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https://www.readbyqxmd.com/read/27875550/an-alternative-approach-to-chip-seq-normalization-enables-detection-of-genome-wide-changes-in-histone-h3-lysine-27-trimethylation-upon-ezh2-inhibition
#1
Brian Egan, Chih-Chi Yuan, Madeleine Lisa Craske, Paul Labhart, Gulfem D Guler, David Arnott, Tobias M Maile, Jennifer Busby, Chisato Henry, Theresa K Kelly, Charles A Tindell, Suchit Jhunjhunwala, Feng Zhao, Charlie Hatton, Barbara M Bryant, Marie Classon, Patrick Trojer
Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3)...
2016: PloS One
https://www.readbyqxmd.com/read/27241916/concentrating-pre-mrna-processing-factors-in-the-histone-locus-body-facilitates-efficient-histone-mrna-biogenesis
#2
Deirdre C Tatomer, Esteban Terzo, Kaitlin P Curry, Harmony Salzler, Ivan Sabath, Grzegorz Zapotoczny, Daniel J McKay, Zbigniew Dominski, William F Marzluff, Robert J Duronio
The histone locus body (HLB) assembles at replication-dependent histone genes and concentrates factors required for histone messenger RNA (mRNA) biosynthesis. FLASH (Flice-associated huge protein) and U7 small nuclear RNP (snRNP) are HLB components that participate in 3' processing of the nonpolyadenylated histone mRNAs by recruiting the endonuclease CPSF-73 to histone pre-mRNA. Using transgenes to complement a FLASH mutant, we show that distinct domains of FLASH involved in U7 snRNP binding, histone pre-mRNA cleavage, and HLB localization are all required for proper FLASH function in vivo...
June 6, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27145109/organ-identity-specification-factor-wge-localizes-to-the-histone-locus-body-and-regulates-histone-expression-to-ensure-genomic-stability-in-drosophila
#3
Nao Ozawa, Hirofumi Furuhashi, Keita Masuko, Eriko Numao, Takashi Makino, Tamaki Yano, Shoichiro Kurata
Over-expression of Winged-Eye (WGE) in the Drosophila eye imaginal disc induces an eye-to-wing transformation. Endogenous WGE is required for organ development, and wge-deficient mutants exhibit growth arrest at the larval stage, suggesting that WGE is critical for normal growth. The function of WGE, however, remains unclear. Here, we analyzed the subcellular localization of WGE to gain insight into its endogenous function. Immunostaining showed that WGE localized to specific nuclear foci called the histone locus body (HLB), an evolutionarily conserved nuclear body required for S phase-specific histone mRNA production...
May 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/26178786/transcriptional-repression-by-prc1-in-the-absence-of-h2a-monoubiquitylation
#4
Ana Raquel Pengelly, Reinhard Kalb, Katja Finkl, Jürg Müller
Histone H2A monoubiquitylation (H2Aub) is considered to be a key effector in transcriptional repression by Polycomb-repressive complex 1 (PRC1). We analyzed Drosophila with a point mutation in the PRC1 subunit Sce that abolishes its H2A ubiquitylase activity or with point mutations in the H2A and H2Av residues ubiquitylated by PRC1. H2Aub is essential for viability and required for efficient histone H3 Lys27 trimethylation by PRC2 early in embryogenesis. However, H2Aub-deficient animals fully maintain repression of PRC1 target genes and do not show phenotypes characteristic of Polycomb group mutants...
July 15, 2015: Genes & Development
https://www.readbyqxmd.com/read/26051888/replication-fork-progression-during-re-replication-requires-the-dna-damage-checkpoint-and-double-strand-break-repair
#5
Jessica L Alexander, M Inmaculada Barrasa, Terry L Orr-Weaver
Replication origins are under tight regulation to ensure activation occurs only once per cell cycle [1, 2]. Origin re-firing in a single S phase leads to the generation of DNA double-strand breaks (DSBs) and activation of the DNA damage checkpoint [2-7]. If the checkpoint is blocked, cells enter mitosis with partially re-replicated DNA that generates chromosome breaks and fusions [5]. These types of chromosomal aberrations are common in numerous human cancers, suggesting that re-replication events contribute to cancer progression...
