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Drosophila chromatin

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https://www.readbyqxmd.com/read/28436983/stable-polycomb-dependent-transgenerational-inheritance-of-chromatin-states-in-drosophila
#1
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Transgenerational epigenetic inheritance (TEI) describes the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known about the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, as defined by differential levels of Polycomb-dependent trimethylation of histone H3 Lys27 (forming H3K27me3)...
April 24, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28428611/transcription-factor-antagonism-controls-enteroendocrine-cell-specification-from-intestinal-stem-cells
#2
Yumei Li, Zhimin Pang, Huanwei Huang, Chenhui Wang, Tao Cai, Rongwen Xi
The balanced maintenance and differentiation of local stem cells is required for Homeostatic renewal of tissues. In the Drosophila midgut, the transcription factor Escargot (Esg) maintains undifferentiated states in intestinal stem cells, whereas the transcription factors Scute (Sc) and Prospero (Pros) promote enteroendocrine cell specification. However, the mechanism through which Esg and Sc/Pros coordinately regulate stem cell differentiation is unknown. Here, by combining chromatin immunoprecipitation analysis with genetic studies, we show that both Esg and Sc bind to a common promoter region of pros...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426351/chromosome-4-in-drosophila-melanogaster-imperfection-or-interesting-exception
#3
Michaelyn A Hartmann, Jeff Sekelsky
Drosophila melanogaster chromosome 4 is an anomaly because of its small size, chromatin structure, and most notably its lack of crossing over during meiosis. Earlier ideas about the absence of crossovers on 4 hypothesize that these unique characteristics function to prevent crossovers. Here, we explore hypotheses about the absence of crossovers on 4, how these have been addressed, and new insights into the mechanism behind this suppression. We review recently published results that indicate that global crossover patterning, in particular the centromere effect, make a major contribution to the prevention of crossovers on 4...
April 20, 2017: Fly
https://www.readbyqxmd.com/read/28421443/genomic-mapping-of-chromatin-proteins-by-using-dam-inv-modification-of-an-flp-dependent-damid-approach
#4
A V Pindyurin
To identify interactions of chromatin proteins with the genome of the cell type of interest that is a part of heterologous tissues and organs of Drosophila, an FLP-dependent DamID approach was recently developed [4], which does not require sorting of cells or nuclei. Here, a modification of this approach, Dam(inv), is described. The modified approach was validated by generating the binding pattern of the LAM protein, a component of the inner membrane of the nuclear envelope, with the genome of glial cells of the Drosophila larval central brains...
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28420691/clustering-of-drosophila-housekeeping-promoters-facilitates-their-expression
#5
Marc Corrales-Berjano, Aranzazu Rosado Diez, Ruggero Cortini, Joris van Arensbergen, Bas van Steensel, Guillaume J Filion
Housekeeping genes of animal genomes cluster in the same chromosomal regions. It has long been suggested that this organization contributes to their steady expression across all the tissues of the organism. Here we show that the activity of Drosophila housekeeping gene promoters depends on the expression of their neighbours. By measuring the expression of ~ 85,000 reporters integrated in Kc167 cells, we identified the best predictors of expression as chromosomal contacts with the promoters and terminators of active genes...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28418397/bap180-baf180-is-required-to-maintain-homeostasis-of-intestinal-innate-immune-response-in-drosophila-and-mice
#6
Xiaomeng He, Junjing Yu, Min Wang, Yang Cheng, Yanan Han, Shuo Yang, Guizhi Shi, Lei Sun, Ying Fang, Si-Tang Gong, Zhong Wang, Yang-Xin Fu, Lei Pan, Hong Tang
Immune homeostasis is a prerequisite to protective immunity against gastrointestinal infections. In Drosophila, immune deficiency (IMD) signalling (tumour necrosis factor receptor/interleukin-1 receptor, TNFR/IL-1R in mammals) is indispensable for intestinal immunity against invading bacteria. However, how this local antimicrobial immune response contributes to inflammatory regulation remains poorly defined. Here, we show that flies lacking intestinal Bap180 (a subunit of the chromatin-remodelling switch/sucrose non-fermentable (SWI/SNF) complex) are susceptible to infection as a result of hyper-inflammation rather than bacterial overload...
