The Mammalian Epigenome

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216

Translating the Histone Code

Jenuwein, T., & Allis, C. D. (2001) · Science · doi:10.1126/science.1063127 · Cited by 9,756

Genome sequencing in microfabricated high-density picolitre reactors

Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693

DNA methylation patterns and epigenetic memory

Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124

DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development

Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143

The fundamental role of epigenetic events in cancer

Jones, P. A., & Baylin, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg816 · Cited by 5,648

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361

Targeted mutation of the DNA methyltransferase gene results in embryonic lethality

Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984

CpG Islands in vertebrate genomes

Gardiner‐Garden, M., & Frommer, M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90689-9 · Cited by 3,417

Epigenetic Reprogramming in Mammalian Development

Reik, W., Dean, W., & Walter, J. (2001) · Science · doi:10.1126/science.1063443 · Cited by 3,078

Polycomb complexes repress developmental regulators in murine embryonic stem cells

Boyer, L. A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L. A., Lee, T. I., Levine, S. S., Wernig, M., Tajonar, A., Ray, M. K., et al. (2006) · Nature · doi:10.1038/nature04733 · Cited by 2,568

Genome sequence, comparative analysis and haplotype structure of the domestic dog

members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568

Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296

The Polycomb group protein EZH2 directly controls DNA methylation

Viré, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., Van Eynde, A., Bernard, D., Vanderwinden, J.-M., et al. (2006) · Nature · doi:10.1038/nature04431 · Cited by 2,204

EUKARYOTIC CYTOSINE METHYLTRANSFERASES

Goll, M. G., & Bestor, T. H. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.010904.153721 · Cited by 2,162

CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer

Weisenberger, D. J., Siegmund, K. D., Campan, M., Young, J. P., Long, T. I., Faasse, M. A., Kang, G. H., Widschwendter, M., Weener, D., Buchanan, D. D., et al. (2006) · Nature Genetics · doi:10.1038/ng1834 · Cited by 1,990

The epigenetic progenitor origin of human cancer

Feinberg, A. P., OHLSSON, R. I., & Henikoff, S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1748 · Cited by 1,885

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S. J., Chan, S. W.-L., Chen, H., Henderson, I. R., Shinn, P., Pellegrini, M. A., Jacobsen, S. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.08.003 · Cited by 1,850

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

Weber, M., Davies, J. J., Wittig, D., Oakeley, E. J., Haase, M., Lam, W. L., & Schübeler, D. (2005) · Nature Genetics · doi:10.1038/ng1598 · Cited by 1,785

Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse

Bernstein, B., Kamal, M., Lindblad‐Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., Gingeras, T., et al. (2005) · Cell · doi:10.1016/j.cell.2005.01.001 · Cited by 1,567

CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus

Hark, A. T., Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., & Tilghman, S. M. (2000) · Nature · doi:10.1038/35013106 · Cited by 1,547

Comprehensive analysis of CpG islands in human chromosomes 21 and 22

Takai, D., & Jones, P. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052410099 · Cited by 1,546

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Pokholok, D., Harbison, C. T., Levine, S. S., Cole, M. F., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, A., Herbolsheimer, E., et al. (2005) · Cell · doi:10.1016/j.cell.2005.06.026 · Cited by 1,477

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402

DNA methylation profiling of human chromosomes 6, 20 and 22

Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V. K., Attwood, J., Burger, M., Burton, J. H., Cox, T. V., Davies, R., Down, T. A., et al. (2006) · Nature Genetics · doi:10.1038/ng1909 · Cited by 1,378

Chromatin signatures of pluripotent cell lines

Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jørgensen, H. F., John, R. M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M., et al. (2006) · Nature Cell Biology · doi:10.1038/ncb1403 · Cited by 1,357

Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitionsPreprint

Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., & Helin, K. (2006) · Genes & Development · doi:10.1101/gad.381706 · Cited by 1,286

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

Meissner, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki901 · Cited by 1,261

Dynamic Reprogramming of DNA Methylation in the Early Mouse Embryo

Santos, F., Hendrich, B., Reik, W., & Dean, W. (2002) · Developmental Biology · doi:10.1006/dbio.2001.0501 · Cited by 1,213

Epigenetic Regulation of Cellular Memory by the Polycomb and Trithorax Group Proteins

Ringrose, L., & Paro, R. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.091907 · Cited by 1,093

Role of transposable elements in heterochromatin and epigenetic control

Lippman, Z., Gendrel, A.-V., Black, M., Vaughn, M. W., Dedhia, N., Richard McCombie, W., Lavine, K., Mittal, V., May, B., Kasschau, K. D., et al. (2004) · Nature · doi:10.1038/nature02651 · Cited by 1,065

Heterochromatin and Epigenetic Control of Gene Expression

Grewal, S. I. S., & Moazed, D. (2003) · Science · doi:10.1126/science.1086887 · Cited by 1,065

Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomainsPreprint

Fischle, W., Wang, Y., Jacobs, S. A., Kim, Y., Allis, C. D., & Khorasanizadeh, S. (2003) · Genes & Development · doi:10.1101/gad.1110503 · Cited by 1,021

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a

Ramsahoye, B. H., Biniszkiewicz, D., Lyko, F., Clark, V. H., Bird, A. P., & Jaenisch, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.10.5237 · Cited by 1,012

Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells

Meshorer, E., Yellajoshyula, D., George, E. M., Scambler, P. J., Brown, D. T., & Misteli, T. (2006) · Developmental Cell · doi:10.1016/j.devcel.2005.10.017 · Cited by 1,008

Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970

A high-resolution map of active promoters in the human genome

Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T., Wu, Y., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 954

A physical map of the human genome

McPherson, J. D., Marra, M. A., Hillier, L., Waterston, R., Chinwalla, A., Wallis, J. W., Sekhon, M., Wylie, K. M., Mardis, E. R., Wilson, R. K., et al. (2001) · Nature · doi:10.1038/35057157 · Cited by 925

Gardening the genome: DNA methylation in Arabidopsis thaliana

Chan, S. W.-L., Henderson, I. R., & Jacobsen, S. E. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1601 · Cited by 903

The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryotePreprint

Schübeler, D., MacAlpine, D. M., Scalzo, D., Wirbelauer, C., Kooperberg, C. L., van Leeuwen, F., Gottschling, D. E., O’Neill, L. P., Turner, B. M., Delrow, J. J., et al. (2004) · Genes & Development · doi:10.1101/gad.1198204 · Cited by 820

The key to development: interpreting the histone code?

Margueron, R., Trojer, P., & Reinberg, D. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.01.005 · Cited by 770

Stem Cells and Cancer

Valk-Lingbeek, M. E., Bruggeman, S. W. M., & van Lohuizen, M. (2004) · Cell · doi:10.1016/j.cell.2004.08.005 · Cited by 743

Histone H3 Lysine 9 Methylation and HP1γ Are Associated with Transcription Elongation through Mammalian Chromatin

Vakoc, C. R., Mandat, S. A., Olenchock, B. A., & Blobel, G. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.06.011 · Cited by 734

The profile of repeat‐associated histone lysine methylation states in the mouse epigenome

Martens, J. H. A., O’Sullivan, R. J., Braunschweig, U., Opravil, S., Radolf, M., Steinlein, P., & Jenuwein, T. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600545 · Cited by 697

Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation

Jackson-Grusby, L., Beard, C., Possemato, R., Tudor, M., Fambrough, D., Csankovszki, G., Dausman, J., Lee, P., Wilson, C., Lander, E., et al. (2001) · Nature Genetics · doi:10.1038/83730 · Cited by 694

Interchromosomal Interactions and Olfactory Receptor Choice

Lomvardas, S., Barnea, G., Pisapia, D. J., Mendelsohn, M. M., Kirkland, J., & Axel, R. (2006) · Cell · doi:10.1016/j.cell.2006.06.035 · Cited by 641

Genome-wide analysis of Polycomb targets in Drosophila melanogaster

Schwartz, Y. B., Kahn, T. G., Nix, D. A., Li, X., Bourgon, R., Biggin, M. D., & Pirrotta, V. (2006) · Nature Genetics · doi:10.1038/ng1817 · Cited by 623

Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation

Pray-Grant, M. G., Daniel, J. A., Schieltz, D. M., Yates, J. R., & Grant, P. A. (2005) · Nature · doi:10.1038/nature03242 · Cited by 529

Genome-scale profiling of histone H3.3 replacement patterns

Mito, Y., Henikoff, J. G., & Henikoff, S. (2005) · Nature Genetics · doi:10.1038/ng1637 · Cited by 526

Distinct epigenetic changes in the stromal cells of breast cancers

Hu, M., Yao, J., Cai, L., Bachman, K., van den Brûle, F., Velculescu, V. E., & Polyák, K. (2005) · Nature Genetics · doi:10.1038/ng1596 · Cited by 520

Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae

Liu, C. L., Kaplan, T., Kim, M., Buratowski, S., Schreiber, S. L., Friedman, N., & Rando, O. J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030328 · Cited by 509

The genomic landscape of histone modifications in human T cells

Roh, T., Cuddapah, S., Cui, K., & Zhao, K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607617103 · Cited by 499

Evidence for an instructive mechanism of de novo methylation in cancer cells

Keshet, I., Schlesinger, Y., Farkash, S., Rand, E., Hecht, M., Segal, E., Pikarsky, E., Young, R. A., Niveleau, A., Cedar, H., et al. (2006) · Nature Genetics · doi:10.1038/ng1719 · Cited by 483