June 15, 2015: Current Biology: CB
https://www.readbyqxmd.com/read/25779050/invadolysin-acts-genetically-via-the-saga-complex-to-modulate-chromosome-structure
#6
Shubha Gururaja Rao, Michal M Janiszewski, Edward Duca, Bryce Nelson, Kanishk Abhinav, Ioanna Panagakou, Sharron Vass, Margarete M S Heck
Identification of components essential to chromosome structure and behaviour remains a vibrant area of study. We have previously shown that invadolysin is essential in Drosophila, with roles in cell division and cell migration. Mitotic chromosomes are hypercondensed in length, but display an aberrant fuzzy appearance. We additionally demonstrated that in human cells, invadolysin is localized on the surface of lipid droplets, organelles that store not only triglycerides and sterols but also free histones H2A, H2Av and H2B...
April 20, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25632158/rrp6-exosc10-is-required-for-the-repair-of-dna-double-strand-breaks-by-homologous-recombination
#7
Consuelo Marin-Vicente, Judit Domingo-Prim, Andrea B Eberle, Neus Visa
The exosome acts on different RNA substrates and plays important roles in RNA metabolism. The fact that short non-coding RNAs are involved in the DNA damage response led us to investigate whether the exosome factor RRP6 of Drosophila melanogaster and its human ortholog EXOSC10 play a role in DNA repair. Here, we show that RRP6 and EXOSC10 are recruited to DNA double-strand breaks (DSBs) in S2 cells and HeLa cells, respectively. Depletion of RRP6/EXOSC10 does not interfere with the phosphorylation of the histone variant H2Av (Drosophila) or H2AX (humans), but impairs the recruitment of the homologous recombination factor RAD51 to the damaged sites, without affecting RAD51 levels...
March 15, 2015: Journal of Cell Science
https://www.readbyqxmd.com/read/25065591/crumbs-interacts-with-xpd-for-nuclear-division-control-in-drosophila
#8
E Yeom, S-T Hong, K-W Choi
Crumbs (Crb) family proteins are crucial for cell polarity. Recent studies indicate that they are also involved in growth regulation and cancer. However, it is not well-understood how Crb participates in mitotic processes. Here, we report that Drosophila Crb is critically involved in nuclear division by interacting with Xeroderma pigmentosum D (XPD). A novel gene named galla-1 was identified from a genetic screen for crb modifiers. Galla-1 protein shows homology to MIP18, a subunit of the mitotic spindle-associated MMS19-XPD complex...
May 21, 2015: Oncogene
https://www.readbyqxmd.com/read/24930966/drosophila-lipid-droplets-buffer-the-h2av-supply-to-protect-early-embryonic-development
#9
Zhihuan Li, Matthew R Johnson, Zhonghe Ke, Lili Chen, Michael A Welte
Assembly of DNA into chromatin requires a delicate balancing act, as both dearth and excess of histones severely disrupt chromatin function [1-3]. In particular, cells need to carefully control histone stoichiometry: if different types of histones are incorporated into chromatin in an imbalanced manner, it can lead to altered gene expression, mitotic errors, and death [4-6]. Both the balance between individual core histones and the balance between core histones and histone variants are critical [5, 7]. Here, we find that in early Drosophila embryos, histone balance in the nuclei is regulated by lipid droplets, cytoplasmic fat-storage organelles [8]...
July 7, 2014: Current Biology: CB
https://www.readbyqxmd.com/read/24833720/a-feed-forward-mechanism-involving-drosophila-fragile-x-mental-retardation-protein-triggers-a-replication-stress-induced-dna-damage-response
#10
Wenxin Zhang, Ying Cheng, Yujing Li, Zhenping Chen, Peng Jin, Dahua Chen
Fragile X syndrome, a common form of inherited mental retardation, is caused by loss of the fragile X mental retardation protein (FMRP). As a selective RNA-binding protein, FMRP is localized predominately in cytoplasm, where it regulates translational control. However, there is a small portion of FMRP present in the nucleus, and its function there has been elusive. Here, we show that Drosophila dFMR1 in nucleus is required for replication stress-induced H2Av phosphorylation in the DNA damage response (DDR)...
