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  1. Content type: Methodology

    DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size o...

    Authors: Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang and Pao-Yang Chen

    Citation: Epigenetics & Chromatin 2017 10:42

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  2. Content type: Research

    The dynamics of histone modifications in Plasmodium falciparum indicates the existence of unique mechanisms that link epigenetic factors with transcription. Here, we studied the impact of acetylated histone code ...

    Authors: Archana P. Gupta, Lei Zhu, Jaishree Tripathi, Michal Kucharski, Alok Patra and Zbynek Bozdech

    Citation: Epigenetics & Chromatin 2017 10:40

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  3. Content type: Research

    The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an ‘open’ local chromatin configuration has long been known. However, the 3D topography of TREs wi...

    Authors: Marion Cremer, Volker J. Schmid, Felix Kraus, Yolanda Markaki, Ines Hellmann, Andreas Maiser, Heinrich Leonhardt, Sam John, John Stamatoyannopoulos and Thomas Cremer

    Citation: Epigenetics & Chromatin 2017 10:39

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  4. Content type: Review

    Accumulating animal and human data indicate that environmental exposures experienced during sensitive developmental periods may strongly influence risk of adult disease. Moreover, the effects triggered by deve...

    Authors: Alexander M. Vaiserman, Alexander K. Koliada and Randy L. Jirtle

    Citation: Epigenetics & Chromatin 2017 10:38

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  5. Content type: Research

    There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail...

    Authors: Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann and Bernhard Horsthemke

    Citation: Epigenetics & Chromatin 2017 10:37

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  6. Content type: Research

    Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that v...

    Authors: Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos

    Citation: Epigenetics & Chromatin 2017 10:36

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  7. Content type: Research

    In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-gl...

    Authors: Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim V. Imakaev, Nezar A. Abdennur, Mikhail S. Gelfand, Alexey A. Gavrilov and Sergey V. Razin

    Citation: Epigenetics & Chromatin 2017 10:35

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  8. Content type: Methodology

    Middle-down mass spectrometry (MS), i.e., analysis of long (~50–60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttransla...

    Authors: Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R. Karch, Chrystian Ruminowicz and Benjamin A. Garcia

    Citation: Epigenetics & Chromatin 2017 10:34

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  9. Content type: Research

    Chromatin insulators shield promoters and chromatin domains from neighboring enhancers or chromatin regions with opposing activities. Insulator-binding proteins and their cofactors mediate the boundary functio...

    Authors: Theresa Jox, Melanie K. Buxa, Dorte Bohla, Ikram Ullah, Igor Mačinković, Alexander Brehm, Marek Bartkuhn and Rainer Renkawitz

    Citation: Epigenetics & Chromatin 2017 10:32

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  10. Content type: Research

    Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and ...

    Authors: Megan Guntrum, Ekaterina Vlasova and Tamara L. Davis

    Citation: Epigenetics & Chromatin 2017 10:31

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  11. Content type: Research

    Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage comp...

    Authors: Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry and Gaël Le Trionnaire

    Citation: Epigenetics & Chromatin 2017 10:30

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  12. Content type: Research

    Melon (Cucumis melo) is an important vegetable crop from the Cucurbitaceae family and a reference model specie for sex determination, fruit ripening and vascular fluxes studies. Nevertheless, the nature and role ...

    Authors: David Latrasse, Natalia Y. Rodriguez-Granados, Alaguraj Veluchamy, Kiruthiga Gayathri Mariappan, Claudia Bevilacqua, Nicolas Crapart, Celine Camps, Vivien Sommard, Cécile Raynaud, Catherine Dogimont, Adnane Boualem, Moussa Benhamed and Abdelhafid Bendahmane

    Citation: Epigenetics & Chromatin 2017 10:22

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  13. Content type: Research

    DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental ...

    Authors: Srihari Radhakrishnan, Robert Literman, Beatriz Mizoguchi and Nicole Valenzuela

    Citation: Epigenetics & Chromatin 2017 10:28

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  14. Content type: Research

    The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutatio...

