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Table of Contents: Epigenetics 2010

COVER

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Epigenetics is the study of inherited changes in phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence. This image represents the structure of a nucleosome. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones.

This collection brings together twenty Research Articles published in five PLoS journals in the area of epigenetics during 2010, along with a Research in Translation article and two Primers. They reflect a range of model systems and organisms, and variously offer phenotypic, mechanistic, and chromatin-based insights.

Produced with support from New England Biolabs. The PLoS journal editors have sole responsibility for the content of this collection.

Download: Complete Collection (62 MB PDF).

Primers

Centromeres Convert but Don't Cross

Paul B. Talbert, Steven Henikoff

Research in Translation

Research Articles

Spatial Epigenetic Control of Mono- and Bistable Gene Expression

János Z. Kelemen, Prasuna Ratna, Simone Scherrer, Attila Becskei

Widespread Gene Conversion in Centromere Cores

Jinghua Shi, Sarah E. Wolf, John M. Burke, Gernot G. Presting, Jeffrey Ross-Ibarra, R. Kelly Dawe

Expression in Aneuploid Drosophila S2 Cells

Yu Zhang, John H. Malone, Sara K. Powell, Vipul Periwal, Eric Spana, David M. MacAlpine, Brian Oliver

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

Sylvain Maenner, Magali Blaud, Laetitia Fouillen, Anne Savoye, Virginie Marchand, Agnès Dubois, Sarah Sanglier-Cianférani, Alain Van Dorsselaer, Philippe Clerc, Philip Avner, Athanase Visvikis, Christiane Branlant

Poised Transcription Factories Prime Silent uPA Gene Prior to Activation

Carmelo Ferrai, Sheila Q. Xie, Paolo Luraghi, Davide Munari, Francisco Ramirez, Miguel R. Branco, Ana Pombo, Massimo P. Crippa

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human

James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette

Altering a Histone H3K4 Methylation Pathway in Glomerular Podocytes Promotes a Chronic Disease Phenotype

Gaelle M. Lefevre, Sanjeevkumar R. Patel, Doyeob Kim, Lino Tessarollo, Gregory R. Dressler

The IG-DMR and the MEG3-DMR at Human Chromosome 14q32.2: Hierarchical Interaction and Distinct Functional Properties as Imprinting Control Centers

Masayo Kagami, Maureen J. O'Sullivan, Andrew J. Green, Yoshiyuki Watabe, Osamu Arisaka, Nobuhide Masawa, Kentarou Matsuoka, Maki Fukami, Keiko Matsubara, Fumiko Kato, Anne C. Ferguson-Smith, Tsutomu Ogata

siRNA–Mediated Methylation of Arabidopsis Telomeres

Jan Vrbsky, Svetlana Akimcheva, J. Matthew Watson, Thomas L. Turner, Lucia Daxinger, Boris Vyskot, Werner Aufsatz, Karel Riha

Initial Genomics of the Human Nucleolus

Attila Németh, Ana Conesa, Javier Santoyo-Lopez, Ignacio Medina, David Montaner, Bálint Péterfia, Irina Solovei, Thomas Cremer, Joaquin Dopazo, Gernot Längst

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome

Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar

Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model

Nina Kaminen-Ahola, Arttu Ahola, Murat Maga, Kylie-Ann Mallitt, Paul Fahey, Timothy C. Cox, Emma Whitelaw, Suyinn Chong

Epigenetic Analysis of KSHV Latent and Lytic Genomes

Zsolt Toth, Dennis T. Maglinte, Sun Hwa Lee, Hye-Ra Lee, Lai-Yee Wong, Kevin F. Brulois, Stacy Lee, Jonathan D. Buckley, Peter W. Laird, Victor E. Marquez, Jae U. Jung

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

Catarina Fonseca Lira-Medeiros, Christian Parisod, Ricardo Avancini Fernandes, Camila Souza Mata, Monica Aires Cardoso, Paulo Cavalcanti Gomes Ferreira

Hepatocellular Carcinoma Displays Distinct DNA Methylation Signatures with Potential as Clinical Predictors

Hector Hernandez-Vargas, Marie-Pierre Lambert, Florence Le Calvez-Kelm, Géraldine Gouysse, Sandrine McKay-Chopin, Sean V. Tavtigian, Jean-Yves Scoazec, Zdenko Herceg

Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding

Christina A. Bormann Chung, Victoria L. Boyd, Kevin J. McKernan, Yutao Fu, Cinna Monighetti, Heather E. Peckham, Melissa Barker

Role for DNA Methylation in the Regulation of miR-200c and miR-141 Expression in Normal and Cancer Cells

Lukas Vrba, Taylor J. Jensen, James C. Garbe, Ronald L. Heimark, Anne E. Cress, Sally Dickinson, Martha R. Stampfer, Bernard W. Futscher

Differential DNA Methylation Correlates with Differential Expression of Angiogenic Factors in Human Heart Failure

Mehregan Movassagh, Mun-Kit Choy, Martin Goddard, Martin R. Bennett, Thomas A. Down, Roger S.-Y. Foo