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  1. 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

    Content type: Research

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  2. 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

    Content type: Research

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Methodology

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  8. 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

    Content type: Research

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  9. 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

    Content type: Methodology

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  10. 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

    Content type: Research

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  11. 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

    Content type: Methodology

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. 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

    Content type: Research

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

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  17. 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

    Content type: Methodology

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  18. 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

    Content type: Research

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  19. 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

    Content type: Methodology

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  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Research

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  24. 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

    Content type: Research

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  25. 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

    Content type: Research

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  26. 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

    Content type: Methodology

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  27. 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

    Content type: Research

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  28. 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

    Content type: Review

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  29. 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

    Content type: Research

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  30. 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

    Content type: Research

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  31. The repair of spontaneous and induced DNA lesions is a multistep process. Depending on the type of injury, damaged DNA is recognized by many proteins specifically involved in distinct DNA repair pathways.

    Authors: Lenka Stixová, Petra Sehnalová, Soňa Legartová, Jana Suchánková, Tereza Hrušková, Stanislav Kozubek, Dmitry V Sorokin, Pavel Matula, Ivan Raška, Aleš Kovařík, Jaroslav Fulneček and Eva Bártová

    Citation: Epigenetics & Chromatin 2014 7:39

    Content type: Research

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  32. The histone variant H3.3 plays a critical role in maintaining the pluripotency of embryonic stem cells (ESCs) by regulating gene expression programs important for lineage specification. H3.3 is deposited by va...

    Authors: Misook Ha, Daniel C Kraushaar and Keji Zhao

    Citation: Epigenetics & Chromatin 2014 7:38

    Content type: Research

    Published on:

  33. The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling...

    Authors: Muhammad A Shah, Emily L Denton, Cheryl H Arrowsmith, Mathieu Lupien and Matthieu Schapira

    Citation: Epigenetics & Chromatin 2014 7:29

    Content type: Research

    Published on:

  34. Genome-wide DNA methylation at a single nucleotide resolution in different primary cells of the mammalian genome helps to determine the characteristics and functions of tissue-specific hypomethylated regions (...

    Authors: Raghunath Chatterjee, Ximiao He, Di Huang, Peter FitzGerald, Andrew Smith and Charles Vinson

    Citation: Epigenetics & Chromatin 2014 7:35

    Content type: Research

    Published on:

  35. The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with tra...

    Authors: Ximiao He, Raghunath Chatterjee, Desiree Tillo, Andrew Smith, Peter FitzGerald and Charles Vinson

    Citation: Epigenetics & Chromatin 2014 7:34

    Content type: Research

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  36. Transcription factors (TFs) and histone modifications (HMs) play critical roles in gene expression by regulating mRNA transcription. Modelling frameworks have been developed to integrate high-throughput omics ...

    Authors: David M Budden, Daniel G Hurley, Joseph Cursons, John F Markham, Melissa J Davis and Edmund J Crampin

    Citation: Epigenetics & Chromatin 2014 7:36

    Content type: Research

    Published on:

  37. Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to t...

    Authors: Maria Tsompana and Michael J Buck

    Citation: Epigenetics & Chromatin 2014 7:33

    Content type: Review

    Published on:

  38. Chromatin consists of ordered nucleosomal arrays that are controlled by highly conserved adenosine triphosphate (ATP)-dependent chromatin remodeling complexes. One such remodeler, chromodomain helicase DNA bin...

    Authors: Daechan Park, Haridha Shivram and Vishwanath R Iyer

    Citation: Epigenetics & Chromatin 2014 7:32

    Content type: Research

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  39. The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in ...

    Authors: Lisette C M Anink-Groenen, Timo R Maarleveld, Pernette J Verschure and Frank J Bruggeman

    Citation: Epigenetics & Chromatin 2014 7:30

    Content type: Research

    Published on:

  40. DNA methylation is thought to play an important role in the regulation of mammalian gene expression, partly based on the observation that a lack of CpG island methylation in gene promoters is associated with h...

    Authors: Rachel Edgar, Powell Patrick Cheng Tan, Elodie Portales-Casamar and Paul Pavlidis

    Citation: Epigenetics & Chromatin 2014 7:28

    Content type: Research

    Published on:

  41. Epigenetic modifications such as histone and DNA methylation are essential for silencing pluripotency genes during embryonic stem cell (ESC) differentiation. G9a is the major histone H3 Lys9 (H3K9) methyltrans...

    Authors: Danielle Bittencourt, Brian H Lee, Lu Gao, Daniel S Gerke and Michael R Stallcup

    Citation: Epigenetics & Chromatin 2014 7:27

    Content type: Research

    Published on:

  42. Epigenetic reprogramming during early mammalian embryonic and germ cell development is a genome-wide process. CpG islands (CGIs), central to the regulation of mammalian gene expression, are exceptional in term...

    Authors: Heba Saadeh and Reiner Schulz

    Citation: Epigenetics & Chromatin 2014 7:26

    Content type: Research

    Published on:

  43. Repression of retrotransposons is essential for genome integrity and the development of germ cells. Among retrotransposons, the establishment of CpG DNA methylation and epigenetic silencing of LINE1 (L1) eleme...

    Authors: Monica Di Giacomo, Stefano Comazzetto, Srihari C Sampath, Srinath C Sampath and Dónal O’Carroll

    Citation: Epigenetics & Chromatin 2014 7:24

    Content type: Research

    Published on:

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