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https://www.readbyqxmd.com/read/27903907/chromatin-binding-of-gcn5-in-drosophila-is-largely-mediated-by-cp190
#1
Tamer Ali, Marcus Krüger, Sabin Bhuju, Michael Jarek, Marek Bartkuhn, Rainer Renkawitz
Centrosomal 190 kDa protein (CP190) is a promoter binding factor, mediates long-range interactions in the context of enhancer-promoter contacts and in chromosomal domain formation. All Drosophila insulator proteins bind CP190 suggesting a crucial role in insulator function. CP190 has major effects on chromatin, such as depletion of nucleosomes, high nucleosomal turnover and prevention of heterochromatin expansion. Here, we searched for enzymes, which might be involved in CP190 mediated chromatin changes. Eighty percent of the genomic binding sites of the histone acetyltransferase Gcn5 are colocalizing with CP190 binding...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899608/tfbsbank-a-platform-to-dissect-the-big-data-of-protein-dna-interaction-in-human-and-model-species
#2
Dongsheng Chen, Sanjie Jiang, Xiaoyan Ma, Fang Li
Genome-wide transcription factors (TFs) binding data has been extensively generated in the past few years, which poses a great challenge to data interpretation. Therefore, comprehensive and dedicated functional annotation databases for TF-DNA interaction are in great demands to manage, explore and utilize those invaluable data resources. Here, we constructed a platform 'TFBSbank' which houses the annotation of 1870 chromatin immunoprecipitation (ChIP) datasets of 585 TFs in five species (human, mouse, fly, worm and yeast)...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#3
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899510/identification-and-in-silico-modeling-of-enhancers-reveals-new-features-of-the-cardiac-differentiation-network
#4
Denis Seyres, Yad Ghavi-Helm, Guillaume Junion, Ouarda Taghli-Lamallem, Céline Guichard, Laurence Röder, Charles Girardot, Eileen E M Furlong, Laurent Perrin
Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27881472/an-unexpected-regulatory-cascade-governs-a-core-function-of-the-drosophila-prc1-chromatin-protein-su-z-2
#5
Son C Nguyen, Stephanie Yu, Elaine Oberlick, Chao-Ting Wu
Polycomb group (PcG) proteins are major chromatin-bound factors that can read and modify chromatin states to maintain gene silencing throughout development. Here we focus on a close homolog of the PcG protein Posterior sex combs in order to better understand how these proteins affect regulation. This homolog, called Suppressor 2 of zeste, or Su(z)2 is comprised of two regions: the N-terminal "homology region" (HR), which serves as a hub for protein interactions, and the C-terminal region (CTR), which is believed to harbor the core activity of compacting chromatin...
November 23, 2016: Genetics
https://www.readbyqxmd.com/read/27880074/what-does-the-fruitless-gene-tell-us-about-nature-versus-nurture-in-the-sex-life-of-drosophila
#6
Daisuke Yamamoto, Soh Kohatsu
The fruitless (fru) gene in Drosophila has been proposed to play a master regulator role in the formation of neural circuitries for male courtship behavior, which is typically considered to be an innate behavior composed of a fixed action pattern as generated by the central pattern generator. However, recent studies have shed light on experience-dependent changes and sensory-input-guided plasticity in courtship behavior. For example, enhanced male-male courtship, a fru mutant "hallmark," disappears when fru-mutant males are raised in isolation...
November 23, 2016: Fly
https://www.readbyqxmd.com/read/27879204/establishment-and-maintenance-of-heritable-chromatin-structure-during-early-drosophila-embryogenesis
#7
Shelby A Blythe, Eric F Wieschaus
During embryogenesis, the initial chromatin state is established during a period of rapid proliferative activity. We have measured with three-minute time resolution how heritable patterns of chromatin structure are initially established and maintained during the midblastula transition (MBT). We find that regions of accessibility are established sequentially, where enhancers are opened in advance of promoters and insulators. These open states are stably maintained in highly condensed mitotic chromatin to ensure faithful inheritance of prior accessibility status across cell divisions...
November 23, 2016: ELife
https://www.readbyqxmd.com/read/27876811/unlocking-sperm-chromatin-at-fertilization-requires-a-dedicated-egg-thioredoxin-in-drosophila
#8
Samantha Tirmarche, Shuhei Kimura, Raphaëlle Dubruille, Béatrice Horard, Benjamin Loppin
In most animals, the extreme compaction of sperm DNA is achieved after the massive replacement of histones with sperm nuclear basic proteins (SNBPs), such as protamines. In some species, the ultracompact sperm chromatin is stabilized by a network of disulfide bonds connecting cysteine residues present in SNBPs. Studies in mammals have established that the reduction of these disulfide crosslinks at fertilization is required for sperm nuclear decondensation and the formation of the male pronucleus. Here, we show that the Drosophila maternal thioredoxin Deadhead (DHD) is specifically required to unlock sperm chromatin at fertilization...
