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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. The formation of chromatin domains is an important step in lineage commitment. In human hematopoietic stem and progenitor cells (HSPCs), G9a/GLP-dependent H3K9me2 chromatin territories form de novo during lineage...

    Authors: Dustin E Schones, Xiaoji Chen, Candi Trac, Ryan Setten and Patrick J Paddison
    Citation: Epigenetics & Chromatin 2014 7:23
  28. Stored, soluble histones in eggs are essential for early development, in particular during the maternally controlled early cell cycles in the absence of transcription. Histone post-translational modifications ...

    Authors: Wei-Lin Wang, Lissa C Anderson, Joshua J Nicklay, Hongshan Chen, Matthew J Gamble, Jeffrey Shabanowitz, Donald F Hunt and David Shechter
    Citation: Epigenetics & Chromatin 2014 7:22
  29. Dendritic cells (DCs) are important mediators of innate and adaptive immune responses, but the gene networks governing their lineage differentiation and maturation are poorly understood. To gain insight into t...

    Authors: Xue Zhang, Ashley Ulm, Hari K Somineni, Sunghee Oh, Matthew T Weirauch, Hong-Xuan Zhang, Xiaoting Chen, Maria A Lehn, Edith M Janssen and Hong Ji
    Citation: Epigenetics & Chromatin 2014 7:21
  30. Targeted gene silencing is an important approach in both drug development and basic research. However, the selection of a potent suppressor has become a significant hurdle to implementing maximal gene inhibiti...

    Authors: Ai-Niu Ma, Hong Wang, Rui Guo, Yong-Xiang Wang, Wei Li, Jiuwei Cui, Guanjun Wang, Andrew R Hoffman and Ji-Fan Hu
    Citation: Epigenetics & Chromatin 2014 7:20
  31. Epigenetic reprogramming of fetal germ cells involves the genome-wide erasure and subsequent re-establishment of DNA methylation. Mouse studies indicate that DNA demethylation may be initiated at embryonic day...

    Authors: Catherine M Rose, Sander van den Driesche, Richard M Sharpe, Richard R Meehan and Amanda J Drake
    Citation: Epigenetics & Chromatin 2014 7:19
  32. The recent introduction of pathology tissue-chromatin immunoprecipitation (PAT-ChIP), a technique allowing chromatin immunoprecipitation from formalin-fixed and paraffin-embedded (FFPE) tissues, has expanded t...

    Authors: Stefano Amatori, Marco Ballarini, Alice Faversani, Elena Belloni, Fulvia Fusar, Silvano Bosari, Pier Giuseppe Pelicci, Saverio Minucci and Mirco Fanelli
    Citation: Epigenetics & Chromatin 2014 7:18
  33. Methyl-CpG binding protein 2 (MECP2) is a protein that specifically binds methylated DNA, thus regulating transcription and chromatin organization. Mutations in the gene have been identified as the principal c...

    Authors: Congdi Song, Yana Feodorova, Jacky Guy, Leo Peichl, Katharina Laurence Jost, Hiroshi Kimura, Maria Cristina Cardoso, Adrian Bird, Heinrich Leonhardt, Boris Joffe and Irina Solovei
    Citation: Epigenetics & Chromatin 2014 7:17
  34. Within the nucleus of eukaryotic cells, chromatin is organized into compact, silent regions called heterochromatin and more loosely packaged regions of euchromatin where transcription is more active. Although ...

    Authors: Na Xu, Alexander V Emelyanov, Dmitry V Fyodorov and Arthur I Skoultchi
    Citation: Epigenetics & Chromatin 2014 7:16
  35. The chromatin remodeler NAP1L1, which is upregulated in small intestinal neuroendocrine neoplasms (NENs), has been implicated in cell cycle progression. As p57Kip2 (CDKN1C), a negative regulator of proliferation ...

    Authors: Simon Schimmack, Andrew Taylor, Ben Lawrence, Daniele Alaimo, Hubertus Schmitz-Winnenthal, Markus W Büchler, Irvin M Modlin and Mark Kidd
    Citation: Epigenetics & Chromatin 2014 7:15
  36. Acetylation of lysine residues in histone tails plays an important role in the regulation of gene transcription. Bromdomains are the readers of acetylated histone marks, and, consequently, bromodomain-containi...

