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  1. Content type: Research

    Specific genomic loci, termed Piwi-interacting RNA (piRNA) clusters, manufacture piRNAs that serve as guides for the inactivation of complementary transposable elements (TEs). The piRNA pathway has been accura...

    Authors: Phillip George, Silke Jensen, Romain Pogorelcnik, Jiyoung Lee, Yi Xing, Emilie Brasset, Chantal Vaury and Igor V. Sharakhov

    Citation: Epigenetics & Chromatin 2015 8:50

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  2. Content type: Research

    CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. CBP plays an important role in embryonic development and cell differentiation and mutations in CB...

    Authors: Philge Philip, Ann Boija, Roshan Vaid, Allison M. Churcher, David J. Meyers, Philip A. Cole, Mattias Mannervik and Per Stenberg

    Citation: Epigenetics & Chromatin 2015 8:48

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    The Erratum to this article has been published in Epigenetics & Chromatin 2016 9:38

  3. Content type: Research

    Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more com...

    Authors: Patrick Coit, Mikhail Ognenovski, Elizabeth Gensterblum, Kathleen Maksimowicz-McKinnon, Jonathan D. Wren and Amr H. Sawalha

    Citation: Epigenetics & Chromatin 2015 8:49

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  4. Content type: Research

    Previous studies of higher order chromatin organization in nuclei of mammalian species revealed both structural consistency and species-specific differences between cell lines and during early embryonic develo...

    Authors: Barbara Hübner, Mariana Lomiento, Fabiana Mammoli, Doris Illner, Yolanda Markaki, Sergio Ferrari, Marion Cremer and Thomas Cremer

    Citation: Epigenetics & Chromatin 2015 8:47

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  5. Content type: Research

    RNA:DNA hybrids represent a non-canonical nucleic acid structure that has been associated with a range of human diseases and potential transcriptional regulatory functions. Mapping of RNA:DNA hybrids in human ...

    Authors: Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N. Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe and John M. Greally

    Citation: Epigenetics & Chromatin 2015 8:46

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  6. Content type: Research

    Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip...

    Authors: Sarina Ravens, Changwei Yu, Tao Ye, Matthieu Stierle and Laszlo Tora

    Citation: Epigenetics & Chromatin 2015 8:45

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  7. Content type: Research

    The death domain-associated protein (DAXX) collaborates with accessory proteins to deposit the histone variant H3.3 into mouse telomeric and pericentromeric repeat DNA. Pericentromeric repeats are the main gen...

    Authors: Lindsy M. Rapkin, Kashif Ahmed, Stanimir Dulev, Ren Li, Hiroshi Kimura, Alexander M. Ishov and David P. Bazett-Jones

    Citation: Epigenetics & Chromatin 2015 8:44

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  8. Content type: Research

    Disease risk and incidence between males and females reveal differences, and sex is an important component of any investigation of the determinants of phenotypes or disease etiology. Further striking differenc...

    Authors: Paula Singmann, Doron Shem-Tov, Simone Wahl, Harald Grallert, Giovanni Fiorito, So-Youn Shin, Katharina Schramm, Petra Wolf, Sonja Kunze, Yael Baran, Simonetta Guarrera, Paolo Vineis, Vittorio Krogh, Salvatore Panico, Rosario Tumino, Anja Kretschmer…

    Citation: Epigenetics & Chromatin 2015 8:43

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  9. Content type: Research

    DNA methylation is important for the maintenance of the silent state of genes on the inactive X chromosome (Xi). Here, we screened for siRNAs and chemicals that reactivate an Xi-linked reporter in the presence...

    Authors: Alissa Minkovsky, Anna Sahakyan, Giancarlo Bonora, Robert Damoiseaux, Elizabeth Dimitrova, Liudmilla Rubbi, Matteo Pellegrini, Caius G. Radu and Kathrin Plath

    Citation: Epigenetics & Chromatin 2015 8:42

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  10. Content type: Research

    Supernumerary chromosomes have been found in many organisms. In fungi, these “accessory” or “dispensable” chromosomes are present at different frequencies in populations and are usually characterized by higher...