November 23, 2016: Nature Communications
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
#9
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/27866148/identification-of-genes-mediating-drosophila-follicle-cell-progenitor-differentiation-by-screening-for-modifiers-of-gal4-uas-variegation
#10
Ming-Chia Lee, Andrew D Skora, Allan C Spradling
The Drosophila melanogaster ovarian follicle cell lineage provides a powerful system for investigating how epigenetic changes contribute to differentiation. Downstream from an epithelial stem cell, follicle progenitors undergo nine mitotic cell cycles before transitioning to the endocycle and initiating differentiation. During their proliferative phase, follicle progenitors experience Lsd1-dependent changes in epigenetic stability that can be monitored using GAL4::UAS variegation. Eventually, follicle progenitors acquire competence to respond to Delta, a Notch ligand present in the environment, which signals them to cease division and initiate differentiation...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27864380/setd5-is-essential-for-mammalian-development-and-co-transcriptional-regulation-of-histone-acetylation
#11
Anna B Osipovich, Rama Gangula, Pedro G Vianna, Mark A Magnuson
SET-domain containing proteins play a vital role in regulating gene expression during development through modifications in chromatin structure. Here we show that SET domain containing 5 (Setd5) is divergently transcribed with Gt(ROSA26)Sor, is necessary for mammalian development, and interacts with the PAF1 co-transcriptional complex and other proteins. Setd5-deficient embryos exhibit severe defects in neural tube formation, somitogenesis, and cardiac development, have aberrant vasculogenesis in embryos, yolk sacs, and placentas; and die between embryonic day 10...
November 18, 2016: Development
https://www.readbyqxmd.com/read/27858939/chromatin-remodeling-during-in-vivo-neural-stem-cells-differentiating-to-neurons-in-early-drosophila-embryos
#12
Youqiong Ye, Min Li, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang
Neurons are a key component of the nervous system and differentiate from multipotent neural stem cells (NSCs). Chromatin remodeling has a critical role in the differentiation process. However, its in vivo epigenetic regulatory role remains unknown. We show here that nucleosome depletion regions (NDRs) form in both proximal promoters and distal enhancers during NSCs differentiating into neurons in the early Drosophila embryonic development. NDR formation in the regulatory regions involves nucleosome shift and eviction...
November 18, 2016: Cell Death and Differentiation
https://www.readbyqxmd.com/read/27852975/rpd3-interacts-with-insulin-signaling-in-drosophila-longevity-extension
#13
Jared K Woods, Tahereh Ziafazeli, Blanka Rogina
Histone deacetylase (HDAC) 1 regulates chromatin compaction and gene expression by removing acetyl groups from lysine residues within histones. HDAC1 affects a variety of processes including proliferation, development, metabolism, and cancer. Reduction or inhibition of Rpd3, yeast and fly HDAC1 orthologue, extends longevity. However, the mechanism of rpd3's effects on longevity remains unclear. Here we report an overlap between rpd3 and the Insulin/Insulin-like growth factor signaling (IIS) longevity pathways...
November 14, 2016: Aging
https://www.readbyqxmd.com/read/27846223/combgap-promotes-ovarian-niche-development-and-chromatin-association-of-ecr-binding-regions-in-br-c
#14
Anna Hitrik, Malka Popliker, Dana Gancz, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Amos Tanay, Lilach Gilboa
The development of niches for tissue-specific stem cells is an important aspect of stem cell biology. Determination of niche size and niche numbers during organogenesis involves precise control of gene expression. How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein Combgap (Cg) supports correct ovarian niche formation in Drosophila by controlling ecdysone-Receptor (EcR)- mediated transcription and long-range chromatin contacts in the broad locus (BR-C)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27816064/increased-wnt-and-notch-signaling-a-clue-to-the-renal-disease-in-schimke-immuno-osseous-dysplasia
#15
Marie Morimoto, Clara Myung, Kimberly Beirnes, Kunho Choi, Yumi Asakura, Arend Bokenkamp, Dominique Bonneau, Milena Brugnara, Joel Charrow, Estelle Colin, Amira Davis, Georges Deschenes, Mattia Gentile, Mario Giordano, Andrew K Gormley, Rajeshree Govender, Mark Joseph, Kory Keller, Evelyne Lerut, Elena Levtchenko, Laura Massella, Christy Mayfield, Behzad Najafian, David Parham, Jurgen Spranger, Peter Stenzel, Uluc Yis, Zhongxin Yu, Jonathan Zonana, Glenda Hendson, Cornelius F Boerkoel
BACKGROUND: Schimke immuno-osseous dysplasia (SIOD) is a multisystemic disorder caused by biallelic mutations in the SWI/SNF-related matrix-associated actin-dependent regulator of chromatin, subfamily A-like 1 (SMARCAL1) gene. Changes in gene expression underlie the arteriosclerosis and T-cell immunodeficiency of SIOD; therefore, we hypothesized that SMARCAL1 deficiency causes the focal segmental glomerulosclerosis (FSGS) of SIOD by altering renal gene expression. We tested this hypothesis by gene expression analysis of an SIOD patient kidney and verified these findings through immunofluorescent analysis in additional SIOD patients and a genetic interaction analysis in Drosophila...
