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Epigenetics & Chromatin

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https://www.readbyqxmd.com/read/28701172/vitamin-c-induces-specific-demethylation-of-h3k9me2-in-mouse-embryonic-stem-cells-via-kdm3a-b
#1
Kevin T Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G Acker, Martin Hirst, Benjamin A Garcia, Miguel Ramalho-Santos
BACKGROUND: Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. RESULTS: We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells...
July 12, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28693562/activation-of-the-alpha-globin-gene-expression-correlates-with-dramatic-upregulation-of-nearby-non-globin-genes-and-changes-in-local-and-large-scale-chromatin-spatial-structure
#2
Sergey V Ulianov, Aleksandra A Galitsyna, Ilya M Flyamer, Arkadiy K Golov, Ekaterina E Khrameeva, Maxim V Imakaev, Nezar A Abdennur, Mikhail S Gelfand, Alexey A Gavrilov, Sergey V Razin
BACKGROUND: In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2...
July 11, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28683815/metabolic-labeling-in-middle-down-proteomics-allows-for-investigation-of-the-dynamics-of-the-histone-code
#3
Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R Karch, Chrystian Ruminowicz, Benjamin A Garcia
BACKGROUND: Middle-down mass spectrometry (MS), i.e., analysis of long (~50-60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities...
July 6, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28676122/genome-wide-search-for-zelda-like-chromatin-signatures-identifies-gaf-as-a-pioneer-factor-in-early-fly-development
#4
Arbel Moshe, Tommy Kaplan
BACKGROUND: The protein Zelda was shown to play a key role in early Drosophila development, binding thousands of promoters and enhancers prior to maternal-to-zygotic transition (MZT), and marking them for transcriptional activation. Recently, we showed that Zelda acts through specific chromatin patterns of histone modifications to mark developmental enhancers and active promoters. Intriguingly, some Zelda sites still maintain these chromatin patterns in Drosophila embryos lacking maternal Zelda protein...
July 4, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28676099/drosophila-cp190-and-dctcf-mediated-enhancer-blocking-is-augmented-by-sumoylation
#5
Theresa Jox, Melanie K Buxa, Dorte Bohla, Ikram Ullah, Igor Mačinković, Alexander Brehm, Marek Bartkuhn, Rainer Renkawitz
BACKGROUND: Chromatin insulators shield promoters and chromatin domains from neighboring enhancers or chromatin regions with opposing activities. Insulator-binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the small ubiquitin-like modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. RESULTS: Here we addressed the impact of dSUMO in respect of insulator function, chromatin binding of insulator factors and formation of insulator speckles in Drosophila...
July 4, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28706564/vitamin-c-induces-specific-demethylation-of-h3k9me2-in-mouse-embryonic-stem-cells-via-kdm3a-b
#6
Kevin T Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G Acker, Martin Hirst, Benjamin A Garcia, Miguel Ramalho-Santos
BACKGROUND: Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. RESULTS: We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28680483/drosophila-cp190-and-dctcf-mediated-enhancer-blocking-is-augmented-by-sumoylation
#7
Theresa Jox, Melanie K Buxa, Dorte Bohla, Ikram Ullah, Igor Mačinković, Alexander Brehm, Marek Bartkuhn, Rainer Renkawitz
BACKGROUND: Chromatin insulators shield promoters and chromatin domains from neighboring enhancers or chromatin regions with opposing activities. Insulator-binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the small ubiquitin-like modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. RESULTS: Here we addressed the impact of dSUMO in respect of insulator function, chromatin binding of insulator factors and formation of insulator speckles in Drosophila...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28649282/asymmetric-dna-methylation-of-cpg-dyads-is-a-feature-of-secondary-dmrs-associated-with-the-dlk1-gtl2-imprinting-cluster-in-mouse
#8
Megan Guntrum, Ekaterina Vlasova, Tamara L Davis
BACKGROUND: Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28638443/dosage-compensation-and-sex-specific-epigenetic-landscape-of-the-x-chromosome-in-the-pea-aphid
#9
Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry, Gaël Le Trionnaire
BACKGROUND: Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage compensation mechanisms involving gene expression and chromatin accessibility regulations have emerged throughout evolution. In insects, these mechanisms have been extensively characterized only in Drosophila but not in insects of agronomical importance. Aphids are indeed major pests of a wide range of crops...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28592995/the-quest-for-epigenetic-regulation-underlying-unisexual-flower-development-in-cucumis-melo
#10
David Latrasse, Natalia Y Rodriguez-Granados, Alaguraj Veluchamy, Kiruthiga Gayathri Mariappan, Claudia Bevilacqua, Nicolas Crapart, Celine Camps, Vivien Sommard, Cécile Raynaud, Catherine Dogimont, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane
