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Drosophila chromatin

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https://www.readbyqxmd.com/read/29339751/jmjc-domain-proteins-modulate-circadian-behaviors-and-sleep-in-drosophila
#1
Nevine A Shalaby, Jorge H Pinzon, Anjana S Narayanan, Eugene Jennifer Jin, Morgan P Ritz, Rachel J Dove, Heike Wolfenberg, Aylin R Rodan, Michael Buszczak, Adrian Rothenfluh
Jumonji (JmjC) domain proteins are known regulators of gene expression and chromatin organization by way of histone demethylation. Chromatin modification and remodeling provides a means to modulate the activity of large numbers of genes, but the importance of this class of predicted histone-modifying enzymes for different aspects of post-developmental processes remains poorly understood. Here we test the function of all 11 non-lethal members in the regulation of circadian rhythms and sleep. We find loss of every Drosophila JmjC gene affects different aspects of circadian behavior and sleep in a specific manner...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335486/high-resolution-tads-reveal-dna-sequences-underlying-genome-organization-in-flies
#2
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke
Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29323275/rna-damid-reveals-cell-type-specific-binding-of-rox-rnas-at-chromatin-entry-sites
#3
Seth W Cheetham, Andrea H Brand
Thousands of long noncoding RNAs (lncRNAs) have been identified in eukaryotic genomes, many of which are expressed in spatially and temporally restricted patterns. Nonetheless, the roles of the majority of these transcripts are still unknown. One of the mechanisms by which lncRNAs function is through the modulation of chromatin states. To assess the functions of lncRNAs, we developed RNA-DamID, a novel approach that detects lncRNA-genome interactions in a cell-type-specific manner in vivo with high sensitivity and accuracy...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29305387/simple-and-complex-centromeric-satellites-in-drosophila-sibling-species
#4
Paul Talbert, Sivakanthan Kasinathan, Steven Henikoff
Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appear to be present at all centromeres, and none of which are found only at centromeres...
January 5, 2018: Genetics
https://www.readbyqxmd.com/read/29298422/winged-eye-induces-transdetermination-of-drosophila-imaginal-disc-by-acting-in-concert-with-a-histone-methyltransferase-su-var-3-9
#5
Keita Masuko, Naoyuki Fuse, Kanae Komaba, Tomonori Katsuyama, Rumi Nakajima, Hirofumi Furuhashi, Shoichiro Kurata
Drosophila imaginal disc cells exhibit a remarkable ability to convert cell fates in response to various perturbations, a phenomenon called transdetermination (TD). We previously identified winged eye (wge) as a factor that induces eye-to-wing TD upon overexpression in eye imaginal discs, but the molecular mechanisms underlying TD have remained largely unclear. Here, we found that wge induces various histone modifications and enhances the methylation of Lys9 on histone H3 (H3K9), a feature of heterochromatin...
January 2, 2018: Cell Reports
https://www.readbyqxmd.com/read/29281702/the-drosophila-clamp-protein-associates-with-diverse-proteins-on-chromatin
#6
Jennifer A Urban, John M Urban, Guray Kuzu, Erica N Larschan
Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP)...
2017: PloS One
https://www.readbyqxmd.com/read/29281014/systematic-genetic-interaction-studies-identify-histone-demethylase-utx-as-potential-target-for-ameliorating-huntington-s-disease
#7
Wan Song, Nóra Zsindely, Anikó Faragó, J Lawrence Marsh, László Bodai
Huntington's Disease (HD) is a dominantly inherited neurodegenerative disease caused by alterations in the huntingtin gene (htt). Transcriptional dysregulation is an early event in HD progression. Protein acetylation and methylation particularly on histones regulates chromatin structure thereby preventing or facilitating transcription. Although protein acetylation has been found to affect HD symptoms, little is known about the potential role of protein methylation in HD pathology. In recent years, a series of proteins have been described that are responsible for methylating and demethylating histones as well as other proteins...
December 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29273756/chromatin-state-changes-during-neural-development-revealed-by-in-vivo-cell-type-specific-profiling
#8
Owen J Marshall, Andrea H Brand
A key question in developmental biology is how cellular differentiation is controlled during development. While transitions between trithorax-group (TrxG) and polycomb-group (PcG) chromatin states are vital for the differentiation of ES cells to multipotent stem cells, little is known regarding the role of chromatin states during development of the brain. Here we show that large-scale chromatin remodelling occurs during Drosophila neural development. We demonstrate that the majority of genes activated during neuronal differentiation are silent in neural stem cells (NSCs) and occupy black chromatin and a TrxG-repressive state...
December 22, 2017: Nature Communications
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
#9
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/29242386/dosage-dependent-expression-variation-suppressed-on-the-drosophila-male-x-chromosome
#10
Hangnoh Lee, Dong-Yeon Cho, Damian Wojtowicz, Susan T Harbison, Steven Russell, Brian Oliver, Teresa Przytycka
DNA copy number variation is associated with many high phenotypic heterogeneity disorders. We systematically examined the impact of Drosophila melanogaster deletions on gene expression profiles to ask if increased expression variability due to reduced gene dose might underlie this phenotypic heterogeneity. Indeed, we find that one dose genes have higher gene expression variability relative to two dose genes. We then asked if this increase in variability could be explained by intrinsic noise within cells, due to stochastic biochemical events, or if expression variability is due to extrinsic noise arising from more complex interactions...