October 1, 2014: Human Molecular Genetics
https://www.readbyqxmd.com/read/24639513/histone-h3-lysine-4-trimethylation-regulates-cotranscriptional-h2a-variant-exchange-by-tip60-complexes-to-maximize-gene-expression
#11
Thomas Kusch, Amanda Mei, Camtu Nguyen
Histone H3 lysine 4 trimethylation (H3K4me3) and the acetylated H2A variant, H2A.Z/v (H2Avac), are enriched at promoters of highly transcribed loci including the stress response genes. Using the inducible Drosophila hsp70 loci as a model, we study here the roles of the dSet1 and dTip60 complexes in the generation of these two chromatin modifications. We find that Heat Shock Factor recruits the dTip60 complex to the hsp70 loci in cells treated with salicylate, which triggers chromatin remodeling at these loci without transcription activation...
April 1, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/24508391/kinase-mediated-changes-in-nucleosome-conformation-trigger-chromatin-decondensation-via-poly-adp-ribosyl-ation
#12
Colin J Thomas, Elena Kotova, Mark Andrake, Jared Adolf-Bryfogle, Robert Glaser, Catherine Regnard, Alexei V Tulin
Dynamically controlled posttranslational modifications of nucleosomal histones alter chromatin condensation to regulate transcriptional activation. We report that a nuclear tandem kinase, JIL-1, controls gene expression by activating poly(ADP-ribose) polymerase-1 (PARP-1). JIL-1 phosphorylates the C terminus of the H2Av histone variant, which stimulates PARP-1 enzymatic activity in the surrounding chromatin, leading to further modification of histones and chromatin loosening. The H2Av nucleosome has a higher surface representation of PARP-1 binding patch, consisting of H3 and H4 epitopes...
March 6, 2014: Molecular Cell
https://www.readbyqxmd.com/read/23833215/the-development-of-a-monoclonal-antibody-recognizing-the-drosophila-melanogaster-phosphorylated-histone-h2a-variant-%C3%AE-h2av
#13
Cathleen M Lake, Julie Korda Holsclaw, Stephanie P Bellendir, Jeff Sekelsky, R Scott Hawley
The recognition of DNA double-strand breaks (DSBs) using a phospho-specific antibody to the histone 2A variant has become the gold standard assay for DNA damage detection. Here we report on the development of the first monoclonal antibody to the phospho-specific form of Drosophila H2AV and characterize the specificity of this antibody to programmed DSBs in oocytes and rereplication sites in endocycling cells by immunofluorescence assays and to DSBs resulting from irradiation in both cell culture and whole tissue by Western blot assays...
September 2013: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/23438598/the-complex-containing-drosophila-myb-and-rb-e2f2-regulates-cytokinesis-in-a-histone-h2av-dependent-manner
#14
Heather DeBruhl, Hong Wen, Joseph S Lipsick
In Drosophila, mutation of the oncogene Myb reduced the expression of mitotic genes, such as polo and ial, and caused multiple mitotic defects, including disrupted chromosome condensation and abnormal spindles. We now show that binucleate cells, the hallmark phenotype of cytokinesis failure, accumulate in Myb-null ovarian follicle cell and wing disc epithelia. Myb functions as an activator in the generally repressive Drosophila RBF, E2F2, and Myb (dREAM)/Myb-MuvB complex. Absence of the dREAM subunit Mip130 or E2F2 suppressed the Myb-null cytokinesis defect...
May 2013: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/23084995/lipid-droplets-control-the-maternal-histone-supply-of-drosophila-embryos
#15
Zhihuan Li, Katharina Thiel, Peter J Thul, Mathias Beller, Ronald P Kühnlein, Michael A Welte
BACKGROUND: Histones are essential for chromatin packing, yet free histones not incorporated into chromatin are toxic. While in most cells multiple regulatory mechanisms prevent accumulation of excess histones, early Drosophila embryos contain massive extranuclear histone stores, thought to be essential for development. Excess histones H2A, H2B, and H2Av are bound to lipid droplets, ubiquitous fat storage organelles especially abundant in embryos. It has been proposed that sequestration on lipid droplets allows safe transient storage of supernumerary histones...
