epigenetics

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2. Bradley E Bernstein, Chih Long Liu, Emily L Humphrey, Ethan O Perlstein and Stuart L Schreiber (2004): Global nucleosome occupancy in yeast. - Genome.Biol., 5:R62.
3. Julius Brennecke, Colin D. Malone, Alexei A. Aravin, Ravi Sachidanandam, Alexander Stark and Gregory J. Hannon (2008): An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. - Science, 322:1387--1392.
4. Simon W.-L Chan, Xiaoyu Zhang, Yana V. Bernatavichute and Steven E. Jacobsen (2006): Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats. - PLoS Biol, 4:e363.
5. Z Jeffrey Chen and Lu Tian (2007): Roles of dynamic and reversible histone acetylation in plant development and polyploidy. - Biochim Biophys Acta, 1769(5-6):295-307.
6. Shawn J. Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D. Haudenschild, Sriharsa Pradhan, Stanley F. Nelson, Matteo Pellegrini and Steven E. Jacobsen (2008): Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. - Nature.
7. Roel van Driel, Paul F Fransz and Pernette J Verschure (2003): The eukaryotic genome: a system regulated at different hierarchical levels. - Journal of Cell Science, 116:4067–4075.
8. Sevinc Ercan and Jason D Lieb (2006): New evidence that DNA encodes its packaging. - Nat Genet, 38(10):1104-5.
9. Klavs R Hansen, Gavin Burns, Juan Mata, Thomas A Volpe, Robert A Martienssen, Jurg Bahler and Genevieve Thon (2005): Global Effects on Gene Expression in Fission Yeast by Silencing and RNA Interference Machineries. - Molecular and Cellular Biology, 25:590–601.
10. Ian R. Henderson, Xiaoyu Zhang, Cheng Lu, Lianna Johnson, Blake C. Meyers, Pamela J. Green and Steven E. Jacobsen (2006): Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. - Nat Genet, 38:721--725.
11. Ian R. Henderson and Steven E. Jacobsen (2007): Epigenetic inheritance in plants. - Nature, 447:418--424.
12. Ilya P Ioshikhes, Istvan Albert, Sara J Zanton and B Franklin Pugh (2006): Nucleosome positions predicted through comparative genomics. - Nat Genet, 38(10):1210-5.
13. R A Irizarry, H Wu and A P Feinberg (2009): A species-generalized probabilistic model-based definition of CpG islands. - Mamm Genome.
14. Dean A Jackson (2005): The amazing complexity of transcription factories. - Briefings in Functional Genomics and Proteomics, 4:143–157.
15. Steven E. Jacobsen and Elliot M. Meyerowitz (1997): Hypermethylated SUPERMAN Epigenetic Alleles in Arabidopsis. - Science, 277:1100--1103.
16. Frank Johannes, Vincent Colot and Ritsert C. Jansen (2008): Epigenome dynamics: a quantitative genetics perspective. - Nat Rev Genet, 9:883--890.
17. Ilana Keshet, Yeshayahu Schlesinger, Shlomit Farkash, Eyal Rand, Merav Hecht, Eran Segal, Eli Pikarski, Richard A Young, Alain Niveleau, Howard Cedar and Itamar Simon (2006): Evidence for an instructive mechanism of de novo methylation in cancer cells. - Nat.Genet., 38:149–153.
18. Ryan Lister, Mattia Pelizzola, Robert H. Dowen, R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren and Joseph R. Ecker (2009): Human DNA methylomes at base resolution show widespread epigenomic differences. - Nature, advance online publication.
19. Ryan Lister and Joseph R. Ecker (2009): Finding the fifth base: Genome-wide sequencing of cytosine methylation. - Genome Research, 19:959--966.
20. Chih Long Liu, Tommy Kaplan, Minkyu Kim, Stephen Buratowski, Stuart L Schreiber, Nir Friedman and Oliver J Rando (2005): Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae. - PLoS Biology, 3 EP -.
21. Olivier Mathieu, Jon Reinders, Marian Caikovski, Chotika Smathajitt and Jerzy Paszkowski (2007): Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. - Cell, 130(5):851-62.
22. Taisuke Nishimura and Jerzy Paszkowski (2007): Epigenetic transitions in plants not associated with changes in DNA or histone modification. - Biochim Biophys Acta, 1769(5-6):393-8.