Active chromatin domains are defined by acetylation islands revealed by genome-wide mappingPreprint

Roh, T., Cuddapah, S., & Zhao, K. (2005) · Genes & Development · doi:10.1101/gad.1272505 · Cited by 469

Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process

Bruniquel, D., & Schwartz, R. H. (2003) · Nature Immunology · doi:10.1038/ni887 · Cited by 460

Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains

Sims, R. J., Chen, C.-F., Santos-Rosa, H., Kouzarides, T., Patel, S. S., & Reinberg, D. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.c500395200 · Cited by 423

Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band

Frigola, J., Song, J. Z., Stirzaker, C., Hinshelwood, R. A., Peinado, M. A., & Clark, S. J. (2006) · Nature Genetics · doi:10.1038/ng1781 · Cited by 417

Large-scale structure of genomic methylation patternsPreprint

Rollins, R. A., Haghighi, F. G., Edwards, J. R., Das, R., Zhang, M. Q., Ju, J., & Bestor, T. H. (2005) · Genome Research · doi:10.1101/gr.4362006 · Cited by 400

Comparative isoschizomer profiling of cytosine methylation: The HELP assayPreprint

Khulan, B., Thompson, R. F., Ye, K. Q., Fazzari, M. J., Suzuki, M., Stasiek, E., Figueroa, M. E., Glass, J. L., Chen, Q., Montagna, C., et al. (2006) · Genome Research · doi:10.1101/gr.5273806 · Cited by 400

Signaling Network Model of Chromatin

Schreiber, S. L., & Bernstein, B. (2002) · Cell · doi:10.1016/s0092-8674(02)01196-0 · Cited by 399

Epigenetic Control of Mouse Oct-4 Gene Expression in Embryonic Stem Cells and Trophoblast Stem Cells

Hattori, N., Nishino, K., Ko, Y., Hattori, N., Ohgane, J., Tanaka, S., & Shiota, K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309002200 · Cited by 397

Highly parallel genomic assays

Fan, J., Chee, M. S., & Gunderson, K. L. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1901 · Cited by 389

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

Tolhuis, B., Muijrers, I., de Wit, E., Teunissen, H., Talhout, W., van Steensel, B., & van Lohuizen, M. (2006) · Nature Genetics · doi:10.1038/ng1792 · Cited by 380

DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project

Rakyan, V. K., Hildmann, T., Novik, K. L., Lewin, J., Tost, J., Cox, A. V., Andrews, T. D., Howe, K., Otto, T., Olek, A., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020405 · Cited by 368

Global and Hox-specific roles for the MLL1 methyltransferase

Guenther, M. G., Jenner, R. G., Chevalier, B. S., Nakamura, T., Croce, C. M., Canaani, E., & Young, R. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503072102 · Cited by 360

Epigenomics: beyond CpG islands

Fazzari, M. J., & Greally, J. M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1349 · Cited by 360

CpG-binding Protein (CXXC Finger Protein 1) Is a Component of the Mammalian Set1 Histone H3-Lys4 Methyltransferase Complex, the Analogue of the Yeast Set1/COMPASS Complex

Lee, J., & Skalnik, D. G. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508312200 · Cited by 339

Chromatin profiling using targeted DNA adenine methyltransferase

van Steensel, B., Delrow, J. J., & Henikoff, S. (2001) · Nature Genetics · doi:10.1038/85871 · Cited by 331

Suz12 binds to silenced regions of the genome in a cell-type-specific mannerPreprint

Squazzo, S. L., O’Geen, H., Komashko, V., Krig, S. R., Jin, V. X., Jang, S.-W., Margueron, R., Reinberg, D., Green, R., & Farnham, P. (2006) · Genome Research · doi:10.1101/gr.5306606 · Cited by 324

Histone variants, nucleosome assembly and epigenetic inheritance

Henikoff, S., Furuyama, T., & Ahmad, K. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.05.004 · Cited by 310

Reprogramming Efficiency Following Somatic Cell Nuclear Transfer Is Influenced by the Differentiation and Methylation State of the Donor Nucleus

Blelloch, R. H., Wang, Z., Meissner, A., Pollard, S. M., Smith, A. G., & Jaenisch, R. (2006) · Stem Cells · doi:10.1634/stemcells.2006-0050 · Cited by 277

Human embryonic stem cells have a unique epigenetic signaturePreprint

Bibikova, M. V., Chudin, E., Wu, B., Zhou, L., Wickham‐Garcia, E., Liu, Y., Shin, S., Plaia, T. W., Auerbach, J. M., Arking, D. E., et al. (2006) · Genome Research · doi:10.1101/gr.5319906 · Cited by 272

Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations

O’Neill, L. P., VerMilyea, M. D., & Turner, B. M. (2006) · Nature Genetics · doi:10.1038/ng1820 · Cited by 265

Chromosomal Distribution of PcG Proteins during Drosophila Development

Negre, N. N., Hennetin, J., Sun, L. V., Lavrov, S. A., Bellis, M., White, K. P., & Cavalli, G. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040170 · Cited by 246

Immunoprecipitation of native chromatin: NChIP.