April 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28404631/regulatory-functions-and-chromatin-loading-dynamics-of-linker-histone-h1-during-endoreplication-in-drosophila
#7
Evgeniya N Andreyeva, Travis J Bernardo, Tatyana D Kolesnikova, Xingwu Lu, Lyubov A Yarinich, Boris A Bartholdy, Xiaohan Guo, Olga V Posukh, Sean Healton, Michael A Willcockson, Alexey V Pindyurin, Igor F Zhimulev, Arthur I Skoultchi, Dmitry V Fyodorov
Eukaryotic DNA replicates asynchronously, with discrete genomic loci replicating during different stages of S phase. Drosophila larval tissues undergo endoreplication without cell division, and the latest replicating regions occasionally fail to complete endoreplication, resulting in underreplicated domains of polytene chromosomes. Here we show that linker histone H1 is required for the underreplication (UR) phenomenon in Drosophila salivary glands. H1 directly interacts with the Suppressor of UR (SUUR) protein and is required for SUUR binding to chromatin in vivo...
March 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28398229/controlling-the-master-chromatin-dynamics-at-the-myc-promoter-integrate-developmental-signaling
#8
REVIEW
Olga Zaytseva, Leonie M Quinn
The transcription factor and cell growth regulator MYC is potently oncogenic and estimated to contribute to most cancers. Decades of attempts to therapeutically target MYC directly have not resulted in feasible clinical applications, and efforts have moved toward indirectly targeting MYC expression, function and/or activity to treat MYC-driven cancer. A multitude of developmental and growth signaling pathways converge on the MYC promoter to modulate transcription through their downstream effectors. Critically, even small increases in MYC abundance (<2 fold) are sufficient to drive overproliferation; however, the details of how oncogenic/growth signaling networks regulate MYC at the level of transcription remain nebulous even during normal development...
April 11, 2017: Genes
https://www.readbyqxmd.com/read/28388407/chromatin-architecture-emerges-during-zygotic-genome-activation-independent-of-transcription
#9
Clemens B Hug, Alexis G Grimaldi, Kai Kruse, Juan M Vaquerizas
Chromatin architecture is fundamental in regulating gene expression. To investigate when spatial genome organization is first established during development, we examined chromatin conformation during Drosophila embryogenesis and observed the emergence of chromatin architecture within a tight time window that coincides with the onset of transcription activation in the zygote. Prior to zygotic genome activation, the genome is mostly unstructured. Early expressed genes serve as nucleation sites for topologically associating domain (TAD) boundaries...
April 6, 2017: Cell
https://www.readbyqxmd.com/read/28378812/ecr-recruits-dmi-2-and-increases-efficiency-of-dmi-2-mediated-remodelling-to-constrain-transcription-of-hormone-regulated-genes
#10
Judith Kreher, Kristina Kovač, Karim Bouazoune, Igor Mačinković, Anna Luise Ernst, Erik Engelen, Roman Pahl, Florian Finkernagel, Magdalena Murawska, Ikram Ullah, Alexander Brehm
Gene regulation by steroid hormones plays important roles in health and disease. In Drosophila, the hormone ecdysone governs transitions between key developmental stages. Ecdysone-regulated genes are bound by a heterodimer of ecdysone receptor (EcR) and Ultraspiracle. According to the bimodal switch model, steroid hormone receptors recruit corepressors in the absence of hormone and coactivators in its presence. Here we show that the nucleosome remodeller dMi-2 is recruited to ecdysone-regulated genes to limit transcription...
April 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28367077/protein-and-genetic-composition-of-four-chromatin-types-in-drosophila-melanogaster-cell-lines
#11
Lidiya V Boldyreva, Fyodor P Goncharov, Olga V Demakova, Tatyana Yu Zykova, Victor G Levitsky, Nikolay N Kolesnikov, Alexey V Pindyurin, Valeriy F Semeshin, Igor F Zhimulev
BACKGROUND: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS: Here, we describe the properties of these chromatin types across different cell lines...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28363744/dref-plays-multiple-roles-during-drosophila-development
#12
REVIEW
Nguyen Trong Tue, Yasuhide Yoshioka, Megumi Mizoguchi, Hideki Yoshida, Mario Zurita, Masamitsu Yamaguchi
DREF was originally identified as a transcription factor that coordinately regulates the expression of DNA replication- and proliferation-related genes in Drosophila. Subsequent studies demonstrated that DREF is involved in tumor suppressor pathways including p53 and Hippo signaling. DREF also regulates the expression of genes encoding components of the JNK and EGFR pathways during Drosophila development. DREF itself is under the control of the TOR pathway during cell and tissue growth responding to nutrition...