    Authors: Martin Philpott, Catherine M Rogers, Clarence Yapp, Chris Wells, Jean-Philippe Lambert, Claire Strain-Damerell, Nicola A Burgess-Brown, Anne-Claude Gingras, Stefan Knapp and Susanne Müller
    Citation: Epigenetics & Chromatin 2014 7:14
  37. X chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions...

    Authors: Alissa Minkovsky, Anna Sahakyan, Elyse Rankin-Gee, Giancarlo Bonora, Sanjeet Patel and Kathrin Plath
    Citation: Epigenetics & Chromatin 2014 7:12
  38. Silencing of the paternal X chromosome (Xp), a phenomenon known as imprinted X-chromosome inactivation (I-XCI), characterises, amongst mouse extraembryonic lineages, the primitive endoderm and the extraembryon...

    Authors: Sarra Merzouk, Jane Lynda Deuve, Agnès Dubois, Pablo Navarro, Philip Avner and Céline Morey
    Citation: Epigenetics & Chromatin 2014 7:11
  39. Significant efforts have recently been put into the investigation of the spatial organization and the chromatin-interaction networks of genomes. Chromosome conformation capture (3C) technology and its derivati...

    Authors: Petros Kolovos, Harmen JG van de Werken, Nick Kepper, Jessica Zuin, Rutger WW Brouwer, Christel EM Kockx, Kerstin S Wendt, Wilfred FJ van IJcken, Frank Grosveld and Tobias A Knoch
    Citation: Epigenetics & Chromatin 2014 7:10

    The Related Article to this article has been published in Nature Protocols 2018 13:nprot.2017.132

  40. Differential distribution of DNA methylation on the parental alleles of imprinted genes distinguishes the alleles from each other and dictates their parent of origin-specific expression patterns. While differe...

    Authors: Alyssa Gagne, Abigail Hochman, Mahvish Qureshi, Celia Tong, Jessica Arbon, Kayla McDaniel and Tamara L Davis
    Citation: Epigenetics & Chromatin 2014 7:9
  41. A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quant...

    Authors: Daniel Smeets, Yolanda Markaki, Volker J Schmid, Felix Kraus, Anna Tattermusch, Andrea Cerase, Michael Sterr, Susanne Fiedler, Justin Demmerle, Jens Popken, Heinrich Leonhardt, Neil Brockdorff, Thomas Cremer, Lothar Schermelleh and Marion Cremer
    Citation: Epigenetics & Chromatin 2014 7:8

    The Related Article to this article has been published in Nature Protocols 2017 12:nprot.2017.020

  42. Histone post-translational modifications (PTMs) are key epigenetic regulators in chromatin-based processes. Increasing evidence suggests that vast combinations of PTMs exist within chromatin histones. These co...

    Authors: Zhangli Su, Melissa D Boersma, Jin-Hee Lee, Samuel S Oliver, Shichong Liu, Benjamin A Garcia and John M Denu
    Citation: Epigenetics & Chromatin 2014 7:7
  43. Genomic imprinting is the epigenetic marking of genes that results in parent-of-origin monoallelic expression. Most imprinted domains are associated with differentially DNA methylated regions (DMRs) that origi...

    Authors: Franck Court, Cristina Camprubi, Cristina Vicente Garcia, Amy Guillaumet-Adkins, Angela Sparago, Davide Seruggia, Juan Sandoval, Manel Esteller, Alex Martin-Trujillo, Andrea Riccio, Lluis Montoliu and David Monk
    Citation: Epigenetics & Chromatin 2014 7:5
  44. Regulation of chromatin structure involves deposition of selective histone variants into nucleosome arrays. Numerous histone H3 variants become differentially expressed by individual nanochromosomes in the cou...

    Authors: Sakeh Forcob, Aneta Bulic, Franziska Jönsson, Hans J Lipps and Jan Postberg
    Citation: Epigenetics & Chromatin 2014 7:4

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