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Drosophila epigenetics

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https://www.readbyqxmd.com/read/29760717/reduced-neuronal-transcription-of-escargot-the-drosophila-gene-encoding-a-snail-type-transcription-factor-promotes-longevity
#1
Alexander V Symonenko, Natalia V Roshina, Anna V Krementsova, Elena G Pasyukova
In recent years, several genes involved in complex neuron specification networks have been shown to control life span. However, information on these genes is scattered, and studies to discover new neuronal genes and gene cascades contributing to life span control are needed, especially because of the recognized role of the nervous system in governing homeostasis, aging, and longevity. Previously, we demonstrated that several genes that encode RNA polymerase II transcription factors and that are involved in the development of the nervous system affect life span in Drosophila melanogaster ...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29740006/identification-of-target-genes-regulated-by-the-drosophila-histone-methyltransferase-eggless-reveals-a-role-of-decapentaplegic-in-apoptotic-signaling
#2
Igojo Kang, Yourim Choi, Sueun Jung, Jae Yun Lim, Dooyoung Lee, Sumeet Gupta, Woongjoon Moon, Chanseok Shin
Epigenetic gene regulation is essential for developmental processes. Eggless (Egg), the Drosophila orthologue of the mammalian histone methyltransferase, SETDB1, is known to be involved in the survival and differentiation of germline stem cells and piRNA cluster transcription during Drosophila oogenesis; however the detailed mechanisms remain to be determined. Here, using high-throughput RNA sequencing, we investigated target genes regulated by Egg in an unbiased manner. We show that Egg plays diverse roles in particular piRNA pathway gene expression, some long non-coding RNA expression, apoptosis-related gene regulation, and Decapentaplegic (Dpp) signaling during Drosophila oogenesis...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29661849/feedback-regulation-by-antagonistic-epigenetic-factors-potentially-maintains-homeostasis-in-drosophila
#3
Devendran A Sadasivam, Der-Hwa Huang
Polycomb group (PcG) repressors confer epigenetically heritable silencing on key regulatory genes through histone H3 trimethylation on lysine 27 (H3K27me3). How the silencing state withstands antagonistic activities from co-expressed trithorax group (trxG) activators is unclear. Using overexpression of Trx H3K4 methylase to perturb the silenced state, we find a dynamic process triggered in a stepwise fashion to neutralize the inductive impacts from excess Trx. Shortly after Trx overexpression, there are global increases in H3K4 trimethylation and RNA polymerase II phosphorylation, marking active transcription...
April 16, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29626011/centromere-transcription-allows-cenp-a-to-transit-from-chromatin-association-to-stable-incorporation
#4
Georg O M Bobkov, Nick Gilbert, Patrick Heun
Centromeres are essential for chromosome segregation and are specified epigenetically by the presence of the histone H3 variant CENP-A. In flies and humans, replenishment of the centromeric mark is uncoupled from DNA replication and requires the removal of H3 "placeholder" nucleosomes. Although transcription at centromeres has been previously linked to the loading of new CENP-A, the underlying molecular mechanism remains poorly understood. Here, we used Drosophila melanogaster tissue culture cells to show that centromeric presence of actively transcribing RNA polymerase II temporally coincides with de novo deposition of dCENP-A...
April 6, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29606905/polytene-chromosomes-a-portrait-of-functional-organization-of-the-drosophila-genome
#5
REVIEW
Tatyana Yu Zykova, Victor G Levitsky, Elena S Belyaeva, Igor F Zhimulev
This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures - bands and interbands. Generally, densely packed chromatin forms black bands, moderately condensed regions form grey loose bands, whereas decondensed regions of the genome appear as interbands. Recent progress in the annotation of the Drosophila genome and epigenome has made it possible to compare the banding pattern and the structural organization of genes, as well as their activity. This was greatly aided by our ability to establish the borders of bands and interbands on the physical map, which allowed to perform comprehensive side-by-side comparisons of cytology, genetic and epigenetic maps and to uncover the association between the morphological structures and the functional domains of the genome...
April 2018: Current Genomics
https://www.readbyqxmd.com/read/29560857/a-switch-in-transcription-and-cell-fate-governs-the-onset-of-an-epigenetically-deregulated-tumor-in-drosophila
#6
Joana Torres, Remo Monti, Ariane L Moore, Makiko Seimiya, Yanrui Jiang, Niko Beerenwinkel, Christian Beisel, Jorge V Beira, Renato Paro
Tumor initiation is often linked to a loss of cellular identity. Transcriptional programs determining cellular identity are preserved by epigenetically-acting chromatin factors. Although such regulators are among the most frequently mutated genes in cancer, it is not well understood how an abnormal epigenetic condition contributes to tumor onset. In this work, we investigated the gene signature of tumors caused by disruption of the Drosophila epigenetic regulator, polyhomeotic (ph). In larval tissue ph mutant cells show a shift towards an embryonic-like signature...
