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Drosophila epigenetics

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https://www.readbyqxmd.com/read/29348326/symmetry-from-asymmetry-or-asymmetry-from-symmetry
#1
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
#2
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
#3
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...
December 14, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/29242288/a-role-for-mono-methylation-of-histone-h3-k27-in-gene-activity-in-drosophila
#4
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 mono-methyltransferase...
December 14, 2017: Genetics
https://www.readbyqxmd.com/read/29190361/shaping-epigenetic-memory-via-genomic-bookmarking
#5
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...
November 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29177687/epigenetic-factors-polycomb-pc-and-suppressor-of-zeste-su-z-2-negatively-regulate-longevity-in-drosophila-melanogaster
#6
Vasanthi Dasari, Surabhi Srivastava, Shagufta Khan, Rakesh K Mishra
The process of aging is a hallmark of the natural life span of all organisms and individuals within a population show variability in the measures of age related performance. Longevity and the rate of aging are influenced by several factors such as genetics, nutrition, stress, and environment. Many studies have focused on the genes that impact aging and there is increasing evidence that epigenetic factors regulate these genes to control life span. Polycomb (PcG) and trithorax (trxG) protein complexes maintain the expression profiles of developmentally important genes and regulate many cellular processes...
November 27, 2017: Biogerontology
https://www.readbyqxmd.com/read/29177663/chromatin-immunoprecipitation-chip-of-heat-shock-protein-90-hsp90
#7
Aneliya Yoveva, Ritwick Sawarkar
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used technique for genome-wide mapping of protein-DNA interactions and epigenetic marks in vivo. Recent studies have suggested an important role of heat shock protein 90 (Hsp90) at chromatin. This molecular chaperone assists other proteins to acquire their mature and functional conformation and helps in the assembly of many complexes. In this chapter, we provide specific details on how to perform Hsp90 ChIP-seq from Drosophila Schneider (S2) cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29175436/3d-chromatin-architecture-of-large-plant-genomes-determined-by-local-a-b-compartments
#8
Pengfei Dong, Xiaoyu Tu, Po-Yu Chu, Peitao Lü, Ning Zhu, Donald Grierson, Baijuan Du, Pinghua Li, Silin Zhong
The spatial organization of the genome plays an important role in the regulation of gene expression. However, the core structural features of animal genomes, such as topologically associated domains (TADs) and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we have examined the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin and gene expression, of maize, tomato, sorghum, foxtail millet and rice with genome sizes ranging from 0...
November 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29174947/rbfox1-encoding-a-splicing-regulator-is-a-candidate-gene-for-aggressive-behavior
#9
Noèlia Fernàndez-Castillo, Gabriela Gan, Marjolein M J van Donkelaar, Mariliis Vaht, Heike Weber, Wolfgang Retz, Andreas Meyer-Lindenberg, Barbara Franke, Jaanus Harro, Andreas Reif, Stephen V Faraone, Bru Cormand
The RBFOX1 gene (or A2BP1) encodes a splicing factor important for neuronal development that has been related to autism spectrum disorder and other neurodevelopmental phenotypes. Evidence from complementary sources suggests that this gene contributes to aggressive behavior. Suggestive associations with RBFOX1 have been identified in genome-wide association studies (GWAS) of anger, conduct disorder, and aggressive behavior. Nominal association signals in RBFOX1 were also found in an epigenome-wide association study (EWAS) of aggressive behavior...
November 23, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29170434/single-cell-absolute-contact-probability-detection-reveals-chromosomes-are-organized-by-multiple-low-frequency-yet-specific-interactions
#10
Diego I Cattoni, Andrés M Cardozo Gizzi, Mariya Georgieva, Marco Di Stefano, Alessandro Valeri, Delphine Chamousset, Christophe Houbron, Stephanie Déjardin, Jean-Bernard Fiche, Inma González, Jia-Ming Chang, Thomas Sexton, Marc A Marti-Renom, Frédéric Bantignies, Giacomo Cavalli, Marcelo Nollmann
At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type...
November 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133298/functional-redundancy-of-variant-and-canonical-histone-h3-lysine-9-modification-in-drosophila
#11
Taylor J R Penke, Daniel J McKay, Brian D Strahl, A Gregory Matera, Robert J Duronio
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin...
November 13, 2017: Genetics
https://www.readbyqxmd.com/read/29130960/piwi-proteins-and-piwi-interacting-rna-emerging-roles-in-cancer
#12
Yi-Neng Han, Yuan Li, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNAs (ncRNAs) and interact with PIWI proteins. piRNAs were primarily described in the germline, but emerging evidence revealed that piRNAs are expressed in a tissue-specific manner among multiple human somatic tissue types as well and play important roles in transposon silencing, epigenetic regulation, gene and protein regulation, genome rearrangement, spermatogenesis and germ stem-cell maintenance. PIWI proteins were first discovered in Drosophila and they play roles in spermatogenesis, germline stem-cell maintenance, self-renewal, retrotransposons silencing and the male germline mobility control...
November 3, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29078350/epigenetic-mechanisms-modulate-differences-in-drosophila-foraging-behavior
#13
Ina Anreiter, Jamie M Kramer, Marla B Sokolowski
Little is known about how genetic variation and epigenetic marks interact to shape differences in behavior. The foraging (for) gene regulates behavioral differences between the rover and sitter Drosophila melanogaster strains, but the molecular mechanisms through which it does so have remained elusive. We show that the epigenetic regulator G9a interacts with for to regulate strain-specific adult foraging behavior through allele-specific histone methylation of a for promoter (pr4). Rovers have higher pr4 H3K9me dimethylation, lower pr4 RNA expression, and higher foraging scores than sitters...
