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Drosophila chromatin

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https://www.readbyqxmd.com/read/29779112/border-structure-of-intercalary-heterochromatin-bands-of-drosophila-melanogaster-polytene-chromosomes
#1
V A Khoroshko, T Yu Zykova, O O Popova, I F Zhimulev
The precise genomic localization of the borders of 62 intercalary heterochromatin bands in Drosophila polytene chromosomes was determined. A new type of bands containing chromatin of different states was identified. This type is a combination of the gray band and the intercalary heterochromatin band, creating a genetic structure that with a light microscope is identified as a continuous band. The border structure of such bands includes the coding regions of genes with ubiquitous activity.
March 2018: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29776334/swi-snf-regulates-half-of-its-targets-without-the-need-of-atp-driven-nucleosome-remodeling-by-brahma
#2
Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann-Kristin Östlund Farrants, Neus Visa
BACKGROUND: Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. RESULTS: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764959/a-targeted-rnai-screen-reveals-drosophila-female-sterile-genes-that-control-the-size-of-germline-stem-cell-niche-during-development
#3
Yueh Cho, Chun-Ming Lai, Kun-Yang Lin, Hwei-Jan Hsu
Adult stem cells maintain tissue homeostasis. This unique capability largely depends on the stem cell niche, a specialized microenvironment, which preserves stem cell identity through physical contacts and secreted factors. In many cancers, latent tumor cell niches are thought to house stem cells and aid tumor initiation. However, in developing tissue and cancer it is unclear how the niche is established. The well-characterized germline stem cells (GSCs) and niches in the Drosophila melanogaster ovary provide an excellent model to address this fundamental issue...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29764501/eya4-inhibits-hepatocellular-carcinoma-growth-and-invasion-by-suppressing-nf-%C3%AE%C2%BAb-dependent-rap1-transactivation
#4
Shi-Jing Mo, Xun Hou, Xiao-Yi Hao, Jian-Peng Cai, Xin Liu, Wei Chen, Dong Chen, Xiao-Yu Yin
BACKGROUND: Our previous studies demonstrated that eyes absent homolog 4 (EYA4), a member of the eye development-related EYA family in Drosophila, is frequently methylated and silenced in hepatocellular carcinoma (HCC) specimens and associated with shorter survival. The current work aimed to explore the mechanisms through which EYA4 functions as a tumor suppressor in HCC. METHODS: Stable EYA4-expressing plasmid (pEYA4) transfectants of the human HCC cell lines Huh-7 and PLC/PRF/5 (PLC) were established...
April 3, 2018: Cancer communications
https://www.readbyqxmd.com/read/29759374/dependence-of-chromatosome-structure-on-linker-histone-sequence-and-posttranslational-modification
#5
Mehmet Ali Öztürk, Vlad Cojocaru, Rebecca C Wade
Linker histone (LH) proteins play a key role in higher-order structuring of chromatin for the packing of DNA in eukaryotic cells and in the regulation of genomic function. The common fruit fly (Drosophila melanogaster) has a single somatic isoform of the LH (H1). It is thus a useful model organism for investigating the effects of the LH on nucleosome compaction and the structure of the chromatosome, the complex formed by binding of an LH to a nucleosome. The structural and mechanistic details of how LH proteins bind to nucleosomes are debated...
May 11, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29754899/dynamic-fluctuations-in-subcellular-localization-of-the-hippo-pathway-effector-yorkie-in-vivo
#6
Samuel A Manning, Lucas G Dent, Shu Kondo, Ziqing W Zhao, Nicolas Plachta, Kieran F Harvey
The Hippo pathway is an evolutionarily conserved signaling network that integrates diverse cues to control organ size and cell fate. The central downstream pathway protein in Drosophila is the transcriptional co-activator Yorkie (YAP and TAZ in humans), which regulates gene expression with the Scalloped/TEA domain family member (TEAD) transcription factors [1-8]. A central regulatory step in the Hippo pathway is phosphorylation of Yorkie by the NDR family kinase Warts, which promotes Yorkie cytoplasmic localization by stimulating association with 14-3-3 proteins [9-12]...
