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https://www.readbyqxmd.com/read/29156628/-differentially-expressed-trna-derived-small-rnas-co-sediment-primarily-with-non-polysomal-fractions-in-drosophila
#1
Çağdaş Göktaş, Hatice Yiğit, Mehmet İlyas Coşacak, Bünyamin Akgül
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0-1 and 7-8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5'ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29155736/high-resolution-fluorescent-in-situ-hybridization-in-drosophila-embryos-and-tissues-using-tyramide-signal-amplification
#2
Allison Jandura, Jack Hu, Ronit Wilk, Henry M Krause
In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of tissues, we have developed numerous modifications and improvements to our original fluorescent in situ hybridization (FISH) protocol. To facilitate throughput and cost effectiveness, all steps, from probe generation to signal detection, are performed using exon 96-well microtiter plates. Digoxygenin (DIG)-labelled antisense RNA probes are produced using either cDNA clones or genomic DNA as templates...
October 19, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29150614/spatial-regulation-of-contractility-by-neuralized-and-bearded-during-furrow-invagination-in-drosophila
#3
Gantas Perez-Mockus, Khalil Mazouni, Vanessa Roca, Giulia Corradi, Vito Conte, François Schweisguth
Embryo-scale morphogenesis arises from patterned mechanical forces. During Drosophila gastrulation, actomyosin contractility drives apical constriction in ventral cells, leading to furrow formation and mesoderm invagination. It remains unclear whether and how mechanical properties of the ectoderm influence this process. Here, we show that Neuralized (Neur), an E3 ubiquitin ligase active in the mesoderm, regulates collective apical constriction and furrow formation. Conversely, the Bearded (Brd) proteins antagonize maternal Neur and lower medial-apical contractility in the ectoderm: in Brd-mutant embryos, the ventral furrow invaginates properly but rapidly unfolds as medial MyoII levels increase in the ectoderm...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29148971/convergence-of-topological-domain-boundaries-insulators-and-polytene-interbands-revealed-by-high-resolution-mapping-of-chromatin-contacts-in-the-early-drosophila-melanogaster-embryo
#4
Michael R Stadler, Jenna E Haines, Michael Eisen
High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters...
November 17, 2017: ELife
https://www.readbyqxmd.com/read/29130209/live-imaging-of-mrna-synthesis-in-drosophila
#5
Hernan G Garcia, Thomas Gregor
mRNA synthesis is one of the earliest readouts of the activity of a transcribed gene, which is of particular interest in the context of metazoan cell fate specification. These processes are intrinsically dynamic and stochastic, which makes in vivo single-cell measurements inevitable. Here, we present the application of a technology that has been widely used in single celled organisms to measure transcriptional activity in developing embryos of the fruit fly Drosophila melanogaster. The method allows for quantification of instantaneous polymerase occupancy of active gene loci and thereby enables the development and testing of models of gene regulation in development...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130194/single-mrna-molecule-detection-in-drosophila
#6
Shawn C Little, Thomas Gregor
Single molecule fluorescent in situ hybridization (smFISH) enables quantitative measurements of gene expression and mRNA localization. The technique is increasingly popular for analysis of cultured cells but is not widely applied to intact organisms. Here, we describe a method for labeling and detection of single mRNA molecules in whole embryos of the fruit fly Drosophila melanogaster. This method permits measurements of gene expression in absolute units, enabling new studies of transcriptional mechanisms underlying precision and reproducibility in cell specification...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129537/a-moving-source-of-matrix-components-is-essential-for-de-novo-basement-membrane-formation
#7
Yutaka Matsubayashi, Adam Louani, Anca Dragu, Besaiz J Sánchez-Sánchez, Eduardo Serna-Morales, Lawrence Yolland, Attila Gyoergy, Gema Vizcay, Roland A Fleck, John M Heddleston, Teng-Leong Chew, Daria E Siekhaus, Brian M Stramer
The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo...
November 2, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29127725/a-loss-of-function-homozygous-mutation-in-ddx59-implicates-a-conserved-dead-box-rna-helicase-in-nervous-system-development-and-function
#8
Vincenzo Salpietro, Stephanie Efthymiou, Andreea Manole, Bhawana Maurya, Sarah Wiethoff, Balasubramaniem Ashokkumar, Maria Concetta Cutrupi, Valeria Dipasquale, Sara Manti, Juan A Botia, Mina Ryten, Jana Vandrovcova, Oscar D Bello, Conceicao Bettencourt, Kshitij Mankad, Ashim Mukherjee, Mousumi Mutsuddi, Henry Houlden
We report on a homozygous frameshift deletion in DDX59 (c.185del: p.Phe62fs*13) in a family presenting with oro-facio-digital syndrome phenotype associated to a broad neurological involvement characterized by microcephaly, intellectual disability, epilepsy, and white matter signal abnormalities associated with cortical and sub-cortical ischemic events. DDX59 encodes a DEAD-box RNA helicase and its role in brain function and neurological diseases is unclear. We showed a reduction of mutant cDNA and perturbation of SHH signalling from patient-derived cell lines; furthermore, analysis of human brain gene expression provides evidence that DDX59 is enriched in oligodendrocytes and might act within pathways of leukoencephalopathies associated genes...