    Authors: Paul R. Hillman, Sarah G. B. Christian, Ryan Doan, Noah D. Cohen, Kranti Konganti, Kory Douglas, Xu Wang, Paul B. Samollow and Scott V. Dindot

    Citation: Epigenetics & Chromatin 2017 10:27

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  15. Content type: Research

    Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established larg...

    Authors: Lenka Gahurova, Shin-ichi Tomizawa, Sébastien A. Smallwood, Kathleen R. Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R. Andrews, Taiping Chen and Gavin Kelsey

    Citation: Epigenetics & Chromatin 2017 10:25

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  16. Content type: Research

    Epigenome editing is expected to manipulate transcription and cell fates and to elucidate the gene expression mechanisms in various cell types. For functional epigenome editing, assessing the chromatin context...

    Authors: Masahiro Okada, Mitsuhiro Kanamori, Kazue Someya, Hiroko Nakatsukasa and Akihiko Yoshimura

    Citation: Epigenetics & Chromatin 2017 10:24

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  17. Content type: Review

    The prevailing views as to the form, function, and regulation of genomic methylation patterns have their origin many years in the past, at a time when the structure of the mammalian genome was only dimly perce...

    Authors: John R. Edwards, Olya Yarychkivska, Mathieu Boulard and Timothy H. Bestor

    Citation: Epigenetics & Chromatin 2017 10:23

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  18. Content type: Research

    The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypot...

    Authors: Lisa M. McEwen, Alexander M. Morin, Rachel D. Edgar, Julia L. MacIsaac, Meaghan J. Jones, William H. Dow, Luis Rosero-Bixby, Michael S. Kobor and David H. Rehkopf

    Citation: Epigenetics & Chromatin 2017 10:21

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  19. Content type: Research

    The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping ...

    Authors: Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark and Clare Stirzaker

    Citation: Epigenetics & Chromatin 2017 10:16

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  20. Content type: Research

    Exposure to environmental stressors during development may lead to latent and transgenerational adverse health effects. To understand the role of DNA methylation in these effects, we used zebrafish as a verteb...

    Authors: Jorke H. Kamstra, Liana Bastos Sales, Peter Aleström and Juliette Legler

    Citation: Epigenetics & Chromatin 2017 10:20

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  21. Content type: Research

    Posttranslational modifications of core histones are correlated with changes in transcriptional status, chromatin fiber folding, and nucleosome dynamics. However, within the centromere-specific histone H3 vari...

    Authors: Minh Bui, Mary Pitman, Arthur Nuccio, Serene Roque, Paul Gregory Donlin-Asp, Aleksandra Nita-Lazar, Garegin A. Papoian and Yamini Dalal

    Citation: Epigenetics & Chromatin 2017 10:17

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  22. Content type: Research

    Despite recent studies on the role of ubiquitin-related SUMO modifier in cell fate decisions, our understanding on precise molecular mechanisms of these processes is limited. Previously, we established that th...

    Authors: Arnab Nayak, Anja Reck, Christian Morsczeck and Stefan Müller

    Citation: Epigenetics & Chromatin 2017 10:15

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  23. Content type: Research

    The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mecha...

    Authors: Johannes Petrus Maree, Megan Lindsay Povelones, David Johannes Clark, Gloria Rudenko and Hugh-George Patterton

    Citation: Epigenetics & Chromatin 2017 10:14

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  24. Content type: Research

    Global epigenetic reprogramming is considered to be essential during embryo development to establish totipotency. In the classic model first described in the mouse, the genome-wide DNA demethylation is asymmet...

    Authors: Sonia Heras, Katrien Smits, Catharina De Schauwer and Ann Van Soom

    Citation: Epigenetics & Chromatin 2017 10:13

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  25. Content type: Research

    Histone posttranslational modifications (PTMs) function to regulate chromatin structure and function in part through the recruitment of effector proteins that harbor specialized “reader” domains. Despite effor...