    Authors: Klaas Schotanus, Jessica L. Soyer, Lanelle R. Connolly, Jonathan Grandaubert, Petra Happel, Kristina M. Smith, Michael Freitag and Eva H. Stukenbrock

    Citation: Epigenetics & Chromatin 2015 8:41

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  11. Content type: Research

    Maternal consumption of alcohol during pregnancy is associated with a range of physical, cognitive and behavioural outcomes in the offspring which are collectively called foetal alcohol spectrum disorders. We ...

    Authors: Christine R. Zhang, Mei-Fong Ho, Michelle C. Sanchez Vega, Thomas H. J. Burne and Suyinn Chong

    Citation: Epigenetics & Chromatin 2015 8:40

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  12. Content type: Research

    In recent years, we have come to recognize that a multitude of in utero exposures have the capacity to induce the development of congenital and metabolic defects. As most of these encounters manifest their eff...

    Authors: Kylee J. Veazey, Scott E. Parnell, Rajesh C. Miranda and Michael C. Golding

    Citation: Epigenetics & Chromatin 2015 8:39

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  13. Content type: Research

    The transcriptional repressor promyelocytic leukemia zinc finger protein (PLZF) is critical for the regulation of normal stem cells maintenance by establishing specific epigenetic landscape. We have previously...

    Authors: Melanie J. McConnell, Laetitia Durand, Emma Langley, Lise Coste-Sarguet, Arthur Zelent, Christine Chomienne, Tony Kouzarides, Jonathan D. Licht and Fabien Guidez

    Citation: Epigenetics & Chromatin 2015 8:38

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  14. Content type: Methodology

    Proteins that ‘read’ the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably...

    Authors: Yanai Zhan, Maria Kost-Alimova, Xi Shi, Elisabetta Leo, Jennifer P. Bardenhagen, Hannah E. Shepard, Srikanth Appikonda, Bhavatarini Vangamudi, Shuping Zhao, Trang N. Tieu, Shiming Jiang, Timothy P. Heffernan, Joseph R. Marszalek, Carlo Toniatti, Giulio Draetta, Jessica Tyler…

    Citation: Epigenetics & Chromatin 2015 8:37

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  15. Content type: Research

    Unraveling transcriptional regulatory networks is a central problem in molecular biology and, in this quest, chromatin immunoprecipitation and sequencing (ChIP-seq) technology has given us the unprecedented ab...

    Authors: Parameswaran Ramachandran, Gareth A. Palidwor and Theodore J. Perkins

    Citation: Epigenetics & Chromatin 2015 8:33

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  16. Content type: Research

    Heterochromatin has been reported to be a major silencing compartment during development and differentiation. Prominent heterochromatin compartments are located at the nuclear periphery and inside the nucleus ...

    Authors: K. Laurence Jost, Bianca Bertulat, Alexander Rapp, Alessandro Brero, Tanja Hardt, Petra Domaing, Claudia Gösele, Herbert Schulz, Norbert Hübner and M. Cristina Cardoso

    Citation: Epigenetics & Chromatin 2015 8:36

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  17. Content type: Research

    The selective incorporation of appropriate histone variants into chromatin is critical for the regulation of genome function. Although many histone variants have been identified, a complete list has not been c...

    Authors: Kazumitsu Maehara, Akihito Harada, Yuko Sato, Masaki Matsumoto, Keiichi I. Nakayama, Hiroshi Kimura and Yasuyuki Ohkawa

    Citation: Epigenetics & Chromatin 2015 8:35

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  18. Content type: Research

    Role of epigenetic mechanisms towards regulation of the complex life cycle/pathogenesis of Plasmodium falciparum, the causative agent of malaria, has been poorly understood. To elucidate stage-specific epigenetic...

