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https://www.readbyqxmd.com/read/28527580/the-function-and-evolution-of-nuclear-receptors-in-insect-embryonic-development
#1
Alys M Cheatle Jarvela, Leslie Pick
Nuclear receptors are a family of transcription factors that are often responsive to small ligands, allowing for efficient gene expression-level responses to a stimulus. The average insect has 21 genes encoding nuclear receptors, whose functions are especially well studied in developmental transitions during the insect life cycle, such as metamorphosis and molting. However, their utility as well-controlled transcriptional regulators also lends them to important roles in embryogenesis, neurogenesis, metabolism, and organogenesis...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28527116/genome-editing-in-drosophila-melanogaster-from-basic-genome-engineering-to-the-multipurpose-crispr-cas9-system
#2
REVIEW
Xingjie Ren, Kristof Holsteens, Haiyi Li, Jin Sun, Yifan Zhang, Lu-Ping Liu, Qingfei Liu, Jian-Quan Ni
Nowadays, genome editing tools are indispensable for studying gene function in order to increase our knowledge of biochemical processes and disease mechanisms. The extensive availability of mutagenesis and transgenesis tools make Drosophila melanogaster an excellent model organism for geneticists. Early mutagenesis tools relied on chemical or physical methods, ethyl methane sulfonate (EMS) and X-rays respectively, to randomly alter DNA at a nucleotide or chromosomal level. Since the discovery of transposable elements and the availability of the complete fly genome, specific genome editing tools, such as P-elements, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have undergone rapid development...
May 1, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28526755/the-matrix-protein-tiggrin-regulates-plasmatocyte-maturation-in-drosophila-larva
#3
Chen U Zhang, Ken M Cadigan
The lymph gland (LG) is a major source of hematopoiesis during Drosophila development. In this tissue, prohemocytes differentiate into multiple lineages including macrophage-like plasmatocytes, which comprise the vast majority of mature hemocytes. Previous studies have uncovered genetic pathways that regulate prohemocyte maintenance and some cell fate choices between hemocyte lineages. However, less is known about how the plasmatocyte pool of the LG is established and matures. Here we report that Tiggrin, a matrix protein expressed in the LG, is a specific regulator of plasmatocyte maturation...
May 19, 2017: Development
https://www.readbyqxmd.com/read/28526029/cell-fixation-and-preservation-for-droplet-based-single-cell-transcriptomics
#4
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks, Nikolaus Rajewsky
BACKGROUND: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. METHODS: Here, we used chemical fixation to address these problems...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28522526/blocking-promiscuous-activation-at-cryptic-promoters-directs-cell-type-specific-gene-expression
#5
Jongmin Kim, Chenggang Lu, Shrividhya Srinivasan, Stephan Awe, Alexander Brehm, Margaret T Fuller
To selectively express cell type-specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation...
May 19, 2017: Science
https://www.readbyqxmd.com/read/28521937/using-drosophila-pigmentation-traits-to-study-the-mechanisms-of-cis-regulatory-evolution
#6
REVIEW
Mark Rebeiz, Thomas M Williams
One primary agenda of the developmental evolution field is to elucidate molecular mechanisms governing differences in animal form. While mounting evidence has established an important role for mutations in transcription controlling cis-regulatory elements (CREs), the underlying mechanisms that translate these alterations into differences in gene expression are poorly understood. Emerging studies focused on pigmentation differences among closely related Drosophila species have provided many examples of phenotypically relevant CRE changes, and have begun to illuminate how this process works at the level of regulatory sequence function and transcription factor binding...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28521739/drosophila-melanogaster-positive-transcriptional-elongation-factors-regulate-metabolic-and-sex-biased-expression-in-adults
#7
Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
BACKGROUND: Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. RESULTS: We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28520736/the-bantam-microrna-acts-through-numb-to-exert-cell-growth-control-and-feedback-regulation-of-notch-in-tumor-forming-stem-cells-in-the-drosophila-brain
#8
Yen-Chi Wu, Kyu-Sun Lee, Yan Song, Stephan Gehrke, Bingwei Lu
Notch (N) signaling is central to the self-renewal of neural stem cells (NSCs) and other tissue stem cells. Its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases. How N regulates stem cell behavior in health and disease is not well understood. Here we show that N regulates bantam (ban) microRNA to impact cell growth, a process key to NSC maintenance and particularly relied upon by tumor-forming cancer stem cells. Notch signaling directly regulates ban expression at the transcriptional level, and ban in turn feedback regulates N activity through negative regulation of the Notch inhibitor Numb...