April 24, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29752350/the-domino-swi2-snf2-gene-product-represses-cell-death-in-drosophila-melanogaster
#7
Kaitlyn Ellis, Joanna Wardwell-Ozgo, Kenneth H Moberg, Barry Yedvobnick
The Drosophila domino locus encodes DNA-dependent ATPases of the SWI2/SNF2 class. This class of chromatin remodeler is associated with an array of cellular activities encompassing transcription, replication, repair and recombination. Moreover, domino was observed initially to maintain a repressive chromatin state via genetic interaction studies with homeotic genes. Although domino mutations were also characterized with a cell death phenotype, its association with a death pathway has not been investigated. Here we have used targeted RNA interference to depress domino function in the wing...
May 11, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29751847/asf1-is-required-to-load-histones-on-the-hira-complex-in-preparation-of-paternal-chromatin-assembly-at-fertilization
#8
Béatrice Horard, Laure Sapey-Triomphe, Emilie Bonnefoy, Benjamin Loppin
BACKGROUND: Anti-Silencing Factor 1 (ASF1) is a conserved H3-H4 histone chaperone involved in both Replication-Coupled and Replication-Independent (RI) nucleosome assembly pathways. At DNA replication forks, ASF1 plays an important role in regulating the supply of H3.1/2 and H4 to the CAF-1 chromatin assembly complex. ASF1 also provides H3.3-H4 dimers to HIRA and DAXX chaperones for RI nucleosome assembly. The early Drosophila embryo is an attractive system to study chromatin assembly in a developmental context...
May 11, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29746464/rif1-prolongs-the-embryonic-s-phase-at-the-drosophila-mid-blastula-transition
#9
Charles A Seller, Patrick H O'Farrell
In preparation for dramatic morphogenetic events of gastrulation, rapid embryonic cell cycles slow at the mid-blastula transition (MBT). In Drosophila melanogaster embryos, down-regulation of cyclin-dependent kinase 1 (Cdk1) activity initiates this slowing by delaying replication of heterochromatic satellite sequences and extending S phase. We found that Cdk1 activity inhibited the chromatin association of Rap1 interacting factor 1 (Rif1), a candidate repressor of replication. Furthermore, Rif1 bound selectively to satellite sequences following Cdk1 down-regulation at the MBT...
May 10, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29739818/spermiogenesis-and-male-fertility-require-the-function-of-suppressor-of-hairy-wing-in-somatic-cyst-cells-of-drosophila
#10
Tingting Duan, Pamela K Geyer
Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is an example of a multivalent transcription factor. Although best known for its role in establishing the chromatin insulator of the gypsy retrotransposon, Su(Hw) functions as an activator and repressor at non- gypsy genomic sites. It remains unclear how the different regulatory activities of Su(Hw) are utilized during development. Motivated from observations of spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis to advance an understanding of its developmental contributions as an insulator, repressor and activator protein...
May 8, 2018: Genetics
https://www.readbyqxmd.com/read/29738688/regulated-gene-expression-as-a-tool-for-analysis-of-heterochromatin-position-effect-in-drosophila
#11
A S Shatskikh, O M Olenkina, A A Solodovnikov, S A Lavrov
Position effect variegation (PEV) is a perturbation of genes expression resulting from the changes in their chromatin organization due to the abnormal juxtaposition with heterochromatin. The exact molecular mechanisms of PEV remain enigmatic in spite of the long history of PEV studies. Here, we developed a genetic model consisting of PEV-inducing chromosome rearrangement and a reporter gene under control of the UAS regulatory element. Expression of the reporter gene could be regulated by adjustment of the GAL4 transactivator activity...
May 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29727464/patterns-of-chromatin-accessibility-along-the-anterior-posterior-axis-in-the-early-drosophila-embryo
#12
Jenna E Haines, Michael B Eisen
As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear how regions of activity are established during early embryogenesis, and if they are the product of spatially restricted or ubiquitous processes. To shed light on this question, we probed chromatin accessibility across the anterior-posterior axis (A-P) of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos...
May 4, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29714689/temporospatial-induction-of-homeodomain-gene-cut-dictates-natural-lineage-reprogramming
#13
Ke Xu, Xiaodan Liu, Yuchun Wang, Chouin Wong, Yan Song
Understanding how cellular identity naturally interconverts with high efficiency and temporospatial precision is crucial for regenerative medicine. Here we revealed a natural midgut-to-renal lineage conversion event during Drosophila metamorphosis and identified the evolutionarily-conserved homeodomain protein Cut as a master switch in this process. A steep Wnt/Wingless morphogen gradient intersects with a pulse of steroid hormone ecdysone to induce cut expression in a subset of midgut progenitors and reprogram them into renal progenitors...
