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Tissue specific gene network

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https://www.readbyqxmd.com/read/28527696/essential-roles-of-g9a-in-cell-proliferation-and-differentiation-during-tooth-development
#1
Taichi Kamiunten, Hisashi Ideno, Akemi Shimada, Yoshinori Arai, Tatsuo Terashima, Yasuhiro Tomooka, Yoshiki Nakamura, Kazuhisa Nakashima, Hiroshi Kimura, Yoichi Shinkai, Makoto Tachibana, Akira Nifuji
Teeth develop through interactions between epithelial and mesenchymal tissues mediated by a signaling network comprised of growth factors and transcription factors However, little is known about how epigenetic modifiers affect signaling pathways and thereby regulate tooth formation. We previously reported that the histone 3 lysine 9 (H3K9) methyltransferase (MTase) G9a is specifically enriched in the tooth mesenchyme during mouse development. In this study, we investigated the functions of G9a in tooth development using G9a conditional knockout (KO) mice...
May 17, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28520732/differential-gene-expression-along-the-animal-vegetal-axis-in-the-ascidian-embryo-is-maintained-by-a-dual-functional-protein-foxd
#2
Shin-Ichi Tokuhiro, Miki Tokuoka, Kenji Kobayashi, Atsushi Kubo, Izumi Oda-Ishii, Yutaka Satou
In many animal embryos, a specific gene expression pattern is established along the animal-vegetal axis soon after zygotic transcription begins. In the embryo of the ascidian Ciona intestinalis, soon after the division that separates animal and vegetal hemispheres into distinct blastomeres, maternal Gata.a and β-catenin activate specific genes in the animal and vegetal blastomeres, respectively. On the basis of these initial distinct gene expression patterns, gene regulatory networks promote animal cells to become ectodermal tissues and vegetal cells to become endomesodermal tissues and a part of the nerve cord...
May 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#3
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
May 17, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28504698/dendritic-cells-enter-lymph-vessels-by-hyaluronan-mediated-docking-to-the-endothelial-receptor-lyve-1
#4
Louise A Johnson, Suneale Banerji, William Lawrance, Uzi Gileadi, Gennaro Prota, Kayla A Holder, Yaowaluck M Roshorm, Tomáš Hanke, Vincenzo Cerundolo, Nicholas W Gale, David G Jackson
Trafficking of tissue dendritic cells (DCs) via lymph is critical for the generation of cellular immune responses in draining lymph nodes (LNs). In the current study we found that DCs docked to the basolateral surface of lymphatic vessels and transited to the lumen through hyaluronan-mediated interactions with the lymph-specific endothelial receptor LYVE-1, in dynamic transmigratory-cup-like structures. Furthermore, we show that targeted deletion of the gene Lyve1, antibody blockade or depletion of the DC hyaluronan coat not only delayed lymphatic trafficking of dermal DCs but also blunted their capacity to prime CD8(+) T cell responses in skin-draining LNs...
May 15, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28501625/circular-rnas-roll-into-the-regulatory-network-of-plants
#5
Quan-Feng Li, Yu-Chan Zhang, Yue-Qin Chen, Yang Yu
As a novel class of endogenous non-coding RNAs, circular RNAs (circRNAs) have become a new research hotspot in recent years. The wide distribution of circRNAs in different plant species has been proven. Furthermore, circRNAs show significant tissue-specific expression patterns in plant development and are responsive to a variety of biotic and abiotic stresses, indicating that circRNAs might have important biological functions in plant development. Here, we summarize the current knowledge of plant circRNAs in recent years and discuss views and perspectives on the possible regulatory roles of plant circRNAs, including the function of miRNA sponges, regulating the expression of their parental genes or linear mRNAs, translating into peptides or proteins and responses to different stresses...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28499866/identification-and-characterization-of-novel-lncrnas-in-arabidopsis-thaliana
#6
Zhaogeng Lu, Xiao Xia, Bei Jiang, Kaibiao Ma, Likui Zhu, Li Wang, Biao Jin
Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation...
May 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28498428/differential-expression-profiles-of-micrornas-as-potential-biomarkers-for-the-early-diagnosis-of-lung-cancer
#7
Yanqiu Zhang, Jing Sui, Xian Shen, Chengyun Li, Wenzhuo Yao, Weiwei Hong, Hui Peng, Yuepu Pu, Lihong Yin, Geyu Liang
Lung cancer is one of the most lethal malignancies worldwide. To reduce the high morbidity and mortality of the disease, sensitive and specific biomarkers for early detection are urgently needed. Tumor-specific microRNAs (miRNAs) seem to be potential biomarkers for the early diagnosis and treatment of cancer. In this study, the microarray of miRNAs and mRNAs on the same samples was performed and the intersection taken with The Cancer Genome Atlas (TCGA) lung cancer miRNA/RNAseq dataset. Then, miRNA-mRNA regulatory network was constructed to identify miRNA candidates associated with lung cancer through integrating gene expression and miRNA-target prediction...