    Authors: Erin K. Shanle, Stephen A. Shinsky, Joseph B. Bridgers, Narkhyun Bae, Cari Sagum, Krzysztof Krajewski, Scott B. Rothbart, Mark T. Bedford and Brian D. Strahl

    Citation: Epigenetics & Chromatin 2017 10:12

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  26. Content type: Research

    In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-bi...

    Authors: Aristea Magaraki, Godfried van der Heijden, Esther Sleddens-Linkels, Leonidas Magarakis, Wiggert A. van Cappellen, Antoine H. F. M. Peters, Joost Gribnau, Willy M. Baarends and Maureen Eijpe

    Citation: Epigenetics & Chromatin 2017 10:11

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  27. Content type: Research

    Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene ATRX. The mechanisms involved in the ATR-X pathology are not completely understood, but may i...

    Authors: Laila C. Schenkel, Kristin D. Kernohan, Arran McBride, Ditta Reina, Amanda Hodge, Peter J. Ainsworth, David I. Rodenhiser, Guillaume Pare, Nathalie G. Bérubé, Cindy Skinner, Kym M. Boycott, Charles Schwartz and Bekim Sadikovic

    Citation: Epigenetics & Chromatin 2017 10:10

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  28. Content type: Methodology

    Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The ...

    Authors: Stephanie B. Hatch, Clarence Yapp, Raquel C. Montenegro, Pavel Savitsky, Vicki Gamble, Anthony Tumber, Gian Filippo Ruda, Vassilios Bavetsias, Oleg Fedorov, Butrus Atrash, Florence Raynaud, Rachel Lanigan, LeAnne Carmichael, Kathy Tomlin, Rosemary Burke, Susan M. Westaway…

    Citation: Epigenetics & Chromatin 2017 10:9

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  29. Content type: Research

    Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated h...

    Authors: Benjamin L. Kidder, Gangqing Hu, Kairong Cui and Keji Zhao

    Citation: Epigenetics & Chromatin 2017 10:8

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  30. Content type: Research

    Defining how epigenetic information is established in the germline during fetal development is key to understanding how epigenetic information is inherited and impacts on evolution and human health and disease.

    Authors: Lexie Prokopuk, Jessica M. Stringer, Kirsten Hogg, Kirstin D. Elgass and Patrick S. Western

    Citation: Epigenetics & Chromatin 2017 10:7

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  31. Content type: Research

    Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous...

    Authors: Natallia Kalinava, Julie Zhouli Ni, Kimberly Peterman, Esteban Chen and Sam Guoping Gu

    Citation: Epigenetics & Chromatin 2017 10:6

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  32. Content type: Research

    In the mammalian zygote, epigenetic reprogramming is a tightly controlled process of coordinated alterations of histone and DNA modifications. The parental genomes of the zygote show distinct patterns of hist...

    Authors: Jie Lan, Konstantin Lepikhov, Pascal Giehr and Joern Walter

    Citation: Epigenetics & Chromatin 2017 10:5

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  33. Content type: Research

    Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of...

    Authors: Zac Chatterton, Brigham J. Hartley, Man-Ho Seok, Natalia Mendelev, Sean Chen, Maria Milekic, Gorazd Rosoklija, Aleksandar Stankov, Iskra Trencevsja-Ivanovska, Kristen Brennand, Yongchao Ge, Andrew J. Dwork and Fatemeh Haghighi

    Citation: Epigenetics & Chromatin 2017 10:4

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  34. Content type: Research

    In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increa...

    Authors: Pavla Navratilova, Gemma Barbara Danks, Abby Long, Stephen Butcher, John Robert Manak and Eric M. Thompson

    Citation: Epigenetics & Chromatin 2017 10:3

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  35. Content type: Methodology

    Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from pr...

    Authors: Sara El Kennani, Annie Adrait, Alexey K. Shaytan, Saadi Khochbin, Christophe Bruley, Anna R. Panchenko, David Landsman, Delphine Pflieger and Jérôme Govin

    Citation: Epigenetics & Chromatin 2017 10:2

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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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