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https://www.readbyqxmd.com/read/27913635/screening-and-analysis-of-janelia-flylight-project-enhancer-gal4-strains-identifies-multiple-gene-enhancers-active-during-hematopoiesis-in-normal-and-wasp-challenged-drosophila-larvae
#1
Tsuyoshi Tokusumi, Yumiko Tokusumi, Mark S Brahier, Victoria Lam, Jessica R Stoller-Conrad, Paul T Kroeger, Robert A Schulz
A GFP expression screen has been conducted on greater than one thousand Janelia FlyLight Project enhancer-Gal4 lines to identify transcriptional enhancers active in the larval hematopoietic system. A total of 190 enhancers associated with 87 distinct genes showed activity in cells of the third instar larval lymph gland and hemolymph. That is, gene enhancers were active in cells of the lymph gland posterior signaling center (PSC), medullary zone (MZ), and/or cortical zone (CZ), while certain of the transcriptional control regions were active in circulating hemocytes...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27903907/chromatin-binding-of-gcn5-in-drosophila-is-largely-mediated-by-cp190
#2
Tamer Ali, Marcus Krüger, Sabin Bhuju, Michael Jarek, Marek Bartkuhn, Rainer Renkawitz
Centrosomal 190 kDa protein (CP190) is a promoter binding factor, mediates long-range interactions in the context of enhancer-promoter contacts and in chromosomal domain formation. All Drosophila insulator proteins bind CP190 suggesting a crucial role in insulator function. CP190 has major effects on chromatin, such as depletion of nucleosomes, high nucleosomal turnover and prevention of heterochromatin expansion. Here, we searched for enzymes, which might be involved in CP190 mediated chromatin changes. Eighty percent of the genomic binding sites of the histone acetyltransferase Gcn5 are colocalizing with CP190 binding...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27901078/asian-citrus-psyllid-rnai-pathway-rnai-evidence
#3
Clauvis N T Taning, Eduardo C Andrade, Wayne B Hunter, Olivier Christiaens, Guy Smagghe
Diaphorina citri, known as the Asian citrus psyllid, is an important pest of citrus because it transmits a phloem-limited bacteria strongly implicated in huanglongbing (citrus greening disease). Emerging biotechnologies, such as RNA interference, could provide a new sustainable and environmentally friendly strategy for the management of this pest. In this study, genome and functional analysis were performed to verify whether the RNAi core genes are present in the Asian psyllid genome and if the RNAi machinery could be exploited to develop a management strategy for this pest...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899608/tfbsbank-a-platform-to-dissect-the-big-data-of-protein-dna-interaction-in-human-and-model-species
#4
Dongsheng Chen, Sanjie Jiang, Xiaoyan Ma, Fang Li
Genome-wide transcription factors (TFs) binding data has been extensively generated in the past few years, which poses a great challenge to data interpretation. Therefore, comprehensive and dedicated functional annotation databases for TF-DNA interaction are in great demands to manage, explore and utilize those invaluable data resources. Here, we constructed a platform 'TFBSbank' which houses the annotation of 1870 chromatin immunoprecipitation (ChIP) datasets of 585 TFs in five species (human, mouse, fly, worm and yeast)...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899510/identification-and-in-silico-modeling-of-enhancers-reveals-new-features-of-the-cardiac-differentiation-network
#5
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/27898892/transcriptome-analyses-identify-five-transcription-factors-differentially-expressed-in-the-hypothalamus-of-post-versus-prepubertal-brahman-heifers
#6
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/27898741/stable-host-gene-expression-in-the-gut-of-adult-drosophila-melanogaster-with-different-bacterial-mono-associations
#7
Carolyn Elya, Vivian Zhang, William B Ludington, Michael B Eisen
There is growing evidence that the microbes found in the digestive tracts of animals influence host biology, but we still do not understand how they accomplish this. Here, we evaluated how different microbial species commonly associated with laboratory-reared Drosophila melanogaster impact host biology at the level of gene expression in the dissected adult gut and in the entire adult organism. We observed that guts from animals associated from the embryonic stage with either zero, one or three bacterial species demonstrated indistinguishable transcriptional profiles...
