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https://www.readbyqxmd.com/read/27910098/gata-3-specific-dnazyme-a-novel-approach-for-stratified-asthma-therapy
#1
REVIEW
Holger Garn, Harald Renz
It is now well established that type-2 immune mechanisms drive the inflammation in about 50% of asthma patients. The major cellular and molecular players regulating this important network have been identified. In terms of therapeutic intervention, cytokine and cytokine-receptor pathways have been given major attention, since these molecules are relatively easily accessible for a blockade through monoclonal antibodies, and a number of positive clinical results support this concept. However, targeting events controlling the type-2 immunity network upstream of selective cytokine pathways would be equally attractive...
December 2, 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/27909445/identification-and-profiling-of-micrornas-expressed-in-elongating-cotton-fibers-using-small-rna-deep-sequencing
#2
Yanmei Wang, Yan Ding, Jin-Yuan Liu
Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27909059/the-role-of-the-histone-methyltransferase-enhancer-of-zeste-homolog-2-ezh2-in-the-pathobiological-mechanisms-underlying-inflammatory-bowel-disease-ibd
#3
Olga F Sarmento, Phyllis A Svingen, Yuning Xiong, Zhifu Sun, Adebowale O Bamidele, Angela J Mathison, Thomas C Smyrk, Asha A Nair, Michelle M Gonzalez, Mary R Sagstetter, Saurabh Baheti, Dermot P B McGovern, Jessica J Friton, Konstantinos A Papadakis, Goel Gautam, Ramnik J Xavier, Raul A Urrutia, William A Faubion
Regulatory T (Treg) cells expressing the transcription factor FOXP3 play a pivotal role in maintaining immunologic self-tolerance. We and others have previously shown that EZH2 is recruited to the FOXP3 promoter and its targets in Treg cells. To further address the role for EZH2 in Treg cellular function, we have now generated mice that lack EZH2 specifically in Treg cells (EZH2ΔFOXP3+). We find that EZH2 deficiency in FOXP3+ T cells results in lethal multi-organ autoimmunity. We further demonstrate that EZH2ΔFOXP3+ T cells lack a regulatory phenotype in vitro and secrete pro-inflammatory cytokines...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27907090/forkhead-box-c1-regulates-human-primary-keratinocyte-terminal-differentiation
#4
Lianghua Bin, Liehua Deng, Hengwen Yang, Leqing Zhu, Xiao Wang, Michael G Edwards, Brittany Richers, Donald Y M Leung
The epidermis serves as a critical protective barrier between the internal and external environment of the human body. Its remarkable barrier function is established through the keratinocyte (KC) terminal differentiation program. The transcription factors specifically regulating terminal differentiation remain largely unknown. Using a RNA-sequencing (RNA-seq) profiling approach, we found that forkhead box c 1 (FOXC1) was significantly up-regulated in human normal primary KC during the course of differentiation...
2016: PloS One
https://www.readbyqxmd.com/read/27905546/transcriptome-analysis-confers-a-complex-disease-resistance-network-in-wild-rice-oryza-meyeriana-against-xanthomonas-oryzae-pv-oryzae
#5
Xiao-Jie Cheng, Bin He, Lin Chen, Su-Qin Xiao, Jian Fu, Yue Chen, Teng-Qiong Yu, Zai-Quan Cheng, Hong Feng
Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice. It is well established that the wild rice Oryza meyeriana is immune to BB. In this study, the transcriptomic analysis was carried out by RNA sequencing of O. meyeriana leaves, inoculated with Xoo to understand the transcriptional responses and interaction between the host and pathogen. Totally, 57,313 unitranscripts were de novo assembled from 58.7 Gb clean reads and 14,143 unitranscripts were identified after Xoo inoculation...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902487/identification-of-laryngeal-cancer-prognostic-biomarkers-using-an-inflammatory-gene-related-competitive-endogenous-rna-network
#6
Qun He, Linli Tian, Hao Jiang, Jiarui Zhang, Qiang Li, Yanan Sun, Jiannan Zhao, Huijun Li, Ming Liu
Competitive endogenous RNAs (ceRNAs) act as molecular sponges for microRNAs (miRNAs), and are associated with tumorigenesis in various cancers, including laryngeal cancer (LC). In this work, we constructed an LC-specific inflammatory gene-related ceRNA network (IceNet). In IceNet, ceRNAs targeting inflammation-related genes tended to be network hubs. Additionally, the betweenness centralities of these hub ceRNAs were higher than those of the inflammation-related genes themselves, indicating that the hub ceRNAs in this study played critical roles in communication between IceNet molecules...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27900601/rna-seq-expression-analysis-of-enteric-neuron-cells-with-rotenone-treatment-and-prediction-of-regulated-pathways
#7
Qiang Guan, Xijin Wang, Yanyan Jiang, Lijuan Zhao, Zhiyu Nie, Lingjing Jin
The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson's disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes...
