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 · see citing works

Translating the Histone Code

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

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 · see citing works

DNA methylation patterns and epigenetic memory

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

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 3,462 · see citing works

Epigenetic Reprogramming in Mammalian Development

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

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 · see citing works

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 2,518 · see citing works

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 2,238 · see citing works

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 · see citing works

EUKARYOTIC CYTOSINE METHYLTRANSFERASES

Goll, M. G., & Bestor, T. H. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.010904.153721 · Cited by 2,066 · see citing works

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 · see citing works

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., Haase, M., Lam, W., & Schübeler, D. (2005) · Nature Genetics · doi:10.1038/ng1598 · Cited by 1,885 · see citing works

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 1,851 · see citing works

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 1,818 · see citing works

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 · see citing works

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 1,509 · see citing works

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 1,507 · see citing works

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 1,433 · see citing works

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 · see citing works

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 · see citing works

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 1,350 · see citing works

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 1,258 · see citing works

Role of transposable elements in heterochromatin and epigenetic control

Lippman, Z. B., Gendrel, A.-V., Black, M. A., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., et al. (2004) · Nature · doi:10.1038/nature02651 · Cited by 1,231 · see citing works

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 · see citing works

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

Meissner, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki901 · Cited by 1,203 · see citing works

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 1,077 · see citing works

Heterochromatin and Epigenetic Control of Gene Expression

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

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

Kim, T. H., Barrera, L., Zheng, M., Qu, C.-X., Singer, M. A., Richmond, T., Wu, Y. N., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 1,019 · see citing works

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

Ramsahoye, B., Biniszkiewicz, D., Lyko, F., Clark, V. H., Bird, A., & Jaenisch, R. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.97.10.5237 · Cited by 1,018 · see citing works

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 · see citing works

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 993 · see citing works

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 · see citing works

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 · see citing works

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 892 · see citing works

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 795 · see citing works

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 747 · see citing works

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 · see citing works

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 698 · see citing works

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 · see citing works

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 663 · see citing works

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 633 · see citing works

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 610 · see citing works

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 · see citing works

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 516 · see citing works

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 511 · see citing works

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 496 · see citing works

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 491 · see citing works

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 477 · see citing works

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 465 · see citing works

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 457 · see citing works

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 · see citing works

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 409 · see citing works

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 · see citing works

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 396 · see citing works

Signaling Network Model of Chromatin

Schreiber, S. L., & Bernstein, B. (2002) · Cell · doi:10.1016/s0092-8674(02)01196-0 · Cited by 395 · see citing works

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 389 · see citing works

Highly parallel genomic assays

Fan, J., Chee, M. S., & Gunderson, K. L. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1901 · Cited by 384 · see citing works

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 · see citing works

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 361 · see citing works

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 357 · see citing works

Epigenomics: beyond CpG islands

Fazzari, M. J., & Greally, J. M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1349 · Cited by 352 · see citing works

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 334 · see citing works

Chromatin profiling using targeted DNA adenine methyltransferase

van Steensel, B., Delrow, J. J., & Henikoff, S. (2001) · Nature Genetics · doi:10.1038/85871 · Cited by 328 · see citing works

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 310 · see citing works

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 299 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Immunoprecipitation of native chromatin: NChIP.

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

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 · see citing works

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 219 · see citing works

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 216 · see citing works

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 · see citing works

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 · see citing works

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 188 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Unfinished symphony

Qiu, J. X. J. (2006) · Nature · doi:10.1038/441143a · Cited by 168 · see citing works

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 160 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 108 · see citing works

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

de Wit, E., Greil, F., & van Steensel, B. (2005) · Genome Research · doi:10.1101/gr.3198905 · Cited by 106 · see citing works

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

Mallin, D. R., Myung, J. S., Patton, J. S., & Geyer, P. (1998) · Genetics · doi:10.1093/genetics/148.1.331 · Cited by 78 · see citing works

Strategies for dissecting epigenetic mechanisms in the mouse

Mager, J., & Bartolomei, M. S. (2005) · Nature Genetics · doi:10.1038/ng1664 · Cited by 39 · see citing works

Epigenetic Regulations of GABAergic Neurotransmission: Relevance for Neurological Disorders and Epigenetic Therapy

Shrestha, S., & Offer, S. M. (2016) · Medical Epigenetics · doi:10.1159/000444713 · Cited by 8,949 · see citing works

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works

Epigenetics in Cancer

Esteller, M. (2008) · New England Journal of Medicine · doi:10.1056/nejmra072067 · Cited by 3,681 · see citing works

Persistent epigenetic differences associated with prenatal exposure to famine in humans

Heijmans, B. T., Tobi, E. W., Stein, A. D., Putter, H., Blauw, G. J., Susser, E. S., Slagboom, P. E., & Lumey, L. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806560105 · Cited by 3,082 · see citing works

Direct conversion of fibroblasts to functional neurons by defined factors

Vierbuchen, T., Ostermeier, A., Pang, Z. P., Kokubu, Y., Südhof, T. C., & Wernig, M. (2010) · Nature · doi:10.1038/nature08797 · Cited by 3,017 · see citing works

Epigenetics in cancer

Sharma, S., Kelly, T. K., & Jones, P. A. (2010) · Carcinogenesis · doi:10.1093/carcin/bgp220 · Cited by 2,637 · see citing works

