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Epigenomics

Guest Editor: Alexander Meissner

In this issue of Genome Biology, we present a special collection of Research, Review, Opinion, Research Highlight and Editorial articles focusing on epigenomics. The issue provides a variety of new insights into the biology of DNA methylation, histone modifications and chromatin organization, and includes perspectives on epigenomics past, present and future from leaders in the field.

  1. Content type: Opinion

    Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3' UTR. We present a perspective on current work and new single-...

    Authors: Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D Vilfan, Samie Jaffrey and Christopher E Mason

    Citation: Genome Biology 2012 13:175

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  2. Content type: Meeting report

    A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.

    Authors: Evangelos Bellos, Lachlan JM Coin and Myrsini Kaforou

    Citation: Genome Biology 2012 13:321

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  3. Content type: Review

    Somatic cell reprogramming to induced pluripotent stem (iPS) cells by defined factors is a form of engineered reverse development carried out in vitro. Recent investigation has begun to elucidate the molecular me...

    Authors: Ryan Schmidt and Kathrin Plath

    Citation: Genome Biology 2012 13:251

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  4. Content type: Review

    Epigenomics, the determination of epigenetic landscapes on a genome-wide scale, has progressed at an astounding rate over the past decade. Recent technological developments have enabled base-pair resolution of...

    Authors: Gabriel E Zentner and Steven Henikoff

    Citation: Genome Biology 2012 13:250

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  5. Content type: Research

    DNA methylation plays an essential role in regulating gene expression under a variety of conditions and it has therefore been hypothesized to underlie the transitions between life cycle stages in parasitic nem...

    Authors: Fei Gao, Xiaolei Liu, Xiu-Ping Wu, Xue-Lin Wang, Desheng Gong, Hanlin Lu, Yudong Xia, Yanxia Song, Junwen Wang, Jing Du, Siyang Liu, Xu Han, Yizhi Tang, Huanming Yang, Qi Jin, Xiuqing Zhang…

    Citation: Genome Biology 2012 13:R100

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  6. Content type: Review

    Heritable phenotypic differences caused by epigenetic modifications, rather than DNA sequence mutations, pose a challenge to our understanding of natural variation. Here, we review what is known about plant ep...

    Authors: Detlef Weigel and Vincent Colot

    Citation: Genome Biology 2012 13:249

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  7. Content type: Method

    Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by a variety of chromati...

    Authors: Zhixin Tian, Nikola Tolić, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith and Ljiljana Paša-Tolić

    Citation: Genome Biology 2012 13:R86

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  8. Content type: Research

    The epigenomes of healthy and diseased human hearts were recently examined by genome-wide DNA methylation profiling. Repetitive elements, heavily methylated in post-natal tissue, have variable methylation prof...

    Authors: Syed Haider, Lina Cordeddu, Emma Robinson, Mehregan Movassagh, Lee Siggens, Ana Vujic, Mun-Kit Choy, Martin Goddard, Pietro Lio and Roger Foo

    Citation: Genome Biology 2012 13:R90

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  9. Content type: Research

    Aberrant CpG island promoter DNA hypermethylation is frequently observed in cancer and is believed to contribute to tumor progression by silencing the expression of tumor suppressor genes. Previously, we obser...

    Authors: Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye and Richard R Meehan

    Citation: Genome Biology 2012 13:R84

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  10. Content type: Method

    DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conv...

    Authors: Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei and Wing-Kin Sung

    Citation: Genome Biology 2012 13:R82

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  11. Content type: Research

    Several recent studies reported aging effects on DNA methylation levels of individual CpG dinucleotides. But it is not yet known whether aging-related consensus modules, in the form of clusters of correlated C...

    Authors: Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg and Roel A Ophoff

    Citation: Genome Biology 2012 13:R97

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  12. Content type: Research

    Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to ...

    Authors: Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H Schulte, Rosa Noguera, Raymond L Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman and Jo Vandesompele

    Citation: Genome Biology 2012 13:R95

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  13. Content type: Research

    Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dyna...

    Authors: John P Thomson, Harri Lempiäinen, Jamie A Hackett, Colm E Nestor, Arne Müller, Federico Bolognani, Edward J Oakeley, Dirk Schübeler, Rémi Terranova, Diana Reinhardt, Jonathan G Moggs and Richard R Meehan

    Citation: Genome Biology 2012 13:R93

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  14. Content type: Research

    Transposable elements are often the targets of repressive epigenetic modifications such as DNA methylation that, in theory, have the potential to spread toward nearby genes and induce epigenetic silencing. To ...

    Authors: Rita Rebollo, Katharine Miceli-Royer, Ying Zhang, Sharareh Farivar, Liane Gagnier and Dixie L Mager

    Citation: Genome Biology 2012 13:R89

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  15. Content type: Software

    DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation,cellular specification and cancer development. Here, we describe an R package, methylKit, thatrapidly analyzes g...

    Authors: Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick and Christopher E Mason

    Citation: Genome Biology 2012 13:R87

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  16. Content type: Research

    The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure.

    Authors: Manching Ku, Jacob D Jaffe, Richard P Koche, Esther Rheinbay, Mitsuhiro Endoh, Haruhiko Koseki, Steven A Carr and Bradley E Bernstein

    Citation: Genome Biology 2012 13:R85

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  17. Content type: Software

    Epigenome mapping consortia are generating resources of tremendous value for studying epigenetic regulation. To maximize their utility and impact, new tools are needed that facilitate interactive analysis of e...

    Authors: Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer and Christoph Bock

    Citation: Genome Biology 2012 13:R96

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  18. Content type: Research

    Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, in...

    Authors: Lidija Berke, Gabino F Sanchez-Perez and Berend Snel

    Citation: Genome Biology 2012 13:R94

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  19. Content type: Method

    Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation ...

    Authors: Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith, Michael Ziller, Jennifer L Fostel, Laurie Holmes, Jim Meldrim, Fontina Kelley, Andreas Gnirke and Alexander Meissner

    Citation: Genome Biology 2012 13:R92

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  20. Content type: Research

    Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prosta...

    Authors: Alok K Tewari, Galip Gürkan Yardimci, Yoichiro Shibata, Nathan C Sheffield, Lingyun Song, Barry S Taylor, Stoyan G Georgiev, Gerhard A Coetzee, Uwe Ohler, Terrence S Furey, Gregory E Crawford and Phillip G Febbo

    Citation: Genome Biology 2012 13:R88

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