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  1. 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

  2. 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

  3. 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

  4. Research

    Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

    The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mecha...

    Johannes Petrus Maree, Megan Lindsay Povelones, David Johannes Clark, Gloria Rudenko and Hugh-George Patterton

    Epigenetics & Chromatin 2017 10:14

    Published on: 20 March 2017

  5. Research

    Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions

    Histone posttranslational modifications (PTMs) function to regulate chromatin structure and function in part through the recruitment of effector proteins that harbor specialized “reader” domains. Despite effor...

    Erin K. Shanle, Stephen A. Shinsky, Joseph B. Bridgers, Narkhyun Bae, Cari Sagum, Krzysztof Krajewski, Scott B. Rothbart, Mark T. Bedford and Brian D. Strahl

    Epigenetics & Chromatin 2017 10:12

    Published on: 14 March 2017

  6. Research

    Silencing markers are retained on pericentric heterochromatin during murine primordial germ cell development

    In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-bi...

    Aristea Magaraki, Godfried van der Heijden, Esther Sleddens-Linkels, Leonidas Magarakis, Wiggert A. van Cappellen, Antoine H. F. M. Peters, Joost Gribnau, Willy M. Baarends and Maureen Eijpe

    Epigenetics & Chromatin 2017 10:11

    Published on: 11 March 2017

  7. Research

    Identification of epigenetic signature associated with alpha thalassemia/mental retardation X-linked syndrome

    Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene ATRX. The mechanisms involved in the ATR-X pathology are not completely understood, but may i...

    Laila C. Schenkel, Kristin D. Kernohan, Arran McBride, Ditta Reina, Amanda Hodge, Peter J. Ainsworth, David I. Rodenhiser, Guillaume Pare, Nathalie G. Bérubé, Cindy Skinner, Kym M. Boycott, Charles Schwartz and Bekim Sadikovic

    Epigenetics & Chromatin 2017 10:10

    Published on: 10 March 2017

  8. Methodology

    Assessing histone demethylase inhibitors in cells: lessons learned

    Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The ...

    Stephanie B. Hatch, Clarence Yapp, Raquel C. Montenegro, Pavel Savitsky, Vicki Gamble, Anthony Tumber, Gian Filippo Ruda, Vassilios Bavetsias, Oleg Fedorov, Butrus Atrash, Florence Raynaud, Rachel Lanigan, LeAnne Carmichael, Kathy Tomlin, Rosemary Burke, Susan M. Westaway…

    Epigenetics & Chromatin 2017 10:9

    Published on: 1 March 2017

  9. Research

    PRC2 is required for extensive reorganization of H3K27me3 during epigenetic reprogramming in mouse fetal germ cells

    Defining how epigenetic information is established in the germline during fetal development is key to understanding how epigenetic information is inherited and impacts on evolution and human health and disease.

    Lexie Prokopuk, Jessica M. Stringer, Kirsten Hogg, Kirstin D. Elgass and Patrick S. Western

    Epigenetics & Chromatin 2017 10:7

    Published on: 20 February 2017

  10. Research

    Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

    Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous...

    Natallia Kalinava, Julie Zhouli Ni, Kimberly Peterman, Esteban Chen and Sam Guoping Gu

    Epigenetics & Chromatin 2017 10:6

    Published on: 15 February 2017

  11. Research

    In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain

    Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of...

    Zac Chatterton, Brigham J. Hartley, Man-Ho Seok, Natalia Mendelev, Sean Chen, Maria Milekic, Gorazd Rosoklija, Aleksandar Stankov, Iskra Trencevsja-Ivanovska, Kristen Brennand, Yongchao Ge, Andrew J. Dwork and Fatemeh Haghighi

    Epigenetics & Chromatin 2017 10:4

    Published on: 26 January 2017

  12. Research

    Sex-specific chromatin landscapes in an ultra-compact chordate genome

    In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increa...

    Pavla Navratilova, Gemma Barbara Danks, Abby Long, Stephen Butcher, John Robert Manak and Eric M. Thompson

    Epigenetics & Chromatin 2017 10:3

    Published on: 17 January 2017

  13. Methodology

    MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

    Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from pr...

    Sara El Kennani, Annie Adrait, Alexey K. Shaytan, Saadi Khochbin, Christophe Bruley, Anna R. Panchenko, David Landsman, Delphine Pflieger and Jérôme Govin

    Epigenetics & Chromatin 2017 10:2

    Published on: 10 January 2017

  14. Methodology

    Genome-wide methylation data mirror ancestry information

    Genetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In con...

    Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter, Sam S. Oh, Melanie Waldenberger, Konstantin Strauch, Harald Grallert, Thomas Meitinger, Christian Gieger…

    Epigenetics & Chromatin 2017 10:1

    Published on: 3 January 2017

  15. Research

    The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes

    The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function—the storage, expression, and replication of genetic information—is still one of the central i...

    Tobias A. Knoch, Malte Wachsmuth, Nick Kepper, Michael Lesnussa, Anis Abuseiris, A. M. Ali Imam, Petros Kolovos, Jessica Zuin, Christel E. M. Kockx, Rutger W. W. Brouwer, Harmen J. G. van de Werken, Wilfred F. J. van IJcken, Kerstin S. Wendt and Frank G. Grosveld

    Epigenetics & Chromatin 2016 9:58

    Published on: 24 December 2016

  16. Methodology

    Targeted bisulfite sequencing of the dynamic DNA methylome

    The ability to measure DNA methylation precisely and efficiently continues to drive our understanding of this modification in development and disease. Whole genome bisulfite sequencing has the advantage of the...

    Michael J. Ziller, Elena K. Stamenova, Hongcang Gu, Andreas Gnirke and Alexander Meissner

    Epigenetics & Chromatin 2016 9:55

    Published on: 3 December 2016

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