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Drosophila chromatin

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https://www.readbyqxmd.com/read/29149408/function-of-translationally-controlled-tumor-protein-in-organ-growth-lessons-from-drosophila-studies
#1
Kwang-Wook Choi, Sung-Tae Hong, Thao Phuong Le
Regulation of cell growth and proliferation is crucial for development and function of organs in all animals. Genetic defects in growth control can lead to developmental disorders and cancers. Translationally controlled tumor protein (TCTP) is a family of evolutionarily conserved proteins implicated in cancer. Recent studies have revealed multiple roles of TCTP in diverse cellular events, but TCTP functions in vivo are poorly understood in vertebrate systems. We have used Drosophila melanogaster, the fruit fly, as a model organism for genetic dissection of Tctp function...
2017: Results and Problems in Cell Differentiation
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
#2
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/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#3
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29133298/functional-redundancy-of-variant-and-canonical-histone-h3-lysine-9-modification-in-drosophila
#4
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/29126440/chromatin-organization-changes-during-the-establishment-and-maintenance-of-the-postmitotic-state
#5
Yiqin Ma, Laura Buttitta
BACKGROUND: Genome organization changes during development as cells differentiate. Chromatin motion becomes increasingly constrained and heterochromatin clusters as cells become restricted in their developmental potential. These changes coincide with slowing of the cell cycle, which can also influence chromatin organization and dynamics. Terminal differentiation is often coupled with permanent exit from the cell cycle, and existing data suggest a close relationship between a repressive chromatin structure and silencing of the cell cycle in postmitotic cells...
November 10, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29125381/pleiotropy-in-drosophila-organogenesis-mechanistic-insights-from-combgap-and-the-retinal-determination-gene-network
#6
Trevor L Davis, Ilaria Rebay
Master regulatory transcription factors cooperate in networks to shepherd cells through organogenesis. In the Drosophila eye, a collection of master control proteins known as the retinal determination gene network (RDGN) switches the direction and targets of its output to choreograph developmental transitions, but the molecular partners that enable such regulatory flexibility are not known. We recently showed that two RDGN members, Eyes absent (Eya) and Sine oculis (So), promote exit from the terminal cell cycle known as the second mitotic wave (SMW) to permit differentiation...
November 10, 2017: Fly
https://www.readbyqxmd.com/read/29108672/foxa-transcription-factor-fork-head-maintains-the-intestinal-stem-progenitor-cell-identities-in-drosophila
#7
Qing Lan, Min Cao, Rahul K Kollipara, Jeffrey B Rosa, Ralf Kittler, Huaqi Jiang
Understanding how somatic stem cells respond to tissue needs is important, since aberrant somatic stem cell behaviors may lead to tissue degeneration or tumorigenesis. Here, from an in vivo RNAi screen targeting transcription factors that regulate intestinal regeneration, we uncovered a requirement for the Drosophila FoxA transcription factor Fork head (Fkh) in the maintenance of intestinal stem/progenitor cell identities. FoxA/Fkh maintains the expressions of stem/progenitor cell markers and is required for stem cell proliferation during intestinal homeostasis and regeneration...
September 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29102770/overexpression-of-djmj-differentially-affects-intestinal-stem-cells-and-differentiated-enterocytes
#8
Dang Ngoc Anh Suong, Kouhei Shimaji, Jung-Hoon Pyo, Joung-Sun Park, Hideki Yoshida, Mi-Ae Yoo, Masamitsu Yamaguchi
Jumonji (Jmj)/Jarid2 is a DNA-binding transcriptional repressor mediated via histone methylation. Nevertheless, the well-known function of Jmj is as a scaffold for the recruitment of various complexes including Polycomb repressive complex 2 (PRC2), and required for mouse embryonic stem cell development. However, PRC2 independent function is suggested for Drosophila Jumonji (dJmj). To clarify the function of dJmj during cell differentiation, we used Drosophila adult intestinal stem cell system that allows to follow stem cell behaviors in vivo...
November 2, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29097190/control-of-nerve-cord-formation-by-engrailed-and-gooseberry-neuro-a-multi-step-coordinated-process
#9
Nathalie Bonneaud, Sophie Layalle, Sophie Colomb, Christophe Jourdan, Alain Ghysen, Dany Severac, Christelle Dantec, Nicolas Nègre, Florence Maschat
One way to better understand the molecular mechanisms involved in the construction of a nervous system is to identify the downstream effectors of major regulatory proteins. We previously showed that Engrailed (EN) and Gooseberry-Neuro (GsbN) transcription factors act in partnership to drive the formation of posterior commissures in the central nervous system of Drosophila. In this report, we identified genes regulated by both EN and GsbN through chromatin immunoprecipitation ("ChIP on chip") and transcriptome experiments, combined to a genetic screen relied to the gene dose titration method...