November 30, 2016: Neurochemical Research
https://www.readbyqxmd.com/read/27900352/genomic-data-on-breast-cancer-transcript-profile-modulation-by-17beta-hydroxysteroid-dehydrogenase-type-1-and-17-beta-estradiol
#8
Juliette A Aka, Ezequiel-Luis Calvo, Sheng-Xiang Lin
The data presented here are related to the research article entitled "Estradiol-independent modulation of breast cancer transcript profile by 17beta-hydroxysteroid dehydrogenase type 1" (J.A. Aka, E.L. Calvo, S.X. Lin, 2016) [1]. We evaluated the effect of the steroidal enzyme 17β-HSD1 and its product, the estrogenic hormone 17-beta-estradiol (E2), on gene transcription profile of breast cancer cells. RNA interference technique was used to knock down the 17β-HSD1 gene (HSD17B1) in the hormone-dependent breast cancer cell line T47D in steroid-deprived medium...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27899637/a-genome-wide-dosage-suppressor-network-reveals-genomic-robustness
#9
Biranchi Patra, Yoshiko Kon, Gitanjali Yadav, Anthony W Sevold, Jesse P Frumkin, Ravishankar R Vallabhajosyula, Arend Hintze, Bjørn Østman, Jory Schossau, Ashish Bhan, Bruz Marzolf, Jenna K Tamashiro, Amardeep Kaur, Nitin S Baliga, Elizabeth J Grayhack, Christoph Adami, David J Galas, Alpan Raval, Eric M Phizicky, Animesh Ray
Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899616/the-tissuenet-v-2-database-a-quantitative-view-of-protein-protein-interactions-across-human-tissues
#10
Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F Kirson, Idan Hekselman, Esti Yeger-Lotem
Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899596/chitars-3-1-the-enhanced-chimeric-transcripts-and-rna-seq-database-matched-with-protein-protein-interactions
#11
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#12
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899241/effects-of-nitrogen-metabolism-on-growth-and-aflatoxin-biosynthesis-in-aspergillus-flavus
#13
Bin Wang, Xiaoyun Han, Youhuang Bai, Zhenguo Lin, Mengguang Qiu, Xinyi Nie, Sen Wang, Feng Zhang, Zhenhong Zhuang, Jun Yuan, Shihua Wang
Aflatoxins (AFs), produced mainly by Aspergillus flavus and Aspergillus parasiticus, are strongly toxic and carcinogenic. Here, we showed that glutamine is the optimal nitrogen source for AF-production in A. flavus grown in Czapek Dox medium. Additionally, 4mM glutamine was the threshold for high production of aflatoxin B1. However, no significant impact of glutamine synthetase inhibitor was detected for on AF biosynthesis. In contrast, rapamycin could significantly suppress the glutamine inducing effect on AFs production, simultaneously inhibiting the fungal growth and conidiation...