2016: PloS One
https://www.readbyqxmd.com/read/27898696/regulation-of-gonad-morphogenesis-in-drosophila-melanogaster-by-btb-family-transcription-factors
#8
Diane Silva, Kenneth W Olsen, Magdalena N Bednarz, Andrew Droste, Christopher P Lenkeit, Edwin Chaharbakhshi, Emily R Temple-Wood, Jennifer C Jemc
During embryogenesis, primordial germ cells (PGCs) and somatic gonadal precursor cells (SGPs) migrate and coalesce to form the early gonad. A failure of the PGCs and SGPs to form a gonad with the proper architecture not only affects germ cell development, but can also lead to infertility. Therefore, it is critical to identify the molecular mechanisms that function within both the PGCs and SGPs to promote gonad morphogenesis. We have characterized the phenotypes of two genes, longitudinals lacking (lola) and ribbon (rib), that are required for the coalescence and compaction of the embryonic gonad in Drosophila melanogaster...
2016: PloS One
https://www.readbyqxmd.com/read/27893816/mir-34-modulates-innate-immunity-and-ecdysone-signaling-in-drosophila
#9
Xiao-Peng Xiong, Krishna Kurthkoti, Kung-Yen Chang, Jian-Liang Li, Xingjie Ren, Jian-Quan Ni, Tariq M Rana, Rui Zhou
microRNAs are endogenous small regulatory RNAs that modulate myriad biological processes by repressing target gene expression in a sequence-specific manner. Here we show that the conserved miRNA miR-34 regulates innate immunity and ecdysone signaling in Drosophila. miR-34 over-expression activates antibacterial innate immunity signaling both in cultured cells and in vivo, and flies over-expressing miR-34 display improved survival and pathogen clearance upon Gram-negative bacterial infection; whereas miR-34 knockout animals are defective in antibacterial defense...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27892932/reciprocal-regulation-of-carbon-monoxide-metabolism-and-the-circadian-clock
#10
Roman Klemz, Silke Reischl, Thomas Wallach, Nicole Witte, Karsten Jürchott, Sabrina Klemz, Veronika Lang, Stephan Lorenzen, Miriam Knauer, Steffi Heidenreich, Min Xu, Jürgen A Ripperger, Michael Schupp, Ralf Stanewsky, Achim Kramer
Circadian clocks are cell-autonomous oscillators regulating daily rhythms in a wide range of physiological, metabolic and behavioral processes. Feedback of metabolic signals, such as redox state, NAD(+)/NADH and AMP/ADP ratios, or heme, modulate circadian rhythms and thereby optimize energy utilization across the 24-h cycle. We show that rhythmic heme degradation, which generates the signaling molecule carbon monoxide (CO), is required for normal circadian rhythms as well as circadian metabolic outputs. CO suppresses circadian transcription by attenuating CLOCK-BMAL1 binding to target promoters...
November 28, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27891621/animal-cryptochromes-divergent-roles-in-light-perception-circadian-timekeeping-and-beyond
#11
Alicia K Michael, Jennifer L Fribourgh, Russell N Van Gelder, Carrie L Partch
Cryptochromes are evolutionarily related to the light-dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila-like CRYs that act as non-visual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate-like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors...
November 28, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27888216/drosophila-sulf1-is-required-for-the-termination-of-intestinal-stem-cell-division-during-regeneration
#12
Masahiko Takemura, Hiroshi Nakato
Stem cell division is activated to trigger regeneration in response to tissue damage. The molecular mechanisms by which this stem cell mitotic activity is properly repressed at the end of regeneration are poorly understood. Here we show that a specific modification of heparan sulfate (HS) is critical in regulating Drosophila intestinal stem cell (ISC) division during normal midgut homeostasis and regeneration. Loss of the extracellular HS endosulfatase Sulf1 results in increased ISC division during normal homeostasis, which is caused by upregulation of mitogenic signaling including the JAK/STAT, EGFR, and Hedgehog pathways...
November 25, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27887593/expression-of-barhl2-and-its-relationship-with-pax6-expression-in-the-forebrain-of-the-mouse-embryo
#13
Elisa V Parish, John O Mason, David J Price
BACKGROUND: The transcription factor Barhl2 is an antiproneural transcription factor with roles in neuronal differentiation. The functions of its homologue in Drosophila development are better understood than its functions in mammalian brain development. Existing evidence suggests that its expression in the embryonic forebrain of the mouse is regional and may complement that of another transcription factor that is important for forebrain development, Pax6. The aim of this study is to provide a more detailed description of the Barhl2 expression pattern in the embryonic forebrain than is currently available, to relate its expression domains to those of Pax6 and to examine the effects of Pax6 loss on Barhl2 expression...