    Authors: Krishanpal Karmodiya, Saurabh J. Pradhan, Bhagyashree Joshi, Rahul Jangid, Puli Chandramouli Reddy and Sanjeev Galande

    Citation: Epigenetics & Chromatin 2015 8:32

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  19. Content type: Research

    The genome-wide hyperacetylation of chromatin caused by histone deacetylase inhibitors (HDACi) is surprisingly well tolerated by most eukaryotic cells. The homeostatic mechanisms that underlie this tolerance a...

    Authors: John A Halsall, Nil Turan, Maaike Wiersma and Bryan M Turner

    Citation: Epigenetics & Chromatin 2015 8:29

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  20. Content type: Research

    Genetic recombination plays an important role in evolution, facilitating the creation of new, favorable combinations of alleles and the removal of deleterious mutations by unlinking them from surrounding seque...

    Authors: Michael Walker, Timothy Billings, Christopher L. Baker, Natalie Powers, Hui Tian, Ruth L. Saxl, Kwangbom Choi, Matthew A. Hibbs, Gregory W. Carter, Mary Ann Handel, Kenneth Paigen and Petko M. Petkov

    Citation: Epigenetics & Chromatin 2015 8:31

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  21. Content type: Research

    In the Metazoan nucleus, core histones assemble the genomic DNA to form nucleosome arrays, which are further compacted into dense chromatin structures by the linker histone H1. The extraordinary density of chr...

    Authors: Qian Zhang, Holli A. Giebler, Marisa K. Isaacson and Jennifer K. Nyborg

    Citation: Epigenetics & Chromatin 2015 8:30

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  22. Content type: Research

    Heterochromatin is essential for chromosome segregation, gene silencing and genome integrity. The fission yeast Schizosaccharomyces pombe contains heterochromatin at centromeres, subtelomeres, and mating type gen...

    Authors: Cristina Cotobal, María Rodríguez-López, Caia Duncan, Ayesha Hasan, Akira Yamashita, Masayuki Yamamoto, Jürg Bähler and Juan Mata

    Citation: Epigenetics & Chromatin 2015 8:28

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  23. Content type: Methodology

    DNA methylation has emerged as an important regulator of development and disease, necessitating the design of more efficient and cost-effective methods for detecting and quantifying this epigenetic modificatio...

    Authors: Diana L Bernstein, Vasumathi Kameswaran, John E Le Lay, Karyn L Sheaffer and Klaus H Kaestner

    Citation: Epigenetics & Chromatin 2015 8:27

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  24. Content type: Research

    Epigenomic studies on humans and model species have revealed substantial inter-individual variation in histone modification profiles. However, the pattern of this variation has not been precisely characterized...

    Authors: Fabien Filleton, Florent Chuffart, Muniyandi Nagarajan, Hélène Bottin-Duplus and Gaël Yvert

    Citation: Epigenetics & Chromatin 2015 8:26

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  25. Content type: Methodology

    ChIP-seq is the method of choice for genome-wide studies of protein–DNA interactions. We describe a new method for ChIP-seq sample preparation, termed lobChIP, where the library reactions are performed on cros...

    Authors: Ola Wallerman, Helena Nord, Madhusudhan Bysani, Lisa Borghini and Claes Wadelius

    Citation: Epigenetics & Chromatin 2015 8:25

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  26. Content type: Research

    Stretch enhancers (SEs) are large chromatin-defined regulatory elements that are at least 3,000 base pairs (bps) long, in contrast to the median enhancer length of 800 bps. SEs tend to be cell-type specific, r...

    Authors: Daniel X Quang, Michael R Erdos, Stephen C J Parker and Francis S Collins

    Citation: Epigenetics & Chromatin 2015 8:23

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  27. Content type: Methodology

    The Cancer Genome Atlas (TCGA) offers a multilayered view of genomics and epigenomics data of many human cancer types. However, the retrieval of expression and methylation data from TCGA is a cumbersome and ti...