May 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28516957/asxl2-is-essential-for-haematopoiesis-and-acts-as-a-haploinsufficient-tumour-suppressor-in-leukemia
#9
Jean-Baptiste Micol, Alessandro Pastore, Daichi Inoue, Nicolas Duployez, Eunhee Kim, Stanley Chun-Wei Lee, Benjamin H Durham, Young Rock Chung, Hana Cho, Xiao Jing Zhang, Akihide Yoshimi, Andrei Krivtsov, Richard Koche, Eric Solary, Amit Sinha, Claude Preudhomme, Omar Abdel-Wahab
Additional sex combs-like (ASXL) proteins are mammalian homologues of additional sex combs (Asx), a regulator of trithorax and polycomb function in Drosophila. While there has been great interest in ASXL1 due to its frequent mutation in leukemia, little is known about its paralog ASXL2, which is frequently mutated in acute myeloid leukemia patients bearing the RUNX1-RUNX1T1 (AML1-ETO) fusion. Here we report that ASXL2 is required for normal haematopoiesis with distinct, non-overlapping effects from ASXL1 and acts as a haploinsufficient tumour suppressor...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28514643/yorkie-regulates-epidermal-wound-healing-in-drosophila-larvae-independently-of-cell-proliferation-and-apoptosis
#10
Chang-Ru Tsai, Aimee E Anderson, Sirisha Burra, Juyeon Jo, Michael J Galko
Yorkie (Yki), the transcriptional co-activator of the Hippo signaling pathway, has well-characterized roles in balancing apoptosis and cell division during organ growth control. Yki is also required in diverse tissue regenerative contexts. In most cases this requirement reflects its well-characterized roles in balancing apoptosis and cell division. Whether Yki has repair functions outside of the control of cell proliferation, death, and growth is not clear. Here we show that Yki and Scalloped (Sd) are required for epidermal wound closure in the Drosophila larval epidermis...
May 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28512194/ancient-antagonism-between-celf-and-rbfox-families-tunes-mrna-splicing-outcomes
#11
Matthew R Gazzara, Michael J Mallory, Renat Roytenberg, John Lindberg, Anupama Jha, Kristen W Lynch, Yoseph Barash
Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28510597/ubiquitylation-of-the-acetyltransferase-mof-in-drosophila-melanogaster
#12
Sarah Schunter, Raffaella Villa, Victoria Flynn, Jan B Heidelberger, Anne-Kathrin Classen, Petra Beli, Peter B Becker
The nuclear acetyltransferase MOF (KAT8 in mammals) is a subunit of at least two multi-component complexes involved in transcription regulation. In the context of complexes of the 'Non-Specific-Lethal' (NSL) type it controls transcription initiation of many nuclear housekeeping genes and of mitochondrial genes. While this function is conserved in metazoans, MOF has an additional, specific function in Drosophila in the context of dosage compensation. As a subunit of the male-specific-lethal dosage compensation complex (MSL-DCC) it contributes to the doubling of transcription output from the single male X chromosome by acetylating histone H4...
2017: PloS One
https://www.readbyqxmd.com/read/28510140/nuclear-receptors-ecr-usp-e75-dhr3-and-err-regulate-transcription-of-ecdysone-cascade-genes
#13
M Yu Mazina, E V Kocheryzhkina, J V Nikolenko, A N Krasnov, S G Georgieva, N E Vorobyeva
We found that an increase in the expression level of E75, DHR3, and ERR increases the degree of activation of dhr3 and hr4 genes in Drosophila S2 cells. We also detected a repressing effect of these nuclear receptors on the basal transcription level of these genes. This is the first study to show the ability of nuclear receptors E75, DHR3, and ERR to function as activators or repressors depending on external conditions. We also confirmed the existence of the interaction of all studied nuclear receptors with the promoters of dhr3 and hr4 genes of the ecdysone cascade in vivo...
March 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28507100/the-microrna-machinery-regulates-fasting-induced-changes-in-gene-expression-and-longevity-in-caenorhabditis-elegans
#14
Akiko Kogure, Masaharu Uno, Takako Ikeda, Eisuke Nishida
Intermittent fasting (IF) is a dietary restriction regimen that extends the lifespans of Caenorhabditis elegans and mammals by inducing changes in gene expression. However, how IF induces these changes and promotes longevity remains unclear. One proposed mechanism involves gene regulation by microRNAs (miRNAs), small non-coding RNAs (approximately 22 nucleotides) that repress gene expression and whose expression can be altered by fasting. To test this proposition, we examined the role of the miRNA machinery in fasting-induced transcriptional changes and longevity in C...