March 28, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28349404/analysis-of-chromatin-dynamics-during-drosophila-spermatogenesis
#13
Tim Hundertmark, Ina Theofel, Zeynep Eren-Ghiani, David Miller, Christina Rathke
In the course of spermatogenesis, germ cells undergo dramatic morphological changes that affect almost all cellular components. Therefore, it is impossible to study the process of spermatogenesis in its entirety without detailed morphological analyses. Here, we describe a method to visualize chromatin dynamics in differentiating Drosophila male germ cells using immunofluorescence staining. In addition, we demonstrate how to treat Drosophila sperm before immunofluorescence staining to help reveal epitopes in the highly condensed sperm chromatin that otherwise may be inaccessible to antibodies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28338986/genome-wide-estimates-of-transposable-element-insertion-and-deletion-rates-in-drosophila-melanogaster
#14
Jeffrey R Adrion, Michael J Song, Daniel R Schrider, Matthew W Hahn, Sarah Schaack
Knowing the rate at which transposable elements (TEs) insert and delete is critical for understanding their role in genome evolution. We estimated spontaneous rates of insertion and deletion for all known, active TE superfamilies present in a set of Drosophila melanogaster mutation-accumulation (MA) lines using whole genome sequence data. Our results demonstrate that TE insertions far outpace TE deletions in D. melanogaster. We found a significant effect of background genotype on TE activity, with higher rates of insertions in one MA line...
March 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28336073/visualization-of-the-genomic-loci-that-are-bound-by-specific-multiprotein-complexes-by-bimolecular-fluorescence-complementation-analysis-on-drosophila-polytene-chromosomes
#15
Huai Deng, Tom K Kerppola
We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) complexes on Drosophila polytene chromosomes. BiFC complexes are formed by the facilitated association of two fluorescent protein fragments that are fused to proteins that interact with, or are in close proximity to, each other. The intensity of BiFC complex fluorescence at individual genomic loci is greatly enhanced by the parallel alignment of hundreds of chromatids within the polytene chromosomes...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28302792/propagation-of-polycomb-repressed-chromatin-requires-sequence-specific-recruitment-to-dna
#16
Friederike Laprell, Katja Finkl, Jürg Müller
Epigenetic inheritance models posit that during Polycomb repression, Polycomb repressive complex 2 (PRC2) propagates histone H3 lysine 27 trimethylation (H3K27me3) independently of DNA sequence. We show that insertion of Polycomb response element (PRE) DNA into the Drosophila genome creates extended domains of H3K27me3-modified nucleosomes in the flanking chromatin and causes repression of a linked reporter gene. After excision of PRE DNA, H3K27me3 nucleosomes become diluted with each round of DNA replication, and reporter gene repression is lost...
April 7, 2017: Science
https://www.readbyqxmd.com/read/28296634/constitutive-scaffolding-of-multiple-wnt-enhanceosome-components-by-legless-bcl9
#17
Laurens M van Tienen, Juliusz Mieszczanek, Marc Fiedler, Trevor J Rutherford, Mariann Bienz
Wnt/β-catenin signaling elicits context-dependent transcription switches that determine normal development and oncogenesis. These are mediated by the Wnt enhanceosome, a multiprotein complex binding to the Pygo chromatin reader and acting through TCF/LEF-responsive enhancers. Pygo renders this complex Wnt-responsive, by capturing β-catenin via the Legless/BCL9 adaptor. We used CRISPR/Cas9 genome engineering of Drosophila legless (lgs) and human BCL9 and B9L to show that the C-terminus downstream of their adaptor elements is crucial for Wnt responses...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28282436/regions-of-very-low-h3k27me3-partition-the-drosophila-genome-into-topological-domains
#18
Sherif El-Sharnouby, Bettina Fischer, Jose Paolo Magbanua, Benjamin Umans, Rosalyn Flower, Siew Woh Choo, Steven Russell, Robert White
It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive...
2017: PloS One
https://www.readbyqxmd.com/read/28247044/role-of-chromatin-modifications-in-drosophila-germline-stem-cell-differentiation
#19
Pooja Flora, Alicia McCarthy, Maitreyi Upadhyay, Prashanth Rangan
During Drosophila oogenesis, germline stem cells (GSCs) self-renew and differentiate to give rise to a mature egg. Self-renewal and differentiation of GSCs are regulated by both intrinsic mechanisms such as regulation of gene expression in the germ line and extrinsic signaling pathways from the surrounding somatic niche. Epigenetic mechanisms, including histone-modifying proteins, nucleosome remodeling complexes, and histone variants, play a critical role in regulating intrinsic gene expression and extrinsic signaling cues from the somatic niche...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/28245789/mechanisms-of-groucho-mediated-repression-revealed-by-genome-wide-analysis-of-groucho-binding-and-activity
#20
Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D Gallaher, Albert J Courey
BACKGROUND: The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting...
February 28, 2017: BMC Genomics
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