November 5, 2016: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/27813696/chromatin-changes-in-smarcal1-deficiency-a-hypothesis-for-the-gene-expression-alterations-of-schimke-immuno-osseous-dysplasia
#16
Marie Morimoto, Kunho Choi, Cornelius F Boerkoel, Kyoung Sang Cho
Mutations in SMARCAL1, which encodes a DNA annealing helicase with roles in DNA replication fork restart, DNA repair, and gene expression modulation, cause Schimke immuno-osseous dysplasia (SIOD), an autosomal recessive disease characterized by skeletal dysplasia, renal disease, T-cell immunodeficiency, and arteriosclerosis. The clinical features of SIOD arise from pathological changes in gene expression; however, the underlying mechanism for these gene expression alterations remains unclear. We hypothesized that changes of the epigenome alter gene expression in SIOD...
November 4, 2016: Nucleus
https://www.readbyqxmd.com/read/27810970/the-drosophila-chromosomal-protein-mst77f-is-processed-to-generate-an-essential-component-of-mature-sperm-chromatin
#17
Shuhei Kimura, Benjamin Loppin
In most animals, the bulk of sperm DNA is packaged with sperm nuclear basic proteins (SNBPs), a diverse group of highly basic chromosomal proteins notably comprising mammalian protamines. The replacement of histones with SNBPs during spermiogenesis allows sperm DNA to reach an extreme level of compaction, but little is known about how SNBPs actually function in vivo Mst77F is a Drosophila SNBP with unique DNA condensation properties in vitro, but its role during spermiogenesis remains unclear. Here, we show that Mst77F is required for the compaction of sperm DNA and the production of mature sperm, through its cooperation with protamine-like proteins Mst35Ba/b...
November 2016: Open Biology
https://www.readbyqxmd.com/read/27808254/%C3%AE-synuclein-enhances-histone-h3-lysine-9-dimethylation-and-h3k9me2-dependent-transcriptional-responses
#18
Naoto Sugeno, Sandra Jäckel, Aaron Voigt, Zinah Wassouf, Julia Schulze-Hentrich, Philipp J Kahle
α-Synuclein (αS) is a protein linked to Parkinson's disease (PD) and related neurodegenerative disorders. It is mostly localized within synapses, but αS has also been suggested to play a role in the nucleus. We used transgenic Drosophila and inducible SH-SY5Y neuroblastoma cells to investigate the effects of αS on chromatin with a particular focus on histone modifications. Overexpression of αS in male flies as well as in retinoic acid pre-treated neuroblastoma cells led to an elevation of histone H3K9 methylations, mostly mono- (H3K9me1) and di- (H3K9me2)...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27807477/chromatin-proteins-and-rna-are-associated-with-dna-during-all-phases-of-mitosis
#19
Kathryn L Black, Svetlana Petruk, Tyler K Fenstermaker, Jacob W Hodgson, Jeffrey L Caplan, Hugh W Brock, Alexander Mazo
Mitosis brings about major changes to chromosome and nuclear structure. We used recently developed proximity ligation assay-based techniques to investigate the association with DNA of chromatin-associated proteins and RNAs in Drosophila embryos during mitosis. All groups of tested proteins, histone-modifying and chromatin-remodeling proteins and methylated histones remained in close proximity to DNA during all phases of mitosis. We also found that RNA transcripts are associated with DNA during all stages of mitosis...
2016: Cell Discovery
https://www.readbyqxmd.com/read/27802137/chromatin-profiling-of-drosophila-cns-subpopulations-identifies-active-transcriptional-enhancers
#20
Joseph C Pearson, Daniel J McKay, Jason D Lieb, Stephen T Crews
One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data...
October 15, 2016: Development
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