    Authors: Anna Díez-Villanueva, Izaskun Mallona and Miguel A. Peinado

    Citation: Epigenetics & Chromatin 2015 8:22

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  28. Content type: Research

    Signaling via B cell receptor (BCR) and Toll-like receptors (TLRs) results in activation of B cells with distinct physiological outcomes, but transcriptional regulatory mechanisms that drive activation and dis...

    Authors: Trent Fowler, Alexander S Garruss, Amalendu Ghosh, Supriyo De, Kevin G Becker, William H Wood, Matthew T Weirauch, Stephen T Smale, Bruce Aronow, Ranjan Sen and Ananda L Roy

    Citation: Epigenetics & Chromatin 2015 8:20

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  29. Content type: Research

    DNA methylation is an epigenetic mark that balances plasticity with stability. While DNA methylation exhibits tissue specificity, it can also vary with age and potentially environmental exposures. In studies o...

    Authors: Pau Farré, Meaghan J Jones, Michael J Meaney, Eldon Emberly, Gustavo Turecki and Michael S Kobor

    Citation: Epigenetics & Chromatin 2015 8:19

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  30. Content type: Research

    Cyclins and cyclin-dependent kinases (CDKs) are essential for cell cycle regulation and are functionally associated with proteins involved in epigenetic maintenance of transcriptional patterns in various devel...

    Authors: Camille A Dupont, Delphine Dardalhon-Cuménal, Michael Kyba, Hugh W Brock, Neel B Randsholt and Frédérique Peronnet

    Citation: Epigenetics & Chromatin 2015 8:18

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  31. Content type: Research

    The small non-histone protein Heterochromatin protein 1a (HP1a) plays a vital role in packaging chromatin, most notably in forming constitutive heterochromatin at the centromeres and telomeres. A second major ...

    Authors: Janel R Cabrera, Ursula Olcese and Jamila I Horabin

    Citation: Epigenetics & Chromatin 2015 8:17

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  32. Content type: Research

    Regulated gene expression controls organismal development, and variation in regulatory patterns has been implicated in complex traits. Thus accurate prediction of enhancers is important for further understandi...

    Authors: Nergiz Dogan, Weisheng Wu, Christapher S Morrissey, Kuan-Bei Chen, Aaron Stonestrom, Maria Long, Cheryl A Keller, Yong Cheng, Deepti Jain, Axel Visel, Len A Pennacchio, Mitchell J Weiss, Gerd A Blobel and Ross C Hardison

    Citation: Epigenetics & Chromatin 2015 8:16

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  33. Content type: Methodology

    Histone isoforms and their post-translational modifications (PTMs) play an important role in the control of many chromatin-related processes including transcription and DNA damage. Variants of histones H2A and...

    Authors: Rosalynn C Molden, Natarajan V Bhanu, Gary LeRoy, Anna M Arnaudo and Benjamin A Garcia

    Citation: Epigenetics & Chromatin 2015 8:15

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  34. Content type: Research

    The term CpG island methylator phenotype (CIMP) has been used to describe widespread DNA hypermethylation at CpG-rich genomic regions affecting clinically distinct subsets of cancer patients. Even though there...

    Authors: Francisco Sánchez-Vega, Valer Gotea, Gennady Margolin and Laura Elnitski

    Citation: Epigenetics & Chromatin 2015 8:14

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  35. Content type: Methodology

    Histone variants play further important roles in DNA packaging and controlling gene expression. However, our understanding about their composition and their functions is limited.

    Authors: Kyoung-Jae Won, Inchan Choi, Gary LeRoy, Barry M Zee, Simone Sidoli, Michelle Gonzales-Cope and Benjamin A Garcia

    Citation: Epigenetics & Chromatin 2015 8:13

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  36. Content type: Research

    DNA methylation and histone 3 lysine 9 (H3K9) methylation are considered as epigenetic marks that can be inherited through cell divisions. To explore the functional consequences and stability of these modifica...