October 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29066499/a-mutually-exclusive-stem-loop-arrangement-in-rox2-rna-is-essential-for-x-chromosome-regulation-in-drosophila
#14
Ibrahim Avsar Ilik, Daniel Maticzka, Plamen Georgiev, Noel Marie Gutierrez, Rolf Backofen, Asifa Akhtar
The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX long noncoding RNAs (lncRNAs) harbor several redundant domains to interact with the ubiquitin ligase male-specific lethal 2 (MSL2) and the RNA helicase Maleless (MLE) for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By using the uvCLAP (UV cross-linking and affinity purification) methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA...
October 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/29065309/pwp1-mediates-nutrient-dependent-growth-control-through-nucleolar-regulation-of-ribosomal-gene-expression
#15
Ying Liu, Jaakko Mattila, Sami Ventelä, Leena Yadav, Wei Zhang, Nicole Lamichane, Jari Sundström, Otto Kauko, Reidar Grénman, Markku Varjosalo, Jukka Westermarck, Ville Hietakangas
Ribosome biogenesis regulates animal growth and is controlled by nutrient-responsive mTOR signaling. How ribosome biogenesis is regulated during the developmental growth of animals and how nutrient-responsive signaling adjusts ribosome biogenesis in this setting have remained insufficiently understood. We uncover PWP1 as a chromatin-associated regulator of developmental growth with a conserved role in RNA polymerase I (Pol I)-mediated rRNA transcription. We further observed that PWP1 epigenetically maintains the rDNA loci in a transcription-competent state...
October 23, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29046480/epigenetic-mechanisms-underlying-maternal-diabetes-associated-risk-of-congenital-heart-disease
#16
Madhumita Basu, Jun-Yi Zhu, Stephanie LaHaye, Uddalak Majumdar, Kai Jiao, Zhe Han, Vidu Garg
Birth defects are the leading cause of infant mortality, and they are caused by a combination of genetic and environmental factors. Environmental risk factors may contribute to birth defects in genetically susceptible infants by altering critical molecular pathways during embryogenesis, but experimental evidence for gene-environment interactions is limited. Fetal hyperglycemia associated with maternal diabetes results in a 5-fold increased risk of congenital heart disease (CHD), but the molecular basis for this correlation is unknown...
October 19, 2017: JCI Insight
https://www.readbyqxmd.com/read/29045450/the-genetics-and-development-of-mandibles-and-hypopharyngeal-sclerite-and-cornua-in-larvae-of-drosophila-gaucha
#17
Eduardo Alvarez, Francisco Del Pino, Lilian Jara, Raúl Godoy-Herrera
The genetics and epigenetic processes associated with morphological organization are a principal aim of biology, ranging from cohesion between cells to shape and size of organisms. We investigate the post-embryonic development of Hypopharyngeal sclerite and cornua HPC and mandibles M of Drosophila gaucha larva. Integrated functioning of these Cephalopharyngeal skeleton parts of D. gaucha larva is essential for food acquisition, participating in locomotion and microhabitat selection. We examined two isolates by recording the growth of the HPC and M every 24 h for 8 days in parental, F1, F2 and backcross larvae...
2017: PloS One
https://www.readbyqxmd.com/read/29021174/nutritional-geometry-of-paternal-effects-on-embryo-mortality
#18
Michal Polak, Leigh W Simmons, Joshua B Benoit, Kari Ruohonen, Stephen J Simpson, Samantha M Solon-Biet
Well-established causal links exist between maternal nutritional deficits and embryo health and viability. By contrast, environmental effects operating through the father that could influence embryo mortality have seldom been examined. Yet, ejaculates can require non-trivial resource allocation, and seminal plasma components are increasingly recognized to exert wide-ranging effects on females and offspring, so paternal dietary effects on the embryo should be expected. We test for effects of varying levels of protein (P), carbohydrate (C) and caloric load in adult male diet on embryo mortality in Drosophila melanogaster We demonstrate that macronutrient balance and caloric restriction exert significant effects, and that nutritional effects are more impactful when a prior mating has occurred...
October 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28975408/genome-wide-analysis-of-su-var-3-9-distribution-in-chromosomes-of-drosophila-melanogaster
#19
Daniil A Maksimov, Petr P Laktionov, Olga V Posukh, Stepan N Belyakin, Dmitry E Koryakov
Histone modifications represent one of the key factors contributing to proper genome regulation. One of histone modifications involved in gene silencing is methylation of H3K9 residue. Present in the chromosomes across different eukaryotes, this epigenetic mark is controlled by SU(VAR)3-9 and its orthologs. Despite SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic (salivary glands and brain ganglia) and two germline (ovarian nurse cells and testes) tissues of Drosophila melanogaster...
October 3, 2017: Chromosoma
https://www.readbyqxmd.com/read/28919441/a-unique-ph-dependent-recognition-of-methylated-histone-h3k4-by-pps-and-dido
#20
Adam H Tencer, Jovylyn Gatchalian, Brianna J Klein, Abid Khan, Yi Zhang, Brian D Strahl, Karel H M van Wely, Tatiana G Kutateladze
The protein partner of Sans-fille (PPS) and its human homolog DIDO mediate diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing in Drosophila. Here, we show that the PHD fingers of PPS and DIDO recognize the histone mark H3K4me3 in a pH-dependent manner: the binding is enhanced at high pH values but is decreased at low pH. Structural analysis reveals that the pH dependency is due to the presence of a histidine residue in the K4me3-binding aromatic cage of PPS...
October 3, 2017: Structure
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