23. Jennifer Pfluger and Doris Wagner (2007): Histone modifications and dynamic regulation of genome accessibility in plants. - Curr Opin Plant Biol, 10(6):645-52.
24. Dmitry K Pokholok, Christopher T Harbison, Stuart Levine, Megan Cole, Nancy M Hannett, Tong Ihn Lee, George W Bell, Kimberly Walker, P Alex Rolfe, Elizabeth Herbolsheimer, Julia Zeitlinger, Fran Lewitter, David K Gifford and Richard A Young (2005): Genome-wide map of nucleosome acetylation and methylation in yeast. - Cell., 122:517–27.
25. Katherine S Pollard, David Serre, Xu Wang, Heng Tao, Elin Grundberg, Thomas J Hudson, Andrew G Clark and Kelly Frazer (2008): A genome-wide approach to identifying novel-imprinted genes. - Hum Genet, 122(6):625-34.
26. Nevin Sabet, Sam Volo, Cailin Yu, James P Madigan and Randall H Morse (2004): Genome-wide analysis of the relationship between transcriptional regulationby Rpd3p and the histone H3 and H4 amino termini in budding yeast. - Mol.Cell.Biol., 24:8823–33.
27. Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, AnnChristine Thastrom, Yair Field, Irene K Moore, Ji-Ping Z Wang and Jonathan Widom (2006): A genomic code for nucleosome positioning. - Nature, 442(7104):772-8.
28. Shunsuke Suzuki, Ryuichi Ono, Takanori Narita, Andrew J. Pask, Geoffrey Shaw, Changshan Wang, Takashi Kohda, Amber E. Alsop, Jennifer A. Marshall Graves, Yuji Kohara, Fumitoshi Ishino, Marilyn B. Renfree and Tomoko Kaneko-Ishino (2007): Retrotransposon silencing by dna methylation can drive mammalian genomic imprinting. - PLoS Genetics, 3:e55 EP -.
29. Francisco Ubeda and Jon F Wilkins (2008): Imprinted genes and human disease: an evolutionary perspective. - Adv Exp Med Biol, 626:101-15.
30. Matthew W. Vaughn, Miloš Tanurdžić, Zachary Lippman, Hongmei Jiang, Robert Carrasquillo, Pablo D. Rabinowicz, Neilay Dedhia, W. Richard McCombie, Nicolas Agier, Agnès Bulski, Vincent Colot, R. W. Doerge and Robert A. Martienssen (2007): Epigenetic natural variation in arabidopsis thaliana. - PLoS Biology, 5:e174 EP -.
31. Michael Weber, Ines Hellmann, Michael B Stadler, Liliana Ramos, Svante Paabo, Michael Rebhan and Dirk Schubeler (2007): Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. - Nat Genet, 39(4):457-66.
32. Hye Ryun Woo, Travis A. Dittmer and Eric J. Richards (2008): Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis. - PLoS Genetics, 4:e1000156.
33. Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W.-L. Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve E. Jacobsen and Joseph\^A?R. Ecker (2006): Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. - Cell, 126:1189--1201.
34. Xiaoyu Zhang, Oliver Clarenz, Shawn Cokus, Yana V. Bernatavichute, Matteo Pellegrini, Justin Goodrich and Steven E. Jacobsen (2007): Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis. - PLoS Biol, 5:e129.
35. Xu Zhang, Shinhan Shiu, Andrew Cal and Justin O. Borevitz (2008): Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays. - PLoS Genet, 4:e1000032.
36. Xiaoyu Zhang (2008): The Epigenetic Landscape of Plants. - Science, 320:489--492.
37. Xiaoyu Zhang, Yana Bernatavichute, Shawn Cokus, Matteo Pellegrini and Steven Jacobsen (2009): Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. - Genome Biology, 10:R62.
38. Daniel Zilberman and Steven Henikoff (2005): Epigenetic inheritance in Arabidopsis: selective silence. - Current Opinion in Genetics \& Development, 15:557--562.
39. Elzo de Wit, Frauke Greil and Bas van Steensel (2007): High-resolution mapping reveals links of hp1 with active and inactive chromatin components. - PLoS Genetics, 3:e38 EP -.