March 21, 2018: ELife
https://www.readbyqxmd.com/read/29520020/rapid-and-transient-oxygen-consumption-increase-following-acute-hdac-kdac-inhibition-in-drosophila-tissue
#7
Lore Becker, Melanie Schmitt Nogueira, Caroline Klima, Martin Hrabe de Angelis, Shahaf Peleg
Epigenetic deregulation, such as the reduction of histone acetylation levels, is thought to be causally linked to various maladies associated with aging. Consequently, histone deacetylase inhibitors are suggested to serve as epigenetic therapy by increasing histone acetylation. However, previous work suggests that many non-histone proteins, including metabolic enzymes, are also acetylated and that post transitional modifications may impact their activity. Furthermore, deacetylase inhibitors were recently shown to impact the acetylation of a variety of proteins...
March 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29503869/tads-are-3d-structural-units-of-higher-order-chromosome-organization-in-drosophila
#8
Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I Cattoni, Giorgio L Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear...
February 2018: Science Advances
https://www.readbyqxmd.com/read/29492318/a-phenotypic-hangover-the-predictive-adaptive-response-and-multigenerational-effects-of-altered-nutrition-on-the-transcriptome-of-drosophila-melanogaster
#9
Amy J Osborne, Peter K Dearden
The Developmental Origins of Health and Disease hypothesis predicts that early-life environmental exposures can be detrimental to later-life health and that mismatch between the pre- and post-natal environment may contribute to the growing non-communicable disease epidemic. Within this is an increasingly recognized role for epigenetic mechanisms; for example, epigenetic modifications can be influenced by nutrition and can alter gene expression in mothers and offspring. Currently, there are few whole-genome transcriptional studies of response to nutritional alteration...
October 2017: Environmental Epigenetics
https://www.readbyqxmd.com/read/29466727/in-vivo-analysis-of-centromeric-proteins-reveals-a-stem-cell-specific-asymmetry-and-an-essential-role-in-differentiated-non-proliferating-cells
#10
Ana García Del Arco, Bruce A Edgar, Sylvia Erhardt
Stem cells of the Drosophila midgut (ISCs) are the only mitotically dividing cells of the epithelium and, therefore, presumably the only epithelial cells that require functional kinetochores for microtubule spindle attachment during mitosis. The histone variant CENP-A marks centromeric chromatin as the site of kinetochore formation and spindle attachment during mitotic chromosome segregation. Here, we show that centromeric proteins distribute asymmetrically during ISC division. Whereas newly synthesized CENP-A is enriched in differentiating progeny, CENP-C is undetectable in these cells...
February 20, 2018: Cell Reports
https://www.readbyqxmd.com/read/29432976/epigenomic-and-genomic-landscape-of-drosophila-melanogaster-heterochromatic-genes
#11
Parna Saha, Divya Tej Sowpati, Rakesh K Mishra
Heterochromatin is associated with transcriptional repression. In contrast, several genes in the pericentromeric regions of Drosophila melanogaster are dependent on this heterochromatic environment for their expression. Here we present a comprehensive analysis of the epigenetic landscape of heterochromatic genes across all the developmental stages of Drosophila using the available histone modification and expression data from modENCODE. We find that heterochromatic genes exhibit combinations of active and inactive histone marks that correspond to their level of expression during development...
February 10, 2018: Genomics
https://www.readbyqxmd.com/read/29386085/dna-methylation-is-not-involved-in-dietary-restriction-induced-lifespan-extension-in-adult-drosophila
#12
Ting Lian, Uma Gaur, Q I Wu, Jianbo Tu, Boyuan Sun, Deying Yang, Xiaolan Fan, Xueping Mao, Mingyao Yang
Dietary restriction (DR) is widely regarded as a viable intervention to extend lifespan and healthspan in diverse organisms. The precise molecular regulatory mechanisms are largely unknown. Epigenetic modifications are not stable upon DR and also keep changing with age. Here, we employed whole genome bisulfite sequencing to determine the DNA methylation changes upon DR in adult Drosophila. Our results indicate that although a low level of DNA methylation exists in the adult Drosophila genome, there is no significant difference in DNA methylation levels upon DR when compared to unrestricted flies...
February 1, 2018: Genetics Research
https://www.readbyqxmd.com/read/29372960/-control-of-the-gene-activity-by-polycomb-and-trithorax-group-proteins-in-drosophila
#13
REVIEW
D A Chetverina, P V Elizar’ev, D V Lomaev, P G Georgiev, M M Erokhin
Combinatorial expression of the genes in multicellular organisms leads to the development of different cell types. The important epigenetic regulators of higher eukaryotes are the Polycomb group (PcG) and Trithorax group (TrxG) proteins. These factors control the transcription of a large number of genes involved in various cellular processes. Dysregulation of PcG and TrxG systems leads to developmental abnormalities and cancer. This review focuses on the main characteristics and properties of the Drosophila PRE elements...
