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  1. Content type: Methodology

    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...

    Authors: 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…

    Citation: Epigenetics & Chromatin 2017 10:1

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  2. Content type: Research

    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...

    Authors: 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

    Citation: Epigenetics & Chromatin 2016 9:58

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  3. Content type: Research

    Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is ...

    Authors: Malte Wachsmuth, Tobias A. Knoch and Karsten Rippe

    Citation: Epigenetics & Chromatin 2016 9:57

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  4. Content type: Research

    The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple m...

    Authors: Shan V. Andrews, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen and M. Daniele Fallin

    Citation: Epigenetics & Chromatin 2016 9:56

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  5. Content type: Methodology

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:55

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  6. Content type: Research

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:53

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  7. Content type: Research

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:52

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  8. Content type: Research

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:51

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  9. Content type: Research

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:50

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  10. Content type: Methodology

    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...

    Authors: 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

    Citation: Epigenetics & Chromatin 2016 9:49

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  11. Content type: Research

    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...

    Authors: 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

    Citation: Epigenetics & Chromatin 2016 9:48

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  12. Content type: Research

    During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing ...

    Authors: Charlotte Moretti, Daniel Vaiman, Frederic Tores and Julie Cocquet

    Citation: Epigenetics & Chromatin 2016 9:47

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  13. Content type: Research

    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...

    Authors: 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

    Citation: Epigenetics & Chromatin 2016 9:46

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  14. Content type: Research

    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...

    Authors: 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…

    Citation: Epigenetics & Chromatin 2016 9:45

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  15. Content type: Research

    In C. elegans, in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X...

    Authors: Alyssa C. Lau, Kevin P. Zhu, Elizabeth A. Brouhard, Michael B. Davis and Györgyi Csankovszki

    Citation: Epigenetics & Chromatin 2016 9:44

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  16. Content type: Methodology

    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....

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

    Citation: Epigenetics & Chromatin 2016 9:43

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  17. Content type: Methodology

    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...

    Authors: SriGanesh Jammula and Diego Pasini

    Citation: Epigenetics & Chromatin 2016 9:42

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  18. Content type: Research

    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...

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

    Citation: Epigenetics & Chromatin 2016 9:41

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  19. Content type: Research

    The nucleosome remodeling and deacetylase complex promotes cell fate decisions throughout embryonic development. Its core enzymatic subunit, the SNF2-like ATPase and Helicase Mi2, is well conserved throughout ...

    Authors: Stéphanie Käser-Pébernard, Catherine Pfefferli, Caroline Aschinger and Chantal Wicky

    Citation: Epigenetics & Chromatin 2016 9:39

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  20. Content type: Research

    Pax6 is a key regulator of the entire cascade of ocular lens formation through specific binding to promoters and enhancers of batteries of target genes. The promoters and enhancers communicate with each other ...

    Authors: Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen-Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery-Padan, David Shechter, Deyou Zheng and Ales Cvekl

    Citation: Epigenetics & Chromatin 2016 9:37

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  21. Content type: Research

    Cnidarians are a group of early branching animals including corals, jellyfish and hydroids that are renowned for their high regenerative ability, growth plasticity and longevity. Because cnidarian genomes are ...

    Authors: Anna Török, Philipp H. Schiffer, Christine E. Schnitzler, Kris Ford, James C. Mullikin, Andreas D. Baxevanis, Antony Bacic, Uri Frank and Sebastian G. Gornik

    Citation: Epigenetics & Chromatin 2016 9:36

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  22. Content type: Research

    A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them could generate novel chromatin states, not found in normal cells. The germline-specific transc...

    Authors: Elena M. Pugacheva, Evgeny Teplyakov, Qiongfang Wu, Jingjing Li, Cheng Chen, Chengcheng Meng, Jian Liu, Susan Robinson, Dmitry Loukinov, Abdelhalim Boukaba, Andrew Paul Hutchins, Victor Lobanenkov and Alexander Strunnikov

    Citation: Epigenetics & Chromatin 2016 9:35

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  23. Content type: Research

    How cells respond and adapt to environmental changes, such as nutrient flux, remains poorly understood. Evolutionarily conserved nutrient signaling cascades can regulate chromatin to contribute to genome regul...

    Authors: Hongfeng Chen, Jason J. Workman, Brian D. Strahl and R. Nicholas Laribee

    Citation: Epigenetics & Chromatin 2016 9:34

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  24. Content type: Research

    Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to an...

    Authors: Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller…

    Citation: Epigenetics & Chromatin 2016 9:33

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  25. Content type: Research

    Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30–50 bp downstream of the transcription start site of genes involved in developmental control...

    Authors: Shih-Ying Tsai, Yuh-Long Chang, Krishna B. S. Swamy, Ruei-Lin Chiang and Der-Hwa Huang

    Citation: Epigenetics & Chromatin 2016 9:32

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  26. Content type: Review

    Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that...

    Authors: Kostas A. Triantaphyllopoulos, Ioannis Ikonomopoulos and Andrew J. Bannister

    Citation: Epigenetics & Chromatin 2016 9:31

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  27. Content type: Research

    Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-...

    Authors: Niran Hadad, Dustin R. Masser, Sreemathi Logan, Benjamin Wronowski, Colleen A. Mangold, Nicholas Clark, Laura Otalora, Archana Unnikrishnan, Matthew M. Ford, Cory B. Giles, Jonathan D. Wren, Arlan Richardson, William E. Sonntag, David R. Stanford and Willard Freeman

    Citation: Epigenetics & Chromatin 2016 9:30

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  28. Content type: Research

    Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cel...