November 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/29124738/transcripts-immunoprecipitated-with-sxl-protein-in-primordial-germ-cells-of-drosophila-embryos
#9
Ryoma Ota, Shumpei Morita, Masanao Sato, Shuji Shigenobu, Makoto Hayashi, Satoru Kobayashi
In Drosophila, Sex lethal (Sxl), an RNA binding protein, is required for induction of female sexual identity in both somatic and germline cells. Although the Sxl-dependent feminizing pathway in the soma was previously elucidated, the downstream targets for Sxl in the germline remained elusive. To identify these target genes, we selected transcripts associated with Sxl in primordial germ cells (PGCs) of embryos using RNA immunoprecipitation coupled to sequencing (RIP-seq) analysis. A total of 308 transcripts encoded by 282 genes were obtained...
November 10, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/29121353/secondary-structure-forming-sequences-drive-sd-mmej-repair-of-dna-double-strand-breaks
#10
Varandt Y Khodaverdian, Terrence Hanscom, Amy Marie Yu, Taylor L Yu, Victoria Mak, Alexander J Brown, Steven A Roberts, Mitch McVey
Alternative end-joining (alt-EJ) repair of DNA double-strand breaks is associated with deletions, chromosome translocations, and genome instability. Alt-EJ frequently uses annealing of microhomologous sequences to tether broken ends. When accessible pre-existing microhomologies do not exist, we have postulated that new microhomologies can be created via limited DNA synthesis at secondary-structure forming sequences. This model, called synthesis-dependent microhomology-mediated end joining (SD-MMEJ), predicts that differences between DNA sequences near double-strand breaks should alter repair outcomes in predictable ways...
November 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29117553/drosophila-embryonic-hemocytes-produce-laminins-to-strengthen-migratory-response
#11
Besaiz J Sánchez-Sánchez, José M Urbano, Kate Comber, Anca Dragu, Will Wood, Brian Stramer, María D Martín-Bermudo
The most prominent developmental function attributed to the extracellular matrix (ECM) is cell migration. While cells in culture can produce ECM to migrate, the role of ECM in regulating developmental cell migration is classically viewed as an exogenous matrix presented to the moving cells. In contrast to this view, we show here that Drosophila embryonic hemocytes deposit their own laminins in streak-like structures to migrate efficiently throughout the embryo. With the help of transplantation experiments, live microscopy, and image quantification, we demonstrate that autocrine-produced laminin regulates hemocyte migration by controlling lamellipodia dynamics, stability, and persistence...
November 7, 2017: Cell Reports
https://www.readbyqxmd.com/read/29114912/silencing-pyruvate-kinase-nlpyk-leads-to-reduced-fecundity-in-brown-planthoppers-nilaparvata-lugens-st%C3%A3-l-hemiptera-delphacidae
#12
Lin-Quan Ge, Bo Huang, Xin Li, Hao-Tian Gu, Sui Zheng, Ze Zhou, Hong Miao, Jin-Cai Wu
Pyruvate kinase (PYK) operates in the glycolytic pathway, responsible for regulating the balance between glycolysis and gluconeogenesis. The previous work indicates PYK acts in development of Drosophila embryos and in embryonic muscle growth, from which it may be inferred that PYK acts in insect fecundity. More to the point, as a central enzyme in the glycolytic pathway, PYK acts in many energy-spending functions in most organisms. On the background findings that triazophos (TZP) stimulates fecundity via increase activities of several genes in brown planthoppers, Nilaparvata lugens, we investigated the combined influence of TZP and silencing a N...
November 7, 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/29107549/myosin-2-induced-mitotic-rounding-enables-columnar-epithelial-cells-to-interpret-cortical-spindle-positioning-cues
#13
Soline Chanet, Rishabh Sharan, Zia Khan, Adam C Martin
During epithelial cell proliferation, planar alignment of the mitotic spindle allows the daughter cells to stay within the epithelium. Previous work has identified cortical cues that regulate spindle orientation and the division axis [1, 2]. One such cue is cortical Pins (LGN in vertebrates) [3-6], which recruits the conserved Mud/NuMA protein and the dynein/dynactin complex to the cortex. The dynein/dynactin motor complex pulls astral microtubules to orient the spindle. Cortical Pins can therefore dictate the division axis...