May 1, 2018: ELife
https://www.readbyqxmd.com/read/29695495/multiple-arginine-residues-are-methylated-in-drosophila-mre11-and-required-for-survival-following-ionizing-radiation
#14
Qing Yuan, Ran Tian, Haiying Zhao, Lijuan Li, Xiaolin Bi
Mre11 is a key player for DNA double strand break repair. Previous studies have shown that mammalian Mre11 is methylated at multiple arginines in its C-terminal Glycine-Arginine-Rich motif (GAR) by protein arginine methyltransferase PRMT1. Here, we found that the Drosophila Mre11 is methylated at arginines 559, 563, 565, and 569 in the GAR motif by DART1, the Drosophila homolog of PRMT1. Mre11 interacts with DART1 in S2 cells, and this interaction does not require the GAR motif. Arginines methylated Mre11 localizes exclusively in the nucleus as soluble nuclear protein or chromatin-binding protein...
April 25, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29678692/nucpospred-predicting-species-specific-genomic-nucleosome-positionin-g-via-four-different-modes-of-general-pseknc
#15
Cangzhi Jia, Qing Yang, Quan Zou
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools...
April 17, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29659982/transcription-start-site-analysis-reveals-widespread-divergent-transcription-in-d-melanogaster-and-core-promoter-encoded-enhancer-activities
#16
Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagensø, Torben Heick Jensen, Robin Andersson
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed...
April 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29659604/similarity-in-replication-timing-between-polytene-and-diploid-cells-is-associated-with-the-organization-of-the-drosophila-genome
#17
Tatyana D Kolesnikova, Fedor P Goncharov, Igor F Zhimulev
Morphologically, polytene chromosomes of Drosophila melanogaster consist of compact "black" bands alternating with less compact "grey" bands and interbands. We developed a comprehensive approach that combines cytological mapping data of FlyBase-annotated genes and novel tools for predicting cytogenetic features of chromosomes on the basis of their protein composition and determined the genomic coordinates for all black bands of polytene chromosome 2R. By a PCNA immunostaining assay, we obtained the replication timetable for all the bands mapped...
2018: PloS One
https://www.readbyqxmd.com/read/29650775/mechanotransduction-via-the-linc-complex-regulates-dna-replication-in-myonuclei
#18
Shuoshuo Wang, Elizabeth Stoops, Unnikannan Cp, Barak Markus, Adriana Reuveny, Elly Ordan, Talila Volk
Nuclear mechanotransduction has been implicated in the control of chromatin organization; however, its impact on functional contractile myofibers is unclear. We found that deleting components of the linker of nucleoskeleton and cytoskeleton (LINC) complex in Drosophila melanogaster larval muscles abolishes the controlled and synchronized DNA endoreplication, typical of nuclei across myofibers, resulting in increased and variable DNA content in myonuclei of individual myofibers. Moreover, perturbation of LINC-independent mechanical input after knockdown of β-Integrin in larval muscles similarly led to increased DNA content in myonuclei...
April 12, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29648534/chromatin-associated-rna-sequencing-char-seq-maps-genome-wide-rna-to-dna-contacts
#19
Jason C Bell, David Jukam, Nicole A Teran, Viviana I Risca, Owen K Smith, Whitney L Johnson, Jan M Skotheim, William James Greenleaf, Aaron F Straight
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29642630/aging-and-intermittent-fasting-impact-on-transcriptional-regulation-and-physiological-responses-of-adult-drosophila-neuronal-and-muscle-tissues
#20
Sharon Zhang, Eric P Ratliff, Brandon Molina, Nadja El-Mecharrafie, Jessica Mastroianni, Roxanne W Kotzebue, Madhulika Achal, Ruth E Mauntz, Arysa Gonzalez, Ayeh Barekat, William A Bray, Andrew M Macias, Daniel Daugherty, Greg L Harris, Robert A Edwards, Kim D Finley
The progressive decline of the nervous system, including protein aggregate formation, reflects the subtle dysregulation of multiple functional pathways. Our previous work has shown intermittent fasting (IF) enhances longevity, maintains adult behaviors and reduces aggregates, in part, by promoting autophagic function in the aging Drosophila brain. To clarify the impact that IF-treatment has upon aging, we used high throughput RNA-sequencing technology to examine the changing transcriptome in adult Drosophila tissues...
April 10, 2018: International Journal of Molecular Sciences
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