November 20, 2012: Current Biology: CB
https://www.readbyqxmd.com/read/23035220/baculoviruses-modulate-a-proapoptotic-dna-damage-response-to-promote-virus-multiplication
#16
Jonathan K Mitchell, Paul D Friesen
The baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) initiates apoptosis in diverse insects through events triggered by virus DNA (vDNA) replication. To define the proapoptotic pathway and its role in antivirus defense, we investigated the link between the host's DNA damage response (DDR) and apoptosis. We report here that AcMNPV elicits a DDR in the model insect Drosophila melanogaster. Replication of vDNA activated DDR kinases, as evidenced by ATM-driven phosphorylation of the Drosophila histone H2AX homolog (H2Av), a critical regulator of the DDR...
December 2012: Journal of Virology
https://www.readbyqxmd.com/read/22523743/developmental-regulation-of-chromatin-conformation-by-hox-proteins-in-drosophila
#17
Marios Agelopoulos, Daniel J McKay, Richard S Mann
We present a strategy to examine the chromatin conformation of individual loci in specific cell types during Drosophila embryogenesis. Regulatory DNA is tagged with binding sites (lacO) for LacI, which is used to immunoprecipitate the tagged chromatin from specific cell types. We applied this approach to Distalless (Dll), a gene required for limb development in Drosophila. We show that the local chromatin conformation at Dll depends on the cell type: in cells that express Dll, the 5' regulatory region is in close proximity to the Dll promoter...
April 19, 2012: Cell Reports
https://www.readbyqxmd.com/read/22406835/drosophila-melanogaster-linker-histone-dh1-is-required-for-transposon-silencing-and-to-preserve-genome-integrity
#18
Olivera Vujatovic, Katrin Zaragoza, Alejandro Vaquero, Oscar Reina, Jordi Bernués, Fernando Azorín
Histone H1 is an intrinsic component of chromatin, whose important contribution to chromatin structure is well-established in vitro. Little is known, however, about its functional roles in vivo. Here, we have addressed this question in Drosophila, a model system offering many advantages since it contains a single dH1 variant. For this purpose, RNAi was used to efficiently deplete dH1 in flies. Expression-profiling shows that dH1 depletion affects expression of a relatively small number of genes in a regional manner...
July 2012: Nucleic Acids Research
https://www.readbyqxmd.com/read/22275876/progressive-polycomb-assembly-on-h3k27me3-compartments-generates-polycomb-bodies-with-developmentally-regulated-motion
#19
Thierry Cheutin, Giacomo Cavalli
Polycomb group (PcG) proteins are conserved chromatin factors that maintain silencing of key developmental genes outside of their expression domains. Recent genome-wide analyses showed a Polycomb (PC) distribution with binding to discrete PcG response elements (PREs). Within the cell nucleus, PcG proteins localize in structures called PC bodies that contain PcG-silenced genes, and it has been recently shown that PREs form local and long-range spatial networks. Here, we studied the nuclear distribution of two PcG proteins, PC and Polyhomeotic (PH)...
January 2012: PLoS Genetics
https://www.readbyqxmd.com/read/22024169/drosophila-atm-and-atr-have-distinct-activities-in-the-regulation-of-meiotic-dna-damage-and-repair
#20
Eric F Joyce, Michael Pedersen, Stanley Tiong, Sanese K White-Brown, Anshu Paul, Shelagh D Campbell, Kim S McKim
Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-related (ATR) kinases are conserved regulators of cellular responses to double strand breaks (DSBs). During meiosis, however, the functions of these kinases in DSB repair and the deoxyribonucleic acid (DNA) damage checkpoint are unclear. In this paper, we show that ATM and ATR have unique roles in the repair of meiotic DSBs in Drosophila melanogaster. ATR mutant analysis indicated that it is required for checkpoint activity, whereas ATM may not be...
October 31, 2011: Journal of Cell Biology
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