November 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29101389/pirnas-and-aubergine-cooperate-with-wispy-poly-a-polymerase-to-stabilize-mrnas-in-the-germ-plasm
#14
Jérémy Dufourt, Gwénaëlle Bontonou, Aymeric Chartier, Camille Jahan, Anne-Cécile Meunier, Stéphanie Pierson, Paul F Harrison, Catherine Papin, Traude H Beilharz, Martine Simonelig
Piwi-interacting RNAs (piRNAs) and PIWI proteins play a crucial role in germ cells by repressing transposable elements and regulating gene expression. In Drosophila, maternal piRNAs are loaded into the embryo mostly bound to the PIWI protein Aubergine (Aub). Aub targets maternal mRNAs through incomplete base-pairing with piRNAs and can induce their destabilization in the somatic part of the embryo. Paradoxically, these Aub-dependent unstable mRNAs encode germ cell determinants that are selectively stabilized in the germ plasm...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29097593/maternal-loading-of-a-small-heat-shock-protein-increases-embryo-thermal-tolerance-in-drosophila-melanogaster
#15
Brent L Lockwood, Cole R Julick, Kristi L Montooth
Maternal investment is likely to have direct effects on offspring survival. In oviparous animals whose embryos are exposed to the external environment, maternal provisioning of molecular factors like mRNAs and proteins may help embryos cope with sudden changes in the environment. Here we sought to modify the maternal mRNA contribution to offspring embryos and test for maternal effects on acute thermal tolerance in early embryos of Drosophila melanogaster We drove in vivo overexpression of a small heat shock protein gene (Hsp23) in female ovaries and measured the effects of acute thermal stress on offspring embryonic survival and larval development...
November 2, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29097443/a-facilitated-diffusion-mechanism-establishes-the-drosophila-dorsal-gradient
#16
Sophia N Carrell, Michael D O'Connell, Thomas Jacobsen, Amy E Allen, Stephanie M Smith, Gregory T Reeves
The transcription factor NF-κB plays an important role in the immune system, apoptosis, and inflammation. Dorsal, a Drosophila homolog of NF-κB, patterns the dorsal-ventral axis in the blastoderm embryo. During this stage, Dorsal is sequestered outside the nucleus by the IκB homolog Cactus. Toll signaling on the ventral side breaks the Dorsal/Cactus complex, allowing Dorsal to enter the nucleus to regulate target genes. Fluorescent data show that Dorsal accumulates on the ventral side of the syncytial blastoderm...
November 2, 2017: Development
https://www.readbyqxmd.com/read/29095923/pofut1-point-mutations-that-disrupt-o-fucosyltransferase-activity-destabilize-the-protein-and-abolish-notch1-signaling-during-mouse-somitogenesis
#17
Rieko Ajima, Emiko Suzuki, Yumiko Saga
The segmental pattern of the vertebrate body is established via the periodic formation of somites from the presomitic mesoderm (PSM). This periodical process is controlled by the cyclic and synchronized activation of Notch signaling in the PSM. Protein O-fucosyltransferase1 (Pofut1), which transfers O-fucose to the EGF domains of the Notch1 receptor, is indispensable for Notch signaling activation. The Drosophila homologue Ofut1 was reported to control Notch localization via two different mechanisms, working as a chaperone for Notch or as a regulator of Notch endocytosis...
2017: PloS One
https://www.readbyqxmd.com/read/29095827/co-option-of-the-bzip-transcription-factor-vrille-as-the-activator-of-doublesex1-in-environmental-sex-determination-of-the-crustacean-daphnia-magna
#18
Nur Syafiqah Mohamad Ishak, Quang Dang Nong, Tomoaki Matsuura, Yasuhiko Kato, Hajime Watanabe
Divergence of upstream regulatory pathways of the transcription factor Doublesex (Dsx) serves as a basis for evolution of sex-determining mechanisms in animals. However, little is known about the regulation of Dsx in environmental sex determination. In the crustacean Daphnia magna, environmental sex determination is implemented by male-specific expression of the Dsx ortholog, Dsx1. Transcriptional regulation of Dsx1 comprises at least three phases during embryogenesis: non-sex-specific initiation, male-specific up-regulation, and its maintenance...
November 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29079679/phosphorylation-of-pnut-at-the-early-steps-of-drosophila%C3%A2-embryo-development-affects-association-of-the-septin-complex-with-membrane-and-is-important-for-viability
#19
Katarina Akhmetova, Maxim Balasov, Anton Svitin, Elena Chesnokova, Matthew Renfrow, Igor Chesnokov
Septin proteins are polymerizing GTPases that are found in most eukaryotic species. Septins are important for cytokinesis and participate in many processes involving spatial modifications of the cell cortex. In Drosophila, septin proteins Pnut, Sep1 and Sep2 form a hexameric septin complex. Here, we found that septin protein Pnut is phosphorylated during the first two hours of Drosophila embryo development. To study the effect of Pnut phosphorylation in a live organism, we created a new Drosophila pnut null mutant which allows for the analysis of Pnut mutations during embryogenesis...
October 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29075336/diversity-of-p-element-pirna-production-among-m-and-q-strains-and-its-association-with-p-m-hybrid-dysgenesis-in-drosophila-melanogaster
#20
Keiko Tsuji Wakisaka, Kenji Ichiyanagi, Seiko Ohno, Masanobu Itoh
BACKGROUND: Transposition of P elements in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. For the P strain, the P-M phenotypes are associated with the ability to express a class of small RNAs, called piwi-interacting small RNAs (piRNAs), that suppress the P elements in female gonads. However, little is known about the extent to which piRNAs are involved in the P-M hybrid dysgenesis in M' and Q strains, which show different abilities to regulate the P elements from P strains...
2017: Mobile DNA
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