    Authors: Goran Kungulovski, Suneetha Nunna, Maria Thomas, Ulrich M Zanger, Richard Reinhardt and Albert Jeltsch

    Citation: Epigenetics & Chromatin 2015 8:12

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  37. Content type: Research

    DNA methylation can be abnormally regulated in human disease and associated with effects on gene transcription that appear to be causally related to pathogenesis. The potential to use pharmacological agents th...

    Authors: María-Paz Ramos, Neil Ari Wijetunga, Andrew S McLellan, Masako Suzuki and John M Greally

    Citation: Epigenetics & Chromatin 2015 8:11

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  38. Content type: Research

    Appropriate epigenetic regulation of gene expression during lineage allocation and tissue differentiation is required for normal development. One example is genomic imprinting, which is defined as parent-of-or...

    Authors: Chelsea Marcho, Ariana Bevilacqua, Kimberly D Tremblay and Jesse Mager

    Citation: Epigenetics & Chromatin 2015 8:10

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  39. Content type: Research

    The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a signif...

    Authors: Matthew S Wilken, Joseph A Brzezinski, Anna La Torre, Kyle Siebenthall, Robert Thurman, Peter Sabo, Richard S Sandstrom, Jeff Vierstra, Theresa K Canfield, R Scott Hansen, Michael A Bender, John Stamatoyannopoulos and Thomas A Reh

    Citation: Epigenetics & Chromatin 2015 8:8

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  40. Content type: Research

    Due to the hyper-activation of WNT signaling in a variety of cancer types, there has been a strong drive to develop pathway-specific inhibitors with the eventual goal of providing a chemotherapeutic antagonist...

    Authors: Malaina Gaddis, Diana Gerrard, Seth Frietze and Peggy J Farnham

    Citation: Epigenetics & Chromatin 2015 8:9

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  41. Content type: Research

    Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transduce...

    Authors: Joseph D Fleming, Paul G Giresi, Marianne Lindahl-Allen, Elsa B Krall, Jason D Lieb and Kevin Struhl

    Citation: Epigenetics & Chromatin 2015 8:7

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  42. Content type: Methodology

    The identification and characterisation of differentially methylated regions (DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We present a novel method, DMRcate, that fits replic...

    Authors: Timothy J Peters, Michael J Buckley, Aaron L Statham, Ruth Pidsley, Katherine Samaras, Reginald V Lord, Susan J Clark and Peter L Molloy

    Citation: Epigenetics & Chromatin 2015 8:6

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  43. Content type: Research

    CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation,...

    Authors: Lee Siggens, Lina Cordeddu, Michelle Rönnerblad, Andreas Lennartsson and Karl Ekwall

    Citation: Epigenetics & Chromatin 2015 8:4

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  44. Content type: Review

    Constitutive heterochromatin, mainly formed at the gene-poor regions of pericentromeres, is believed to ensure a condensed and transcriptionally inert chromatin conformation. Pericentromeres consist of repetit...

    Authors: Nehmé Saksouk, Elisabeth Simboeck and Jérôme Déjardin

    Citation: Epigenetics & Chromatin 2015 8:3

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  45. Content type: Research

    The histone H3 variant CENP-A is normally tightly regulated to ensure only one centromere exists per chromosome. Native CENP-A is often found overexpressed in human cancer cells and a range of human tumors. Co...

    Authors: Rajbir K Athwal, Marcin P Walkiewicz, Songjoon Baek, Song Fu, Minh Bui, Jordi Camps, Thomas Ried, Myong-Hee Sung and Yamini Dalal

    Citation: Epigenetics & Chromatin 2015 8:2

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  46. Content type: Research

    DNA methylomes are extensively reprogrammed during mouse pre-implantation and early germ cell development. The main feature of this reprogramming is a genome-wide decrease in 5-methylcytosine (5mC). Standard h...

    Authors: Julia Arand, Mark Wossidlo, Konstantin Lepikhov, Julian R Peat, Wolf Reik and Jörn Walter

    Citation: Epigenetics & Chromatin 2015 8:1

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