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  1. Research

    Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

    The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an ‘open’ local chromatin configuration has long been known. However, the 3D topography of TREs wi...

    Marion Cremer, Volker J. Schmid, Felix Kraus, Yolanda Markaki, Ines Hellmann, Andreas Maiser, Heinrich Leonhardt, Sam John, John Stamatoyannopoulos and Thomas Cremer

    Epigenetics & Chromatin 2017 10:39

    Published on: 7 August 2017

  2. Research

    Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function

    There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail...

    Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann and Bernhard Horsthemke

    Epigenetics & Chromatin 2017 10:37

    Published on: 26 July 2017

  3. Research

    Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b

    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 v...

    Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos

    Epigenetics & Chromatin 2017 10:36

    Published on: 12 July 2017

  4. Research

    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

    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-gl...

    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 and Sergey V. Razin

    Epigenetics & Chromatin 2017 10:35

    Published on: 11 July 2017

  5. Methodology

    Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code

    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 posttransla...

    Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R. Karch, Chrystian Ruminowicz and Benjamin A. Garcia

    Epigenetics & Chromatin 2017 10:34

    Published on: 6 July 2017

  6. Research

    Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

    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 functio...

    Theresa Jox, Melanie K. Buxa, Dorte Bohla, Ikram Ullah, Igor Mačinković, Alexander Brehm, Marek Bartkuhn and Rainer Renkawitz

    Epigenetics & Chromatin 2017 10:32

    Published on: 4 July 2017

  7. Research

    Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid

    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 comp...

    Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry and Gaël Le Trionnaire

    Epigenetics & Chromatin 2017 10:30

    Published on: 15 June 2017

  8. Research

    The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo

    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 ...

    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 and Abdelhafid Bendahmane

    Epigenetics & Chromatin 2017 10:22

    Published on: 6 June 2017

  9. Research

    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

    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 ...

    Srihari Radhakrishnan, Robert Literman, Beatriz Mizoguchi and Nicole Valenzuela

    Epigenetics & Chromatin 2017 10:28

    Published on: 19 May 2017

  10. Research

    Genomic imprinting does not reduce the dosage of UBE3A in neurons

    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 mutatio...

    Paul R. Hillman, Sarah G. B. Christian, Ryan Doan, Noah D. Cohen, Kranti Konganti, Kory Douglas, Xu Wang, Paul B. Samollow and Scott V. Dindot

    Epigenetics & Chromatin 2017 10:27

    Published on: 15 May 2017

  11. Research

    Transcription and chromatin determinants of de novo DNA methylation timing in oocytes

    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 larg...

    Lenka Gahurova, Shin-ichi Tomizawa, Sébastien A. Smallwood, Kathleen R. Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R. Andrews, Taiping Chen and Gavin Kelsey

    Epigenetics & Chromatin 2017 10:25

    Published on: 12 May 2017

  12. Review

    DNA methylation and DNA methyltransferases

    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 perce...

    John R. Edwards, Olya Yarychkivska, Mathieu Boulard and Timothy H. Bestor

    Epigenetics & Chromatin 2017 10:23

    Published on: 8 May 2017

  13. Research

    Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region

    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 hypot...

    Lisa M. McEwen, Alexander M. Morin, Rachel D. Edgar, Julia L. MacIsaac, Meaghan J. Jones, William H. Dow, Luis Rosero-Bixby, Michael S. Kobor and David H. Rehkopf

    Epigenetics & Chromatin 2017 10:21

    Published on: 27 April 2017

  14. Research

    Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

    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 ...

    Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark and Clare Stirzaker

    Epigenetics & Chromatin 2017 10:16

    Published on: 20 April 2017

  15. Research

    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

    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 verteb...

    Jorke H. Kamstra, Liana Bastos Sales, Peter Aleström and Juliette Legler

    Epigenetics & Chromatin 2017 10:20

    Published on: 12 April 2017

  16. Research

    Internal modifications in the CENP-A nucleosome modulate centromeric dynamics

    Posttranslational modifications of core histones are correlated with changes in transcriptional status, chromatin fiber folding, and nucleosome dynamics. However, within the centromere-specific histone H3 vari...

    Minh Bui, Mary Pitman, Arthur Nuccio, Serene Roque, Paul Gregory Donlin-Asp, Aleksandra Nita-Lazar, Garegin A. Papoian and Yamini Dalal

    Epigenetics & Chromatin 2017 10:17

    Published on: 4 April 2017

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