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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. Opinion

    The birth of the Epitranscriptome: deciphering the function of RNA modifications

    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-...

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

    Genome Biology 2012 13:175

    Published on: 31 October 2012

  2. Meeting report

    Bioinformatics: living on the edge

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

    Evangelos Bellos, Lachlan JM Coin and Myrsini Kaforou

    Genome Biology 2012 13:321

    Published on: 26 October 2012

  3. Research highlight

    Balance of DNA methylation and demethylation in cancer development

    Genome-wide 5-hydroxymethylome analysis of a rodent hepatocarcinogen model reveals that 5-hydroxymethylcytosine-dependent active DNA demethylation may be functionally important in the early stages of carcinoge...

    Chun-Xiao Song and Chuan He

    Genome Biology 2012 13:173

    Published on: 23 October 2012

  4. Review

    Surveying the epigenomic landscape, one base at a time

    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...

    Gabriel E Zentner and Steven Henikoff

    Genome Biology 2012 13:250

    Published on: 22 October 2012

  5. Opinion

    DNA methylation studies using twins: what are they telling us?

    Recent studies have identified both heritable DNA methylation effects and differential methylation in disease-discordant identical twins. Larger sample sizes, replication, genetic-epigenetic analyses and longi...

    Jordana T Bell and Tim D Spector

    Genome Biology 2012 13:172

    Published on: 18 October 2012

  6. Research

    Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

    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...

    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…

    Genome Biology 2012 13:R100

    Published on: 17 October 2012

  7. Review

    Epialleles in plant evolution

    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...

    Detlef Weigel and Vincent Colot

    Genome Biology 2012 13:249

    Published on: 11 October 2012

  8. Method

    Enhanced top-down characterization of histone post-translational modifications

    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...

    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

    Genome Biology 2012 13:R86

    Published on: 3 October 2012

  9. Software

    methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

    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...

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

    Genome Biology 2012 13:R87

    Published on: 3 October 2012

  10. Research

    The landscape of DNA repeat elements in human heart failure

    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...

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

    Genome Biology 2012 13:R90

    Published on: 3 October 2012

  11. Research

    Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

    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...

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

    Genome Biology 2012 13:R84

    Published on: 3 October 2012

  12. Method

    BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

    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...

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

    Genome Biology 2012 13:R82

    Published on: 3 October 2012

  13. Research

    Aging effects on DNA methylation modules in human brain and blood tissue

    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...

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

    Genome Biology 2012 13:R97

    Published on: 3 October 2012

  14. Research

    Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

    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 ...

    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

    Genome Biology 2012 13:R95

    Published on: 3 October 2012

  15. Research

    Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

    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...

    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

    Genome Biology 2012 13:R93

    Published on: 3 October 2012

  16. Research

    Epigenetic interplay between mouse endogenous retroviruses and host genes

    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 ...

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

    Genome Biology 2012 13:R89

    Published on: 3 October 2012

  17. Research

    H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

    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.

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

    Genome Biology 2012 13:R85

    Published on: 3 October 2012

  18. Software

    EpiExplorer: live exploration and global analysis of large epigenomic datasets

    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...

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

    Genome Biology 2012 13:R96

    Published on: 3 October 2012

  19. Method

    Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

    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 ...

    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

    Genome Biology 2012 13:R92

    Published on: 3 October 2012

  20. Research

    Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

    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...

    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

    Genome Biology 2012 13:R88

    Published on: 3 October 2012