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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Research

    Widespread recovery of methylation at gametic imprints in hypomethylated mouse stem cells following rescue with DNMT3A2

    Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated reg...

    Avinash Thakur, Sarah-Jayne Mackin, Rachelle E. Irwin, Karla M. O’Neill, Gareth Pollin and Colum Walsh

    Epigenetics & Chromatin 2016 9:53

    Published on: 22 November 2016

  9. Research

    Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes

    The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic de...

    Maaike Wiersma, Marianne Bussiere, John A. Halsall, Nil Turan, Robert Slany, Bryan M. Turner and Karl P. Nightingale

    Epigenetics & Chromatin 2016 9:52

    Published on: 11 November 2016

  10. Research

    Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

    Long noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, He...

    Jian-Jun Jiang, Le-Hua Cheng, Huan Wu, Yong-Han He and Qing-Peng Kong

    Epigenetics & Chromatin 2016 9:51

    Published on: 10 November 2016

  11. Research

    Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

    Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understandin...

    Suhn Kyong Rhie, Yu Guo, Yu Gyoung Tak, Lijing Yao, Hui Shen, Gerhard A. Coetzee, Peter W. Laird and Peggy J. Farnham

    Epigenetics & Chromatin 2016 9:50

    Published on: 9 November 2016

  12. Methodology

    Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq

    The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance betw...

    Michele Busby, Catherine Xue, Catherine Li, Yossi Farjoun, Elizabeth Gienger, Ido Yofe, Adrianne Gladden, Charles B. Epstein, Evan M. Cornett, Scott B. Rothbart, Chad Nusbaum and Alon Goren

    Epigenetics & Chromatin 2016 9:49

    Published on: 4 November 2016

  13. Research

    Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

    A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By c...

    Michiel E. Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E. H. Dahlmans, Lars M. Eijssen, Timothy Beck, Bradly G. Wouters, Jan Willem Voncken and Chris T. A. Evelo

    Epigenetics & Chromatin 2016 9:48

    Published on: 1 November 2016

  14. Research

    Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

    Trimethylation at histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) controls gene activity during development and differentiation. Whether H3K4me3 and H3K27me3 changes dynamically in response to altered m...

    Peggy Prickaerts, Michiel E. Adriaens, Twan van den Beucken, Elizabeth Koch, Ludwig Dubois, Vivian E. H. Dahlmans, Caroline Gits, Chris T. A. Evelo, Michelle Chan-Seng-Yue, Bradly G. Wouters and Jan Willem Voncken

    Epigenetics & Chromatin 2016 9:46

    Published on: 26 October 2016

  15. Research

    Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis

    Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, reg...

    Valerio Pazienza, Concetta Panebianco, Francesca Rappa, Domenico Memoli, Michela Borghesan, Sara Cannito, Asami Oji, Giuseppe Mazza, Domenico Tamburrino, Giuseppe Fusai, Rosario Barone, Giulia Bolasco, Francesc Villarroya, Joan Villarroya, Kiyotaka Hatsuzawa, Francesco Cappello…

    Epigenetics & Chromatin 2016 9:45

    Published on: 25 October 2016

  16. Methodology

    High-throughput assessment of context-dependent effects of chromatin proteins

    Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest....

    Laura Brueckner, Joris van Arensbergen, Waseem Akhtar, Ludo Pagie and Bas van Steensel

    Epigenetics & Chromatin 2016 9:43

    Published on: 18 October 2016

  17. Methodology

    EpiMINE, a computational program for mining epigenomic data

    In epigenetic research, both the increasing ease of high-throughput sequencing and a greater interest in genome-wide studies have resulted in an exponential flooding of epigenetic-related data in public domai...

    SriGanesh Jammula and Diego Pasini

    Epigenetics & Chromatin 2016 9:42

    Published on: 29 September 2016

  18. Research

    Imprinted DNA methylation reconstituted at a non-imprinted locus

    In mammals, tight regulation of cytosine methylation is required for embryonic development and cellular differentiation. The trans-acting DNA methyltransferases that catalyze this modification have been identifi...

    David H. Taylor, Chelsea M. McLean, Warren L. Wu, Alex B. Wang and Paul D. Soloway

    Epigenetics & Chromatin 2016 9:41

    Published on: 22 September 2016

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