    Authors: Tamas Aranyi, Daniel Stockholm, Roseline Yao, Catherine Poinsignon, Thibaut Wiart, Guillaume Corre, Nizar Touleimat, Jörg Tost, Anne Galy and Andràs Paldi

    Citation: Epigenetics & Chromatin 2016 9:29

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  29. Content type: Research

    Functional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of ...

    Authors: Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W. Parks, Aldons J. Lusis, Rama Natarajan and Dustin E. Schones

    Citation: Epigenetics & Chromatin 2016 9:28

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  30. Content type: Research

    Adaptive evolution is not possible without the generation of phenotypic variants. The origin of these variations has been a central topic in evolutionary biology. Up to now, it was commonly accepted that stand...

    Authors: Sara Fneich, André Théron, Céline Cosseau, Anne Rognon, Benoit Aliaga, Jérôme Buard, David Duval, Nathalie Arancibia, Jérôme Boissier, David Roquis, Guillaume Mitta and Christoph Grunau

    Citation: Epigenetics & Chromatin 2016 9:27

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  31. Content type: Review

    DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dy...

    Authors: Wai-Shin Yong, Fei-Man Hsu and Pao-Yang Chen

    Citation: Epigenetics & Chromatin 2016 9:26

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  32. Content type: Research

    Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol’s ef...

    Authors: Elodie Portales-Casamar, Alexandre A. Lussier, Meaghan J. Jones, Julia L. MacIsaac, Rachel D. Edgar, Sarah M. Mah, Amina Barhdadi, Sylvie Provost, Louis-Philippe Lemieux-Perreault, Max S. Cynader, Albert E. Chudley, Marie-Pierre Dubé, James N. Reynolds, Paul Pavlidis and Michael S. Kobor

    Citation: Epigenetics & Chromatin 2016 9:25

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  33. Content type: Research

    During the process of spermatogenesis, male germ cells undergo dramatic chromatin reorganization, whereby most histones are replaced by protamines, as part of the pathway to compact the genome into the small n...

    Authors: Lacey J. Luense, Xiaoshi Wang, Samantha B. Schon, Angela H. Weller, Enrique Lin Shiao, Jessica M. Bryant, Marisa S. Bartolomei, Christos Coutifaris, Benjamin A. Garcia and Shelley L. Berger

    Citation: Epigenetics & Chromatin 2016 9:24

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  34. Content type: Research

    Hematopoietic stem cell renewal and differentiation are regulated through epigenetic processes. The conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC) by ten-eleven-translocation enzymes provid...

    Authors: Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine B. Vågbø, Robert Lyle, Marianne K. Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland and Judith Staerk

    Citation: Epigenetics & Chromatin 2016 9:21

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  35. Content type: Research

    Chromatin containing the histone variant CENP-A (CEN chromatin) exists as an essential domain at every centromere and heritably marks the location of kinetochore assembly. The size of the CEN chromatin domain ...

    Authors: Justyne E. Ross, Kaitlin Stimpson Woodlief and Beth A. Sullivan

    Citation: Epigenetics & Chromatin 2016 9:20

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  36. Content type: Research

    Transcriptional regulation is impacted by multiple layers of genome organization. A general feature of transcriptionally active chromatin is sensitivity to DNase I and association with acetylated histones. How...

    Authors: Sanzida Jahan, Wayne Xu, Shihua He, Carolina Gonzalez, Geneviève P. Delcuve and James R. Davie

    Citation: Epigenetics & Chromatin 2016 9:19

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  37. Content type: Research

    The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation...

    Authors: Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter F. Hickey, Sarah A. Kinkel, Darcy L. Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Catherine Phillips, Miha Pakusch, Christine Biben, Julie M. Sheridan, Benjamin T. Kile…

    Citation: Epigenetics & Chromatin 2016 9:16

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  38. Content type: Research

    Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence featu...

    Authors: Owen K. Smith, RyanGuk Kim, Haiqing Fu, Melvenia M. Martin, Chii Mei Lin, Koichi Utani, Ya Zhang, Anna B. Marks, Marc Lalande, Stormy Chamberlain, Maxwell W. Libbrecht, Eric E. Bouhassira, Michael C. Ryan, William S. Noble and Mirit I. Aladjem

    Citation: Epigenetics & Chromatin 2016 9:18

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  39. Content type: Research

    Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyp...

    Authors: Christopher L. Frank, Dinesh Manandhar, Raluca Gordân and Gregory E. Crawford

    Citation: Epigenetics & Chromatin 2016 9:15

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  40. Content type: Research

    The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in off-loading cohesin to fa...

    Authors: Cary Stelloh, Michael H. Reimer, Kirthi Pulakanti, Steven Blinka, Jonathan Peterson, Luca Pinello, Shuang Jia, Sergei Roumiantsev, Martin J. Hessner, Samuel Milanovich, Guo-Cheng Yuan and Sridhar Rao

    Citation: Epigenetics & Chromatin 2016 9:14

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  41. Content type: Research

    Fragile X syndrome (FXS) is caused by CGG expansion over 200 repeats at the 5′ UTR of the FMR1 gene and subsequent DNA methylation of both the expanded sequence and the CpGs of the promoter region. This epigeneti...

    Authors: Elisabetta Tabolacci, Giorgia Mancano, Stella Lanni, Federica Palumbo, Martina Goracci, Fabrizio Ferrè, Manuela Helmer-Citterich and Giovanni Neri

    Citation: Epigenetics & Chromatin 2016 9:12

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  42. Content type: Research

    There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-indepe...

    Authors: Yuting Chen, Charles E. Breeze, Shao Zhen, Stephan Beck and Andrew E. Teschendorff

    Citation: Epigenetics & Chromatin 2016 9:10

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