April 28, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28490757/transcriptome-and-metabolite-analysis-identifies-nitrogen-utilization-genes-in-tea-plant-camellia-sinensis
#8
Wei Li, Fen Xiang, Micai Zhong, Lingyun Zhou, Hongyan Liu, Saijun Li, Xuewen Wang
Applied nitrogen (N) fertilizer significantly increases the leaf yield. However, most N is not utilized by the plant, negatively impacting the environment. To date, little is known regarding N utilization genes and mechanisms in the leaf production. To understand this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (Camellia sinensis), the most popular beverage crop. We identified 196 and 29 common differentially expressed genes in roots and leaves, respectively, in response to ammonium in two tea varieties...
May 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28485080/pelp1-a-key-mediator-of-estrogen-signaling-and-actions-in-the-brain
#9
REVIEW
Roshni Thakkar, Gangadhara Reddy Sareddy, Quanguang Zhang, Ruimin Wang, Ratna K Vadlamudi, Darrell Brann
Proline-, Glutamic acid-, and Leucine-rich Protein 1 (PELP1) is an estrogen receptor (ER) coregulator protein identified by our collaborative group. Work from our lab and others has shown that PELP1 is a scaffold protein that interacts with ERs, kinase signaling factors, as well as proteins involved in chromatin remodeling and DNA repair. Its role in mediating 17β-Estradiol (E2) signaling and actions has been heavily studied in cancer cells, but only recently has attention turned to its role in the brain. In this review, we discuss the tissue, cellular and subcellular localization of PELP1 in the brain...
May 9, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/28477009/identification-of-the-mirna-mrna-regulatory-network-of-small-cell-osteosarcoma-based-on-rna-seq
#10
Lin Xie, Yedan Liao, Lida Shen, Fengdi Hu, Sunlin Yu, Yonghong Zhou, Ya Zhang, Yihao Yang, Dongqi Li, Minyan Ren, Zhongqin Yuan, Zuozhang Yang
Small cell osteosarcoma (SCO) is a rare subtype of osteosarcoma characterized by highly aggressive progression and a poor prognosis. The miRNA and mRNA expression profiles of peripheral blood mononuclear cells (PBMCs) were obtained in 3 patients with SCO and 10 healthy individuals using high-throughput RNA-sequencing. We identified 37 dysregulated miRNAs and 1636 dysregulated mRNAs in patients with SCO compared to the healthy controls. Specifically, the 37 dysregulated miRNAs consisted of 27 up-regulated miRNAs and 10 down-regulated miRNAs; the 1636 dysregulated mRNAs consisted of 555 up-regulated mRNAs and 1081 down-regulated mRNAs...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28473845/pancreatic-islet-protein-complexes-and-their-dysregulation-in-type-2-diabetes
#11
Helle Krogh Pedersen, Valborg Gudmundsdottir, Søren Brunak
Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential to unveil the full potential of person-specific profiles...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28469556/integrative-analysis-of-brain-region-specific-shank3-interactomes-for-understanding-the-heterogeneity-of-neuronal-pathophysiology-related-to-shank3-mutations
#12
Yeunkum Lee, Hyojin Kang, Bokyoung Lee, Yinhua Zhang, Yoonhee Kim, Shinhyun Kim, Won-Ki Kim, Kihoon Han
Recent molecular genetic studies have identified 100s of risk genes for various neurodevelopmental and neuropsychiatric disorders. As the number of risk genes increases, it is becoming clear that different mutations of a single gene could cause different types of disorders. One of the best examples of such a gene is SHANK3, which encodes a core scaffold protein of the neuronal excitatory post-synapse. Deletions, duplications, and point mutations of SHANK3 are associated with autism spectrum disorders, intellectual disability, schizophrenia, bipolar disorder, and attention deficit hyperactivity disorder...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28466185/tissue-specific-transcription-of-the-neuronal-gene-lim3-affects-drosophila-melanogaster-lifespan-and-locomotion
#13
Olga Y Rybina, Svetlana V Sarantseva, Ekaterina R Veselkina, Olga I Bolschakova, Alexander V Symonenko, Anna V Krementsova, Elena V Ryabova, Natalia V Roshina, Elena G Pasyukova
The identity of neuronal cell types is established and maintained by the expression of neuronal genes coding for ion channels, neurotransmitters, and neuropeptides, among others. Some of these genes have been shown to affect lifespan; however, their role in lifespan control remains largely unclear. The Drosophila melanogaster gene Lim3 encodes a transcription factor involved in complicated motor neuron specification networks. We previously identified Lim3 as a candidate gene affecting lifespan. To obtain direct evidence of the involvement of Lim3 in lifespan control, Lim3 overexpression and RNAi knockdown were induced in the nervous system and muscles of Drosophila using the GAL4-UAS binary system...
