological networks that are enriched by top GWAS findings. Although gene functions are relevant to tissue context, most existing methods analyze tissue-free networks without reflecting phenotypic specificity. Results: We propose a novel module identification framework for imaging genetic studies using the tissue-specific functional interaction network. Our method includes three steps: 1) re-prioritize imaging GWAS findings by applying machine learning methods to incorporate network topological information and enhance the connectivity among top genes; 2) detect densely connected modules based on interactions among top re-prioritized genes; and 3) identify phenotype-relevant modules enriched by top GWAS findings...
May 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575118/comparative-analysis-of-genes-frequently-regulated-by-drugs-based-on-connectivity-map-transcriptome-data
#19
Xinhua Liu, Pan Zeng, Qinghua Cui, Yuan Zhou
Gene expression is perturbated by drugs to different extent. Analyzing genes whose expression is frequently regulated by drugs would be useful for the screening of candidate therapeutic targets and genes implicated in side effect. Here, we obtained the differential expression number (DEN) for genes profiled in Affymetrix microarrays from the Connectivity Map project, and conducted systemic comparative computational analysis between high DEN genes and other genes. Results indicated that genes with higher down-/up-regulation number (down_h/up_h) tended to be clustered in genome, and have lower homologous gene number, higher SNP density and more disease-related SNP...
2017: PloS One
https://www.readbyqxmd.com/read/28562671/integrative-genomic-analyses-for-identification-and-prioritization-of-long-non-coding-rnas-associated-with-autism
#20
Brian L Gudenas, Anand K Srivastava, Liangjiang Wang
Genetic studies have identified many risk loci for autism spectrum disorder (ASD) although causal factors in the majority of cases are still unknown. Currently, known ASD risk genes are all protein-coding genes; however, the vast majority of transcripts in humans are non-coding RNAs (ncRNAs) which do not encode proteins. Recently, long non-coding RNAs (lncRNAs) were shown to be highly expressed in the human brain and crucial for normal brain development. We have constructed a computational pipeline for the integration of various genomic datasets to identify lncRNAs associated with ASD...
2017: PloS One
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