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Drosophila epigenetics

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https://www.readbyqxmd.com/read/28094282/evidence-of-neofunctionalization-after-the-duplication-of-the-highly-conserved-polycomb-group-gene-caf1-55-in-the-obscura-group-of-drosophila
#1
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
Drosophila CAF1-55 protein is a subunit of the Polycomb repressive complex PRC2 and other protein complexes. It is a multifunctional and evolutionarily conserved protein that participates in nucleosome assembly and remodelling, as well as in the epigenetic regulation of a large set of target genes. Here, we describe and analyze the duplication of Caf1-55 in the obscura group of Drosophila. Paralogs exhibited a strong asymmetry in evolutionary rates, which suggests that they have evolved according to a neofunctionalization process...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28076775/nutritional-programming-of-lifespan-by-foxo-inhibition-on-sugar-rich-diets
#2
Adam J Dobson, Marina Ezcurra, Charlotte E Flanagan, Adam C Summerfield, Matthew D W Piper, David Gems, Nazif Alic
Consumption of unhealthy diets is exacerbating the burden of age-related ill health in aging populations. Such diets can program mammalian physiology to cause long-term, detrimental effects. Here, we show that, in Drosophila melanogaster, an unhealthy, high-sugar diet in early adulthood programs lifespan to curtail later-life survival despite subsequent dietary improvement. Excess dietary sugar promotes insulin-like signaling, inhibits dFOXO-the Drosophila homolog of forkhead box O (FOXO) transcription factors-and represses expression of dFOXO target genes encoding epigenetic regulators...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28048969/on-the-developmental-self-regulatory-dynamics-and-evolution-of-individuated-multicellular-organisms
#3
Felipe A Veloso
Changes in gene expression are thought to regulate the cell differentiation process intrinsically through complex epigenetic mechanisms. In fundamental terms, however, this assumed regulation refers only to the intricate propagation of changes in gene expression or else leads to non-explanatory regresses. The developmental self-regulatory dynamics and evolution of individuated multicellular organisms also lack a unified and falsifiable description. To fill this gap, I computationally analyzed publicly available high-throughput data of histone H3 post-translational modifications and mRNA abundance for different Homo sapiens, Mus musculus, and Drosophila melanogaster cell-type/developmental-period samples...
December 31, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28028175/the-transcriptional-corepressor-sin3-directly-regulates-genes-involved-in-methionine-catabolism-and-affects-histone-methylation-linking-epigenetics-and-metabolism
#4
Mengying Liu, Lori A Pile
Chromatin modification and cellular metabolism are tightly connected. Chromatin modifiers regulate the expression of genes involved in metabolism and, in turn, the levels of metabolites. The generated metabolites are utilized by chromatin modifiers to affect epigenetic modification. The mechanism for this cross-talk, however, remains incompletely understood. The corepressor SIN3 controls histone acetylation through association with the histone deacetylase RPD3. The SIN3 complex is known to regulate genes involved in a number of metabolic processes...
December 27, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28018141/what-drives-positive-selection-in-the-drosophila-pirna-machinery-the-genomic-autoimmunity-hypothesis
#5
REVIEW
Justin P Blumenstiel, Alexandra A Erwin, Lucas W Hemmer
In animals, PIWI-interacting RNAs (piRNAs) play a crucial role in genome defense. Moreover, because piRNAs can be maternally transmitted, they contribute to the epigenetic profile of inheritance. Multiple studies, especially in Drosophila, have demonstrated that the machinery of piRNA biogenesis is often the target of positive selection. Because transposable elements (TEs) are a form of genetic parasite, positive selection in the piRNA machinery is often explained by analogy to the signatures of positive selection commonly observed in genes that play a role in host-parasite dynamics...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/27932388/from-embryo-to-adult-pirna-mediated-silencing-throughout-germline-development-in-drosophila
#6
Pauline P Marie, Stéphane Ronsseray, Antoine Boivin
In metazoan germ cells, transposable element activity is repressed by small noncoding PIWI-associated RNAs (piRNAs). Numerous studies in Drosophila have elucidated the mechanism of this repression in the adult germline. However, when and how transposable element repression is established during germline development, has not been addressed. Here, we show that homology-dependent trans silencing is active in female primordial germ cells from late embryogenesis through pupal stages, and that genes related to the adult piRNA pathway are required for silencing during development...
December 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#7
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27907135/the-histone-deacetylase-gene-rpd3-is-required-for-starvation-stress-resistance
#8
Ei Nakajima, Kouhei Shimaji, Takanari Umegawachi, Saki Tomida, Hideki Yoshida, Nana Yoshimoto, Shingo Izawa, Hiroshi Kimura, Masamitsu Yamaguchi
Epigenetic regulation in starvation is important but not fully understood yet. Here we identified the Rpd3 gene, a Drosophila homolog of histone deacetylase 1, as a critical epigenetic regulator for acquiring starvation stress resistance. Immunostaining analyses of Drosophila fat body revealed that the subcellular localization and levels of Rpd3 dynamically changed responding to starvation stress. In response to starvation stress, the level of Rpd3 rapidly increased, and it accumulated in the nucleolus in what appeared to be foci...
2016: PloS One
https://www.readbyqxmd.com/read/27889707/transgenerational-programming-of-longevity-through-e-z-mediated-histone-h3k27-trimethylation-in-drosophila
#9
Brian Xia, Ed Gerstin, Dustin E Schones, Wendong Huang, J Steven de Belle
Transgenerational effects on health and development of early-life nutrition have gained increased attention recently. However, the underlying mechanisms of transgenerational transmission are only starting to emerge, with epigenetics as perhaps the most important mechanism. We recently reported the first animal model to study transgenerational programming of longevity after early-life dietary manipulations, enabling investigations to identify underlying epigenetic mechanisms. We report here that post-eclosion dietary manipulation (PDM) with a low-protein (LP) diet upregulates the protein level of E(z), an H3K27 specific methyltransferase, leading to higher levels of H3K27 trimethylation (H3K27me3)...