BACKGROUND: Melon (Cucumis melo) is an important vegetable crop from the Cucurbitaceae family and a reference model specie for sex determination, fruit ripening and vascular fluxes studies. Nevertheless, the nature and role of its epigenome in gene expression regulation and more specifically in sex determination remains largely unknown. RESULTS: We have investigated genome wide H3K27me3 and H3K9ac histone modifications and gene expression dynamics, in five melon organs...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28539972/site-specific-regulation-of-histone-h1-phosphorylation-in-pluripotent-cell-differentiation
#11
Ruiqi Liao, Craig A Mizzen
BACKGROUND: Structural variation among histone H1 variants confers distinct modes of chromatin binding that are important for differential regulation of chromatin condensation, gene expression and other processes. Changes in the expression and genomic distributions of H1 variants during cell differentiation appear to contribute to phenotypic differences between cell types, but few details are known about the roles of individual H1 variants and the significance of their disparate capacities for phosphorylation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28533820/medip-seq-and-ncpg-analyses-illuminate-sexually-dimorphic-methylation-of-gonadal-development-genes-with-high-historic-methylation-in-turtle-hatchlings-with-temperature-dependent-sex-determination
#12
Srihari Radhakrishnan, Robert Literman, Beatriz Mizoguchi, Nicole Valenzuela
BACKGROUND: DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28515788/genomic-imprinting-does-not-reduce-the-dosage-of-ube3a-in-neurons
#13
Paul R Hillman, Sarah G B Christian, Ryan Doan, Noah D Cohen, Kranti Konganti, Kory Douglas, Xu Wang, Paul B Samollow, Scott V Dindot
BACKGROUND: The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggesting that UBE3A is dosage-sensitive in the brain. The observation that loss of imprinting increases the dosage of UBE3A in brain further suggests that inactivation of the paternal UBE3A allele evolved as a dosage-regulating mechanism...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#14
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28507606/transcription-and-chromatin-determinants-of-de-novo-dna-methylation-timing-in-oocytes
#15
Lenka Gahurova, Shin-Ichi Tomizawa, Sébastien A Smallwood, Kathleen R Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R Andrews, Taiping Chen, Gavin Kelsey
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28503202/stabilization-of-foxp3-expression-by-crispr-dcas9-based-epigenome-editing-in-mouse-primary-t-cells
#16
Masahiro Okada, Mitsuhiro Kanamori, Kazue Someya, Hiroko Nakatsukasa, Akihiko Yoshimura
BACKGROUND: Epigenome editing is expected to manipulate transcription and cell fates and to elucidate the gene expression mechanisms in various cell types. For functional epigenome editing, assessing the chromatin context-dependent activity of artificial epigenetic modifier is required. RESULTS: In this study, we applied clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9-based epigenome editing to mouse primary T cells, focusing on the Forkhead box P3 (Foxp3) gene locus, a master transcription factor of regulatory T cells (Tregs)...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28503201/dna-methylation-and-dna-methyltransferases
#17
REVIEW
John R Edwards, Olya Yarychkivska, Mathieu Boulard, Timothy H Bestor
The prevailing views as to the form, function, and regulation of genomic methylation patterns have their origin many years in the past, at a time when the structure of the mammalian genome was only dimly perceived, when the number of protein-encoding mammalian genes was believed to be at least five times greater than the actual number, and when it was not understood that only ~10% of the genome is under selective pressure and likely to have biological function. We use more recent findings from genome biology and whole-genome methylation profiling to provide a reappraisal of the shape of genomic methylation patterns and the nature of the changes that they undergo during gametogenesis and early development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28465725/differential-dna-methylation-and-lymphocyte-proportions-in-a-costa-rican-high-longevity-region
#18
Lisa M McEwen, Alexander M Morin, Rachel D Edgar, Julia L MacIsaac, Meaghan J Jones, William H Dow, Luis Rosero-Bixby, Michael S Kobor, David H Rehkopf
BACKGROUND: The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population's unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28428825/comprehensive-evaluation-of-genome-wide-5-hydroxymethylcytosine-profiling-approaches-in-human-dna
#19
Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M Gould, Shalima S Nair, Susan J Clark, Clare Stirzaker
BACKGROUND: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28413451/differential-dna-methylation-at-conserved-non-genic-elements-and-evidence-for-transgenerational-inheritance-following-developmental-exposure-to-mono-2-ethylhexyl-phthalate-and-5-azacytidine-in-zebrafish
#20
Jorke H Kamstra, Liana Bastos Sales, Peter Aleström, Juliette Legler
BACKGROUND: Exposure to environmental stressors during development may lead to latent and transgenerational adverse health effects. To understand the role of DNA methylation in these effects, we used zebrafish as a vertebrate model to investigate heritable changes in DNA methylation following chemical-induced stress during early development. We exposed zebrafish embryos to non-embryotoxic concentrations of the biologically active phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP, 30 µM) and the DNA methyltransferase 1 inhibitor 5-azacytidine (5AC, 10 µM)...
2017: Epigenetics & Chromatin
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