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Page 7 of 14

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: Research

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Review

    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

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  23. Content type: Research

    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

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  24. Content type: Research

    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

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  25. Content type: Research

    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

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  26. Content type: Research

    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

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  27. Content type: Research

    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

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  28. Content type: Research

    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

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  29. Content type: Research

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Research

    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

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  33. Content type: Research

    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

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  34. Content type: Methodology

    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

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  35. Content type: Research

    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

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  36. Content type: Research

    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

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  37. Content type: Research

    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

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  38. Content type: Methodology

    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

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  39. Content type: Research

    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

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  40. Content type: Research

    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

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  41. Content type: Research

    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

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    A Related Article has been published.

  42. Content type: Research

    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

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  43. Content type: Research

    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

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    A Related Article has been published.

  44. Content type: Methodology

    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

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