November 25, 2016: Aging
https://www.readbyqxmd.com/read/27880074/what-does-the-fruitless-gene-tell-us-about-nature-vs-nurture-in-the-sex-life-of-drosophila
#10
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/27866148/identification-of-genes-mediating-drosophila-follicle-cell-progenitor-differentiation-by-screening-for-modifiers-of-gal4-uas-variegation
#11
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...
January 5, 2017: G3: Genes—Genomes—Genetics
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/27856695/multiplex-shrna-screening-of-germ-cell-development-by-in-vivo-transfection-of-mouse-testis
#13
Nicholas R Y Ho, Abul R Usmani, Yan Yin, Liang Ma, Donald F Conrad
Spermatozoa are one of the few mammalian cell types that cannot be fully derived in vitro, severely limiting the application of modern genomic techniques to study germ cell biology. The current gold standard approach of characterizing single-gene knockout mice is slow as generation of each mutant line can take 6-9 months. Here, we describe an in vivo approach to rapid functional screening of germline genes based on a new nonsurgical, nonviral in vivo transfection method to deliver nucleic acids into testicular germ cells...
January 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27813696/chromatin-changes-in-smarcal1-deficiency-a-hypothesis-for-the-gene-expression-alterations-of-schimke-immuno-osseous-dysplasia
#14
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 2016: Nucleus
https://www.readbyqxmd.com/read/27687115/ben-domain-protein-elba2-can-functionally-substitute-for-linker-histone-h1-in-drosophila-in-vivo
#15
Na Xu, Xingwu Lu, Harsh Kavi, Alexander V Emelyanov, Travis J Bernardo, Elena Vershilova, Arthur I Skoultchi, Dmitry V Fyodorov
Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo...
September 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27670720/beyond-mice-emerging-and-transdisciplinary-models-for-the-study-of-early-onset-myopathies
#16
Krzysztof Jagla, Benoit Kalman, Thomas Boudou, Sylvie Hénon, Sabrina Batonnet-Pichon
The use of the adapted models to decipher patho-physiological mechanisms of human diseases is always a great challenge. This is of particular importance for early-onset myopathies, in which pathological mutations often impact not only on muscle structure and function but also on developmental processes. Mice are currently the main animal model used to study neuromuscular disorders including the early-onset myopathies. However strategies based on simple animal models and on transdisciplinary approaches exploring mechanical muscle cell properties emerge as attractive, non-exclusive alternatives...
September 23, 2016: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/27659984/determination-of-polycomb-group-of-protein-compartmentalization-through-chromatin-fractionation-procedure
#17
Federica Marasca, Fabrizia Marullo, Chiara Lanzuolo
Epigenetic mechanisms modulate and maintain the transcriptional state of the genome acting at various levels on chromatin. Emerging findings suggest that the position in the nuclear space and the cross talk between components of the nuclear architecture play a role in the regulation of epigenetic signatures. We recently described a cross talk between the Polycomb group of proteins (PcG) epigenetic repressors and the nuclear lamina. This interplay is important for the maintenance of transcriptional repression at muscle-specific genes and for the correct timing of muscle differentiation...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27659974/analysis-of-single-locus-replication-timing-in-asynchronous-cycling-cells
#18
Lo Sardo Federica
In higher eucaryotes, not all the genome is replicated simultaneously: there are parts of the genome that replicate at the beginning of S-phase (early S-phase), others that are replicated later. In each cell, early replicating genomic regions are alternated to late-replicating regions. In general, eucaryotic genomes are organized into structural domains where genes showing the same epigenetic state replicate at the same time.Here, we will describe the protocol that we routinely used for the analysis of replication timing of specific loci in Drosophila embryonic cell lines (S2 and S3) based on BrdU labeling and FACS sorting of different S-phase fractions (early, mid, late) of asynchronous cycling cells...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27635759/acetylation-dependent-control-of-global-poly-a-rna-degradation-by-cbp-p300-and-hdac1-2
#19
Sahil Sharma, Fabian Poetz, Marius Bruer, Thi Bach Nga Ly-Hartig, Johanna Schott, Bertrand Séraphin, Georg Stoecklin
Acetylation of histones and transcription-related factors is known to exert epigenetic and transcriptional control of gene expression. Here we report that histone acetyltransferases (HATs) and histone deacetylases (HDACs) also regulate gene expression at the posttranscriptional level by controlling poly(A) RNA stability. Inhibition of HDAC1 and HDAC2 induces massive and widespread degradation of normally stable poly(A) RNA in mammalian and Drosophila cells. Acetylation-induced RNA decay depends on the HATs p300 and CBP, which acetylate the exoribonuclease CAF1a, a catalytic subunit of the CCR4-CAF1-NOT deadenlyase complex and thereby contribute to accelerating poly(A) RNA degradation...
September 15, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27634414/chromatin-remodeling-during-the-in-vivo-glial-differentiation-in-early-drosophila-embryos
#20
Youqiong Ye, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang
Chromatin remodeling plays a critical role in gene regulation and impacts many biological processes. However, little is known about the relationship between chromatin remodeling dynamics and in vivo cell lineage commitment. Here, we reveal the patterns of histone modification change and nucleosome positioning dynamics and their epigenetic regulatory roles during the in vivo glial differentiation in early Drosophila embryos. The genome-wide average H3K9ac signals in promoter regions are decreased in the glial cells compared to the neural progenitor cells...
2016: Scientific Reports
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