November 25, 2016: BMC Neuroscience
https://www.readbyqxmd.com/read/27887564/the-drosophila-transcriptional-network-is-structured-by-microbiota
#14
Adam J Dobson, John M Chaston, Angela E Douglas
BACKGROUND: Resident microorganisms (microbiota) have far-reaching effects on the biology of their animal hosts, with major consequences for the host's health and fitness. A full understanding of microbiota-dependent gene regulation requires analysis of the overall architecture of the host transcriptome, by identifying suites of genes that are expressed synchronously. In this study, we investigated the impact of the microbiota on gene coexpression in Drosophila. RESULTS: Our transcriptomic analysis, of 17 lines representative of the global genetic diversity of Drosophila, yielded a total of 11 transcriptional modules of co-expressed genes...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27886257/an-evolutionary-conserved-interaction-between-the-gcm-transcription-factor-and-the-sf1-nuclear-receptor-in-the-female-reproductive-system
#15
Pierre B Cattenoz, Claude Delaporte, Wael Bazzi, Angela Giangrande
NR5A1 is essential for the development and for the function of steroid producing glands of the reproductive system. Moreover, its misregulation is associated with endometriosis, which is the first cause of infertility in women. Hr39, the Drosophila ortholog of NR5A1, is expressed and required in the secretory cells of the spermatheca, the female exocrine gland that ensures fertility by secreting substances that attract and capacitate the spermatozoids. We here identify a direct regulator of Hr39 in the spermatheca: the Gcm transcription factor...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27884706/identification-and-functional-characterization-of-a-novel-sp%C3%A3-tzle-gene-in-litopenaeus-vannamei
#16
Kai Yuan, Feng-Hua Yuan, Shao-Ping Weng, Jian-Guo He, Yi-Hong Chen
Shrimp innate immunity is the first line of resistance against pathogenic bacteria. The Toll-like receptor (TLR)-NF-κB pathway is vital in this immunity process. In this study, a novel Spätzle gene (LvSpz4) of Litopenaeus vannamei was cloned and functionally characterized. The open reading frame of LvSpz4 was 918 bp, which encoded a putative protein with 305 amino acids. LvSpz4 was most expressed in the gills of L. vannamei. This expression was induced by Vibrio alginolyticus or Staphylococcus aureus infection or lipopolysaccharide stimulation...
November 21, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27882698/the-cellular-and-molecular-basis-of-cnidarian-neurogenesis
#17
REVIEW
Fabian Rentzsch, Michael Layden, Michaël Manuel
Neurogenesis initiates during early development and it continues through later developmental stages and in adult animals to enable expansion, remodeling, and homeostasis of the nervous system. The generation of nerve cells has been analyzed in detail in few bilaterian model organisms, leaving open many questions about the evolution of this process. As the sister group to bilaterians, cnidarians occupy an informative phylogenetic position to address the early evolution of cellular and molecular aspects of neurogenesis and to understand common principles of neural development...
November 23, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27879206/exon-junction-complex-proteins-bind-nascent-transcripts-independently-of-pre-mrna-splicing-in-drosophila-melanogaster
#18
Subhendu Roy Choudhury, Anand K Singh, Tina McLeod, Marco Blanchette, Boyun Jang, Paul Badenhorst, Aditi Kanhere, Saverio Brogna
Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosome. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells...
November 23, 2016: ELife
https://www.readbyqxmd.com/read/27879204/establishment-and-maintenance-of-heritable-chromatin-structure-during-early-drosophila-embryogenesis
#19
Shelby A Blythe, Eric F Wieschaus
During embryogenesis, the initial chromatin state is established during a period of rapid proliferative activity. We have measured with three-minute time resolution how heritable patterns of chromatin structure are initially established and maintained during the midblastula transition (MBT). We find that regions of accessibility are established sequentially, where enhancers are opened in advance of promoters and insulators. These open states are stably maintained in highly condensed mitotic chromatin to ensure faithful inheritance of prior accessibility status across cell divisions...
November 23, 2016: ELife
https://www.readbyqxmd.com/read/27875550/an-alternative-approach-to-chip-seq-normalization-enables-detection-of-genome-wide-changes-in-histone-h3-lysine-27-trimethylation-upon-ezh2-inhibition
#20
Brian Egan, Chih-Chi Yuan, Madeleine Lisa Craske, Paul Labhart, Gulfem D Guler, David Arnott, Tobias M Maile, Jennifer Busby, Chisato Henry, Theresa K Kelly, Charles A Tindell, Suchit Jhunjhunwala, Feng Zhao, Charlie Hatton, Barbara M Bryant, Marie Classon, Patrick Trojer
Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3)...
2016: PloS One
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