May 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28506986/soxneuro-and-shavenbaby-act-cooperatively-to-shape-denticles-in-the-embryonic-epidermis-of-drosophila
#15
Nicholas P Rizzo, Amy Bejsovec
During development, extracellular signals are integrated by cells to induce the transcriptional circuitry that controls morphogenesis. In the fly epidermis, Wingless (Wg)/Wnt signaling directs cells to produce either a distinctly-shaped denticle or no denticle, resulting in a segmental pattern of denticle belts separated by smooth, or "naked", cuticle. Naked cuticle results from Wg repression of shavenbaby (svb), which encodes a transcription factor required for denticle construction. We have discovered that although the svb promoter responds differentially to altered Wg levels, Svb alone cannot produce the morphological diversity of denticles found in wild-type belts...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28503020/circadian-rhythm-in-mrna-expression-of-the-glutathione-synthesis-gene-gclc-is-controlled-by-peripheral-glial-clocks-in-drosophila-melanogaster
#16
Eileen S Chow, Dani M Long, Jadwiga M Giebultowicz
Circadian coordination of metabolism, physiology, and behaviour is found in all living kingdoms. Clock genes are transcriptional regulators, and their rhythmic activities generate daily rhythms in clock-controlled genes which result in cellular and organismal rhythms. Insects provide numerous examples of rhythms in behaviour and reproduction, but less is known about control of metabolic processes by circadian clocks in insects. Recent data suggest that several pathways involved in protecting cells from oxidative stress may be modulated by the circadian system, including genes involved in glutathione (GSH) biosynthesis...
December 2016: Physiological Entomology
https://www.readbyqxmd.com/read/28502805/distinct-phenotypes-of-three-repeat-and-four-repeat-human-tau-in-a-transgenic-model-of-tauopathy
#17
Megan A Sealey, Ergina Vourkou, Catherine M Cowan, Torsten Bossing, Shmma Quraishe, Sofia Grammenoudi, Efthimios M C Skoulakis, Amritpal Mudher
Tau exists as six closely related protein isoforms in the adult human brain. These are generated from alternative splicing of a single mRNA transcript and they differ in the absence or presence of two N-terminal and three or four microtubule binding domains. Typically all six isoforms have been considered functionally similar. However, their differential involvement in particular tauopathies raises the possibility that there may be isoform-specific differences in physiological function and pathological role...
May 11, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28500052/exploring-the-impact-of-cleavage-and-polyadenylation-factors-on-pre-mrna-splicing-across-eukaryotes
#18
Gildas Lepennetier, Francesco Catania
In human, mouse and Drosophila, the spliceosomal complex U1 snRNP (U1) protects transcripts from premature cleavage and polyadenylation at proximal intronic polyadenylation signals (PAS). These U1-mediated effects preserve transcription integrity and are known as telescripting. The watchtower role of U1 throughout transcription is clear. What is less clear is whether cleavage and polyadenylation factors (CPFs) are simply patrolled or if they may actively antagonize U1 recruitment. In addressing this question, we found that in the introns of human, mouse and Drosophila and of 14 other eukaryotes, including multi- and single-celled species, the conserved AATAAA PAS - a major target for CPFs - is selected against...
May 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28498729/the-distinct-function-of-tep2-and-tep6-in-the-immune-defense-of-drosophila-melanogaster-against-the-pathogen-photorhabdus
#19
Upasana Shokal, Hannah Kopydlowski, Ioannis Eleftherianos
Previous and recent investigations on the innate immune response of Drosophila have identified certain mechanisms that promote pathogen elimination. However, the function of Thioester-containing proteins (TEPs) in the fly still remains elusive. Recently we have shown the contribution of TEP4 in the antibacterial immune defense of Drosophila against non-pathogenic E. coli, and the pathogens Photorhabdus luminescens and P. asymbiotica. Here we studied the function of Tep genes in both humoral and cellular immunity upon E...
May 12, 2017: Virulence
https://www.readbyqxmd.com/read/28497798/phosphorylation-induces-sequence-specific-conformational-switches-in-the-rna-polymerase-ii-c-terminal-domain
#20
Eric B Gibbs, Feiyue Lu, Bede Portz, Michael J Fisher, Brenda P Medellin, Tatiana N Laremore, Yan Jessie Zhang, David S Gilmour, Scott A Showalter
The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization...
May 12, 2017: Nature Communications
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