February 2017: Genetika
https://www.readbyqxmd.com/read/29364877/tet2-promotes-pathogen-infection-induced-myelopoiesis-through-mrna-oxidation
#14
Qicong Shen, Qian Zhang, Yang Shi, Qingzhu Shi, Yanyan Jiang, Yan Gu, Zhiqing Li, Xia Li, Kai Zhao, Chunmei Wang, Nan Li, Xuetao Cao
Varieties of RNA modification form the epitranscriptome for post-transcriptional regulation. 5-Methylcytosine (5-mC) is a sparse RNA modification in messenger RNA (mRNA) under physiological conditions. The function of RNA 5-hydroxymethylcytosine (5-hmC) oxidized by ten-eleven translocation (Tet) proteins in Drosophila has been revealed more recently. However, the turnover and function of 5-mC in mammalian mRNA have been largely unknown. Tet2 suppresses myeloid malignancies mostly in an enzymatic activity-dependent manner, and is important in resolving inflammatory response in an enzymatic activity-independent way...
February 1, 2018: Nature
https://www.readbyqxmd.com/read/29357905/chromosome-nuclear-envelope-attachments-affect-interphase-chromosome-territories-and-entanglement
#15
Nicholas Allen Kinney, Igor V Sharakhov, Alexey V Onufriev
BACKGROUND: It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome territories have biologically significant properties, and understanding how these properties change with time during lifetime of the cell is important. Chromosome-nuclear envelope (Chr-NE) interactions play a role in epigenetic regulation of DNA replication, repair, and transcription. However, their role in maintaining chromosome territories remains unclear...
January 22, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29348326/symmetry-from-asymmetry-or-asymmetry-from-symmetry
#16
Elizabeth W Kahney, Rajesh Ranjan, Ryan J Gleason, Xin Chen
The processes of DNA replication and mitosis allow the genetic information of a cell to be copied and transferred reliably to its daughter cells. However, if DNA replication and cell division were always performed in a symmetric manner, the result would be a cluster of tumor cells instead of a multicellular organism. Therefore, gaining a complete understanding of any complex living organism depends on learning how cells become different while faithfully maintaining the same genetic material. It is well recognized that the distinct epigenetic information contained in each cell type defines its unique gene expression program...
January 18, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29345184/temperature-dependent-small-rna-expression-in-drosophila-melanogaster
#17
Isabel Fast, David Rosenkranz
Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures...
January 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/29249293/epigenetic-crosstalk-pharmacological-inhibition-of-hdacs-can-rescue-defective-synaptic-morphology-and-neurotransmission-phenotypes-associated-with-loss-of-the-chromatin-reader-kismet
#18
REVIEW
Nina K Latcheva, Jennifer M Viveiros, Edward A Waddell, Phuong T T Nguyen, Faith L W Liebl, Daniel R Marenda
We are beginning to appreciate the complex mechanisms by which epigenetic proteins control chromatin dynamics to tightly regulate normal development. However, the interaction between these proteins, particularly in the context of neuronal function, remains poorly understood. Here, we demonstrate that the activity of histone deacetylases (HDACs) opposes that of a chromatin remodeling enzyme at the Drosophila neuromuscular junction (NMJ). Pharmacological inhibition of HDAC function reverses loss of function phenotypes associated with Kismet, a chromodomain helicase DNA-binding (CHD) protein...
March 2018: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/29242288/a-role-for-monomethylation-of-histone-h3-k27-in-gene-activity-in-drosophila
#19
Liangjun Wang, Preeti Joshi, Ellen L Miller, LeeAnn Higgins, Matthew Slattery, Jeffrey A Simon
Polycomb repressive complex 2 (PRC2) is a conserved chromatin-modifying enzyme that methylates histone H3 on lysine-27 (K27). PRC2 can add one, two, or three methyl groups and the fully methylated product, H3-K27me3, is a hallmark of Polycomb-silenced chromatin. Less is known about functions of K27me1 and K27me2 and the dynamics of flux through these states. These modifications could serve mainly as intermediates to produce K27me3 or they could each convey distinct epigenetic information. To investigate this, we engineered a variant of Drosophila melanogaster PRC2 which is converted into a monomethyltransferase...
March 2018: Genetics
https://www.readbyqxmd.com/read/29190361/shaping-epigenetic-memory-via-genomic-bookmarking
#20
Davide Michieletto, Michael Chiang, Davide Colì, Argyris Papantonis, Enzo Orlandini, Peter R Cook, Davide Marenduzzo
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors...
January 9, 2018: Nucleic Acids Research
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