November 21, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27898892/transcriptome-analyses-identify-five-transcription-factors-differentially-expressed-in-the-hypothalamus-of-post-versus-prepubertal-brahman-heifers
#14
M R S Fortes, L T Nguyen, M M D C A Weller, A Cánovas, A Islas-Trejo, L R Porto-Neto, A Reverter, S A Lehnert, G B Boe-Hansen, M G Thomas, J F Medrano, S S Moore
Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27897262/genome-wide-analysis-of-mirnas-in-the-ovaries-of-jining-grey-and-laiwu-black-goats-to-explore-the-regulation-of-fecundity
#15
Xiangyang Miao, Qingmiao Luo, Huijing Zhao, Xiaoyu Qin
Goat fecundity is important for agriculture and varies depending on the genetic background of the goat. Two excellent domestic breeds in China, the Jining Grey and Laiwu Black goats, have different fecundity and prolificacies. To explore the potential miRNAs that regulate the expression of the genes involved in these prolific differences and to potentially discover new miRNAs, we performed a genome-wide analysis of the miRNAs in the ovaries from these two goats using RNA-Seq technology. Thirty miRNAs were differentially expressed between the Jining Grey and Laiwu Black goats...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896996/cerna-search-method-identified-a-met-activated-subgroup-among-egfr-dna-amplified-lung-adenocarcinoma-patients
#16
Halla Kabat, Leo Tunkle, Inhan Lee
Given the diverse molecular pathways involved in tumorigenesis, identifying subgroups among cancer patients is crucial in precision medicine. While most targeted therapies rely on DNA mutation status in tumors, responses to such therapies vary due to the many molecular processes involved in propagating DNA changes to proteins (which constitute the usual drug targets). Though RNA expressions have been extensively used to categorize tumors, identifying clinically important subgroups remains challenging given the difficulty of discerning subgroups within all possible RNA-RNA networks...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896993/frequent-subgraph-mining-of-personalized-signaling-pathway-networks-groups-patients-with-frequently-dysregulated-disease-pathways-and-predicts-prognosis
#17
Arda Durmaz, Tim A D Henderson, Douglas Brubaker, Gurkan Bebek
MOTIVATION: Large scale genomics studies have generated comprehensive molecular characterization of numerous cancer types. Subtypes for many tumor types have been established; however, these classifications are based on molecular characteristics of a small gene sets with limited power to detect dysregulation at the patient level. We hypothesize that frequent graph mining of pathways to gather pathways functionally relevant to tumors can characterize tumor types and provide opportunities for personalized therapies...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27895744/identification-of-targets-of-mirna-221-and-mirna-222-in-fulvestrant-resistant-breast-cancer
#18
Pengfei Liu, Manna Sun, Wenhua Jiang, Jinkun Zhao, Chunyong Liang, Huilai Zhang
The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27894806/genetic-divergence-in-the-transcriptional-engram-of-chronic-alcohol-abuse-a-laser-capture-rna-seq-study-of-the-mouse-mesocorticolimbic-system
#19
Megan K Mulligan, Khyobeni Mozhui, Ashutosh K Pandey, Maren L Smith, Suzhen Gong, Jesse Ingels, Michael F Miles, Marcelo F Lopez, Lu Lu, Robert W Williams
Genetic factors that influence the transition from initial drinking to dependence remain enigmatic. Recent studies have leveraged chronic intermittent ethanol (CIE) paradigms to measure changes in brain gene expression in a single strain at 0, 8, 72 h, and even 7 days following CIE. We extend these findings using LCM RNA-seq to profile expression in 11 brain regions in two inbred strains - C57BL/6J (B6) and DBA/2J (D2) - 72 h following multiple cycles of ethanol self-administration and CIE. Linear models identified differential expression based on treatment, region, strain, or interactions with treatment...
October 15, 2016: Alcohol
https://www.readbyqxmd.com/read/27890424/recent-scenario-of-microrna-as-diagnostic-and-prognostic-biomarkers-of-prostate-cancer
#20
REVIEW
Kamla Kant Shukla, Sanjeev Misra, Puneet Pareek, Vivek Mishra, Barkha Singhal, Praveen Sharma
Prostate cancer (CaP) is a leading cause of cancer death and displays a broad range of clinical behavior from relatively indolent to aggressive metastatic disease. Due to the alteration and incomplete characterization of the CaP genomic markers, the quest for novel cellular metabolic regulatory molecules like micro RNA (miRNA) as a biomarker could be considered for the prognosis and treatment of CaP in future. In this article, we review the existing literature pertaining to CaP. Study provides a comprehensive miRNA profile expressed in CaP...
November 24, 2016: Urologic Oncology
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