May 2, 2017: Biogerontology
https://www.readbyqxmd.com/read/28459834/genome-wide-analysis-of-rice-dehydrin-gene-family-its-evolutionary-conservedness-and-expression-pattern-in-response-to-peg-induced-dehydration-stress
#14
Giti Verma, Yogeshwar Vikram Dhar, Dipali Srivastava, Maria Kidwai, Puneet Singh Chauhan, Sumit Kumar Bag, Mehar Hasan Asif, Debasis Chakrabarty
Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28457792/a-gene-regulatory-network-balances-neural-and-mesoderm-specification-during-vertebrate-trunk-development
#15
Mina Gouti, Julien Delile, Despina Stamataki, Filip J Wymeersch, Yali Huang, Jens Kleinjung, Valerie Wilson, James Briscoe
Transcriptional networks, regulated by extracellular signals, control cell fate decisions and determine the size and composition of developing tissues. One example is the network controlling bipotent neuromesodermal progenitors (NMPs) that fuel embryo elongation by generating spinal cord and trunk mesoderm tissue. Here, we use single-cell transcriptomics to identify the molecular signature of NMPs and reverse engineer the mechanism that regulates their differentiation. Together with genetic perturbations, this reveals a transcriptional network that integrates opposing retinoic acid (RA) and Wnt signals to determine the rate at which cells enter and exit the NMP state...
May 8, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28448485/assessment-of-engineered-cells-using-cellnet-and-rna-seq
#16
Arthur H Radley, Remy M Schwab, Yuqi Tan, Jeesoo Kim, Emily K W Lo, Patrick Cahan
CellNet is a computational platform designed to assess cell populations engineered by either directed differentiation of pluripotent stem cells (PSCs) or direct conversion, and to suggest specific hypotheses to improve cell fate engineering protocols. CellNet takes as input gene expression data and compares them with large data sets of normal expression profiles compiled from public sources, in regard to the extent to which cell- and tissue-specific gene regulatory networks are established. CellNet was originally designed to work with human or mouse microarray expression data for 21 cell or tissue (C/T) types...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28446913/de-novo-transcriptome-analysis-of-miscanthus-lutarioriparius-identifies-candidate-genes-in-rhizome-development
#17
Ruibo Hu, Changjiang Yu, Xiaoyu Wang, Chunlin Jia, Shengqiang Pei, Kang He, Guo He, Yingzhen Kong, Gongke Zhou
HIGHLIGHTDe novo transcriptome profiling of five tissues reveals candidate genes putatively involved in rhizome development in M. lutarioriparius. Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28438184/microbiota-activated-cd103-dcs-stemming-from-microbiota-adaptation-specifically-drive-%C3%AE-%C3%AE-t17-proliferation-and-activation
#18
Chris Fleming, Yihua Cai, Xuan Sun, Venkatakrishna R Jala, Feng Xue, Samantha Morrissey, Yu-Ling Wei, Yueh-Hsiu Chien, Huang-Ge Zhang, Bodduluri Haribabu, Jian Huang, Jun Yan
BACKGROUND: IL-17-producing γδT cells (γδT17) promote autoinflammatory diseases and cancers. Yet, γδT17 peripheral regulation has not been thoroughly explored especially in the context of microbiota-host interaction. The potent antigen-presenting CD103(+) dendritic cell (DC) is a key immune player in close contact with both γδT17 cells and microbiota. This study presents a novel cellular network among microbiota, CD103(+) DCs, and γδT17 cells. METHODS: Immunophenotyping of IL-17r(-/-) mice and IL-17r(-/-) IRF8(-/-) mice were performed by ex vivo immunostaining and flow cytometric analysis...
April 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28436429/human-fetal-heart-specific-coexpression-network-involves-congenital-heart-disease-defect-candidate-genes
#19
Bo Wang, Guoling You, Qihua Fu
Heart development is a complex process requiring dynamic transcriptional regulation. Disturbance of this process will lead to severe developmental defects such as congenital heart disease/defect (CHD). CHD is a group of complex disorder with high genetic heterogeneity, common pathways associated with CHD remains largely unknown. In the manuscript, we focused on the tissue specific genes in human fetal heart samples to explore such pathways. We used the RNA microarray dataset of human fetal tissues from ENCODE project to identify genes with heart tissue specific expression...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28434945/prognostic-biomarker-identification-through-integrating-the-gene-signatures-of-hepatocellular-carcinoma-properties
#20
Jialin Cai, Bin Li, Yan Zhu, Xuqian Fang, Mingyu Zhu, Mingjie Wang, Shupeng Liu, Xiaoqing Jiang, Jianming Zheng, XinXin Zhang, Peizhan Chen
Many molecular classification and prognostic gene signatures for hepatocellular carcinoma (HCC) patients have been established based on genome-wide gene expression profiling; however, their generalizability is unclear. Herein, we systematically assessed the prognostic effects of these gene signatures and identified valuable prognostic biomarkers by integrating these gene signatures. With two independent HCC datasets (GSE14520, N=242 and GSE54236, N=78), 30 published gene signatures were evaluated, and 11 were significantly associated with the overall survival (OS) of postoperative HCC patients in both datasets...
April 12, 2017: EBioMedicine
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