October 30, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29089422/a-cryptic-tudor-domain-links-brwd2-phip-to-compass-mediated-histone-h3k4-methylation
#10
Marc A J Morgan, Ryan A Rickels, Clayton K Collings, Xiaolin He, Kaixiang Cao, Hans-Martin Herz, Kira A Cozzolino, Nebiyu A Abshiru, Stacy A Marshall, Emily J Rendleman, Christie C Sze, Andrea Piunti, Neil L Kelleher, Jeffrey N Savas, Ali Shilatifard
Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4-RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain...
October 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/29077765/enhanced-chromatin-accessibility-of-the-dosage-compensated-drosophila-male-x-chromosome-requires-the-clamp-zinc-finger-protein
#11
Jennifer Urban, Guray Kuzu, Sarah Bowman, Benjamin Scruggs, Telmo Henriques, Robert Kingston, Karen Adelman, Michael Tolstorukov, Erica Larschan
The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes...
2017: PloS One
https://www.readbyqxmd.com/read/29069466/mga-repository-a-curated-data-resource-for-chip-seq-and-other-genome-annotated-data
#12
René Dréos, Giovanna Ambrosini, Romain Groux, Rouayda Cavin Périer, Philipp Bucher
The Mass Genome Annotation (MGA) repository is a resource designed to store published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) in a completely standardised format. Each sample has undergone local processing in order the meet the strict MGA format requirements. The original data source, the reformatting procedure and the biological characteristics of the samples are described in an accompanying documentation file manually edited by data curators...
October 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29065309/pwp1-mediates-nutrient-dependent-growth-control-through-nucleolar-regulation-of-ribosomal-gene-expression
#13
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/29056321/cbp-regulates-recruitment-and-release-of-promoter-proximal-rna-polymerase-ii
#14
Ann Boija, Dig Bijay Mahat, Aman Zare, Per-Henrik Holmqvist, Philge Philip, David J Meyers, Philip A Cole, John T Lis, Per Stenberg, Mattias Mannervik
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide...
November 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29046480/epigenetic-mechanisms-underlying-maternal-diabetes-associated-risk-of-congenital-heart-disease
#15
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/29045822/individual-effects-of-the-copia-and-gypsy-enhancer-and-insulator-on-chromatin-marks-erna-synthesis-and-binding-of-insulator-proteins-in-transfected-genetic-constructs
#16
Daria M Fedoseeva, Olga V Kretova, Maria A Gorbacheva, Nickolai A Tchurikov
Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer...
October 15, 2017: Gene
https://www.readbyqxmd.com/read/29036346/opbp-is-a-new-architectural-insulator-protein-required-for-ribosomal-gene-expression
#17
Nikolay Zolotarev, Oksana Maksimenko, Olga Kyrchanova, Elena Sokolinskaya, Igor Osadchiy, Charles Girardot, Artem Bonchuk, Lucia Ciglar, Eileen E M Furlong, Pavel Georgiev
A special class of poorly characterized architectural proteins is required for chromatin topology and enhancer-promoter interactions. Here, we identify Opbp as a new Drosophila architectural protein, interacting with CP190 both in vivo and in vitro. Opbp binds to a very restrictive set of genomic regions, through a rare sequence specific motif. These sites are co-bound by CP190 in vivo, and generally located at bidirectional promoters of ribosomal protein genes. We show that Opbp is essential for viability, and loss of opbp function, or destruction of its motif, leads to reduced ribosomal protein gene expression, indicating a functional role in promoter activation...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29030848/profiling-open-chromatin-structure-in-the%C3%A2-ovarian-somatic-cells-using-atac-seq
#18
Kensaku Murano, Yuka W Iwasaki, Haruhiko Siomi
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29028826/identification-of-cis-regulatory-sequences-reveals-potential-participation-of-lola-and-deaf1-transcription-factors-in-anopheles-gambiae-innate-immune-response
#19
Bernardo Pérez-Zamorano, Sandra Rosas-Madrigal, Oscar Arturo Migueles Lozano, Manuel Castillo Méndez, Verónica Valverde-Garduño
The innate immune response of Anopheles gambiae involves the transcriptional upregulation of effector genes. Therefore, the cis-regulatory sequences and their cognate binding factors play essential roles in the mosquito's immune response. However, the genetic control of the mosquito's innate immune response is not yet fully understood. To gain further insight on the elements, the factors and the potential mechanisms involved, an open chromatin profiling was carried out on A. gambiae-derived immune-responsive cells...
2017: PloS One
https://www.readbyqxmd.com/read/29021216/multiple-interactions-are-involved-in-a-highly-specific-association-of-the-mod-mdg4-67-2-isoform-with-the-su-hw-sites-in-drosophila
#20
Larisa Melnikova, Margarita Kostyuchenko, Varvara Molodina, Alexander Parshikov, Pavel Georgiev, Anton Golovnin
The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited to the chromatin through interactions with the DNA-binding Su(Hw) protein. It was shown previously that Mod(mdg4)-67.2 is critical for the enhancer-blocking activity of the Su(Hw) insulators and it differs from more than 30 other Mod(mdg4) isoforms by the C-terminal domain required for a specific interaction with Su(Hw) only. The mechanism of the highly specific association between Mod(mdg4)-67...
October 2017: Open Biology
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