December 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29242288/a-role-for-mono-methylation-of-histone-h3-k27-in-gene-activity-in-drosophila
#11
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/29229671/h3s10ph-broadly-marks-early-replicating-domains-in-interphase-escs-and-shows-reciprocal-antagonism-with-h3k9me2
#12
Carol C L Chen, Preeti Goyal, Mohammad M Karimi, Marie H Abildgaard, Hiroshi Kimura, Matthew C Lorincz
Phosphorylation of histone H3 at serine 10 (H3S10ph) by Aurora kinases plays an important role in mitosis; however, H3S10ph also marks regulatory regions of inducible genes in interphase mammalian cells, implicating mitosis-independent functions. Using the fluorescent ubiquitin-mediated cell cycle indicator (FUCCI), we found that 30% of the genome in interphase mouse embryonic stem cells (ESCs) is marked with H3S10ph. H3S10ph broadly demarcates gene-rich regions in G1 and is positively correlated with domains of early DNA replication timing (RT) but negatively correlated with H3K9me2 and lamin-associated domains (LADs)...
December 11, 2017: Genome Research
https://www.readbyqxmd.com/read/29211718/pirna-mediated-regulation-of-transposon-alternative-splicing-in-the-soma-and-germ-line
#13
Felipe Karam Teixeira, Martyna Okuniewska, Colin D Malone, Rémi-Xavier Coux, Donald C Rio, Ruth Lehmann
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29208012/pho-dynamically-interacts-with-spt5-to-facilitate-transcriptional-switches-at-the-hsp70-locus
#14
Allwyn Pereira, Renato Paro
BACKGROUND: Numerous target genes of the Polycomb group (PcG) are transiently activated by a stimulus and subsequently repressed. However, mechanisms by which PcG proteins regulate such target genes remain elusive. RESULTS: We employed the heat shock-responsive hsp70 locus in Drosophila to study the chromatin dynamics of PRC1 and its interplay with known regulators of the locus before, during and after heat shock. We detected mutually exclusive binding patterns for HSF and PRC1 at the hsp70 locus...
December 6, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29190361/shaping-epigenetic-memory-via-genomic-bookmarking
#15
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/29180952/maintenance-of-positional-identity-of-neural-progenitors-in-the-embryonic-and-postnatal-telencephalon
#16
Ryan N Delgado, Daniel A Lim
Throughout embryonic development and into postnatal life, regionally distinct populations of neural progenitor cells (NPCs) collectively generate the many different types of neurons that underlie the complex structure and function of the adult mammalian brain. At very early stages of telencephalic development, NPCs become organized into regional domains that each produce different subsets of neurons. This positional identity of NPCs relates to the regional expression of specific, fate-determining homeodomain transcription factors...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29177663/chromatin-immunoprecipitation-chip-of-heat-shock-protein-90-hsp90
#17
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
#18
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/29158494/mrg15-stimulates-ash1-h3k36-methyltransferase-activity-and-facilitates-ash1-trithorax-group-protein-function-in-drosophila
#19
Chang Huang, Fu Yang, Zhuqiang Zhang, Jing Zhang, Gaihong Cai, Lin Li, Yong Zheng, She Chen, Rongwen Xi, Bing Zhu
Ash1 is a Trithorax group protein that possesses H3K36-specific histone methyltransferase activity, which antagonizes Polycomb silencing. Here we report the identification of two Ash1 complex subunits, Mrg15 and Nurf55. In vitro, Mrg15 stimulates the enzymatic activity of Ash1. In vivo, Mrg15 is recruited by Ash1 to their common targets, and Mrg15 reinforces Ash1 chromatin association and facilitates the proper deposition of H3K36me2. To dissect the functional role of Mrg15 in the context of the Ash1 complex, we identify an Ash1 point mutation (Ash1-R1288A) that displays a greatly attenuated interaction with Mrg15...
November 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/29158441/shep-regulates-drosophila-neuronal-remodeling-by-controlling-transcription-of-its-chromatin-targets
#20
Dahong Chen, Ryan K Dale, Elissa P Lei
Neuronal remodeling is critical to form the mature nervous system and can lead to neuropsychiatric diseases when disrupted. Global gene expression changes in neurons during remodeling as well as the factors that regulate these changes remain poorly defined. To elucidate this process, we performed RNA-seq on isolated Drosophila larval and pupal neurons and found up-regulated synaptic signaling and down-regulated gene expression regulators as a result of normal neuronal metamorphosis. We further tested the role of alan shepard (shep), which encodes an evolutionarily conserved RNA-binding protein required for proper neuronal remodeling...
November 20, 2017: Development
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