O'Neill, L., & Turner, B. (2003) · Methods · doi:10.1016/s1046-2023(03)00090-2 · Cited by 239

Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain

Forsberg, E. C., Downs, K. M., Christensen, H. M., Im, H., Nuzzi, P. A., & Bresnick, E. H. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.26.14494 · Cited by 226

The MT domain of the proto-oncoprotein MLL binds to CpG-containing DNA and discriminates against methylation

Birke, M. T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.4.958 · Cited by 222

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

Bock, C., Paulsen, M., Tierling, S., Mikeska, T., Lengauer, T., & Walter, J. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020026 · Cited by 222

Chromatin Insulator Elements Block the Silencing of a Target Gene by the Drosophila Polycomb Response Element (PRE) but Allow trans Interactions Between PREs on Different Chromosomes

Sigrist, C. J. A., & Pirrotta, V. (1997) · Genetics · doi:10.1093/genetics/147.1.209 · Cited by 210

A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted GenesPreprint

Strichman-Almashanu, L. Z., Lee, R. S., Onyango, P. O., Perlman, E. J., FLAM, F., Frieman, M. B., & Feinberg, A. P. (2002) · Genome Research · doi:10.1101/gr.224102 · Cited by 191

Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4

Morshead, K. B., Ciccone, D. N., Taverna, S. D., Allis, C. D., & Oettinger, M. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1932643100 · Cited by 190

Unfinished symphony

Qiu, J. X. J. (2006) · Nature · doi:10.1038/441143a · Cited by 179

Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis

Orlando, V., Jane, E. P., Chinwalla, V., Harte, P. J., & Paro, R. (1998) · The EMBO Journal · doi:10.1093/emboj/17.17.5141 · Cited by 179

A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21qPreprint

Yamada, Y. M. A., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Sakaki, Y., & Ito, T. (2004) · Genome Research · doi:10.1101/gr.1351604 · Cited by 171

A Blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop

Jones, P. A., & Martienssen, R. A. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-3865 · Cited by 169

DNA Methylation-mediated Control of Sry Gene Expression in Mouse Gonadal Development*

Nishino, K., Hattori, N., Tanaka, S., & Shiota, K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309513200 · Cited by 159

Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3

Ching, T.-T., Maunakea, A. K., Jun, P., Hong, C., Zardo, G., Pinkel, D., Albertson, D. G., Fridlyand, J., Mao, J.-H., Shchors, K., et al. (2005) · Nature Genetics · doi:10.1038/ng1563 · Cited by 159

Computational prediction of methylation status in human genomic sequences

Das, R., Dimitrova, N., Xuan, Z., Rollins, R. A., Haghighi, F., Edwards, J. R., Ju, J., Bestor, T. H., & Zhang, M. Q. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602949103 · Cited by 158

A Complex Chromatin Landscape Revealed by Patterns of Nuclease Sensitivity and Histone Modification within the Mouse β-Globin Locus

Bulger, M., Schübeler, D., Bender, M. A., Hamilton, J., Farrell, C. M., Hardison, R. C., & Groudine, M. T. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.15.5234-5244.2003 · Cited by 157

Formation of an Active Tissue-Specific Chromatin Domain Initiated by Epigenetic Marking at the Embryonic Stem Cell Stage

Szutorisz, H., Canzonetta, C., Georgiou, A., Chow, C.-M., Tora, L., & Dillon, N. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.5.1804-1820.2005 · Cited by 129

Transposon-free regions in mammalian genomesPreprint

Simons, C., Pheasant, M., Makunin, I. V., & Mattick, J. S. (2005) · Genome Research · doi:10.1101/gr.4624306 · Cited by 125

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes

Ng, P. C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl444 · Cited by 124

Allele-Specific Non-CpG Methylation of the Nf1 Gene during Early Mouse Development

Haines, T. R., Rodenhiser, D. I., & Ainsworth, P. (2001) · Developmental Biology · doi:10.1006/dbio.2001.0504 · Cited by 118

Polycomb Complexes and the Propagation of the Methylation Mark at the Drosophila Ubx Gene

Kahn, T. G., Schwartz, Y. B., Dellino, G. I., & Pirrotta, V. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m605430200 · Cited by 112

Genome-wide HP1 binding in Drosophila : Developmental plasticity and genomic targeting signalsPreprint

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Polycomb Group Repression Is Blocked by the Drosophila suppressor of Hairy-wing [su(Hw)] Insulator

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