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

Lister, R., O’Malley, R. C., Tonti‐Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008) · Cell · doi:10.1016/j.cell.2008.03.029 · Cited by 2,424 · see citing works

Combinatorial patterns of histone acetylations and methylations in the human genome

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331 · see citing works

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217 · see citing works

The NIH Roadmap Epigenomics Mapping Consortium

Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1045 · Cited by 1,892 · see citing works

CTCF: Master Weaver of the Genome

Phillips‐Cremins, J. E., & Corces, V. G. (2009) · Cell · doi:10.1016/j.cell.2009.06.001 · Cited by 1,540 · see citing works

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The ENCODE Project Consortium (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001046 · Cited by 1,495 · see citing works

Dissecting direct reprogramming through integrative genomic analysis

Mikkelsen, T. S., Hanna, J. H., Zhang, X., Ku, M., Wernig, M., Schorderet, P., Bernstein, B., Jaenisch, R., Lander, E. S., & Meissner, A. (2008) · Nature · doi:10.1038/nature07056 · Cited by 1,472 · see citing works

Initial genome sequencing and analysis of multiple myeloma

Chapman, M. A., Lawrence, M. S., Keats, J. J., Cibulskis, K., Sougnez, C. L., Schinzel, A. C., Harview, C. L., Brunet, J.-P., Ahmann, G. J., Adli, M., et al. (2011) · Nature · doi:10.1038/nature09837 · Cited by 1,422 · see citing works

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Goldberg, A. D., Banaszynski, L. A., Noh, K., Lewis, P. W., Elsässer, S. J., Stadler, S. C., Dewell, S. B., Law, M. J., Guo, X., Li, X., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.003 · Cited by 1,281 · see citing works

Epigenome-wide association studies for common human diseases

Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3000 · Cited by 1,272 · see citing works

Molecular regulation of stem cell quiescence

Cheung, T. H., & Rando, T. A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3591 · Cited by 1,148 · see citing works

Charting histone modifications and the functional organization of mammalian genomes

Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147 · see citing works

Discovery and characterization of chromatin states for systematic annotation of the human genome

Ernst, J., & Kellis, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1662 · Cited by 1,033 · see citing works

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,043 · see citing works

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,022 · see citing works

Transcriptional control of the inflammatory response

Medzhitov, R., & Horng, T. (2009) · Nature Reviews Immunology · doi:10.1038/nri2634 · Cited by 1,035 · see citing works

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

Ku, M., Koche, R. P., Rheinbay, E., Mendenhall, E. M., Endoh, M., Mikkelsen, T. S., Aiden, A. P., Nusbaum, C., Xie, X. S., Chi, A. S., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000242 · Cited by 996 · see citing works

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

Lupien, M., Eeckhoute, J., Meyer, C. A., Wang, Q., Zhang, Y., Li, W., Carroll, J. S., Liu, X. S., & Brown, M. (2008) · Cell · doi:10.1016/j.cell.2008.01.018 · Cited by 983 · see citing works

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

Mohn, F., Weber, M., Rebhan, M., Roloff, T. C., Richter, J., Stadler, M. B., Bibel, M., & Schübeler, D. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.007 · Cited by 912 · see citing works

The Role of Snail in EMT and Tumorigenesis

Wang, Y., Shi, J., Chai, K., Ying, X., & Zhou, B. P. (2013) · Current Cancer Drug Targets · doi:10.2174/15680096113136660102 · Cited by 871 · see citing works

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Boettiger, A. N., Bintu, B., Moffitt, J. R., Wang, S. S., Beliveau, B. J., Fudenberg, G., Imakaev, M., Mirny, L. A., Wu, C.-T., & Zhuang, X. (2016) · Nature · doi:10.1038/nature16496 · Cited by 877 · see citing works

Epigenetic inheritance in plants

Henderson, I. R., & Jacobsen, S. E. (2007) · Nature · doi:10.1038/nature05917 · Cited by 838 · see citing works

Histone modification levels are predictive for gene expression

Karlić, R., Chung, H., Lasserre, J., Vlahoviček, K., & Vingron, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909344107 · Cited by 794 · see citing works

Rethinking how DNA methylation patterns are maintained

Jones, P. A., & Liang, G. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2651 · Cited by 767 · see citing works

Non-coding RNAs as regulators in epigenetics

Wei, J., Huang, K., Yang, C., & Kang, C. (2016) · Oncology Reports · doi:10.3892/or.2016.5236 · Cited by 750 · see citing works

Mechanisms and Metabolic Implications of Regional Differences among Fat Depots

Tchkonia, T., Thomou, T., Zhu, Y. Z., Karagiannides, I., Pothoulakis, C., Jensen, M. D., & Kirkland, J. L. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.03.008 · Cited by 728 · see citing works

Recent aspects of the effects of zinc on human health

Chasapis, C. T., Ntoupa, P.-S. A., Spiliopoulou, C., & Stefanidou, M. E. (2020) · Archives of Toxicology · doi:10.1007/s00204-020-02702-9 · Cited by 732 · see citing works

Endothelial to Mesenchymal Transition: Role in Physiology and in the Pathogenesis of Human Diseases

Piera-Velázquez, S., & Jiménez, S. A. (2019) · Physiological Reviews · doi:10.1152/physrev.00021.2018 · Cited by 673 · see citing works

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Down, T. A., Rakyan, V. K., Turner, D., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, E. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1414 · Cited by 651 · see citing works

Chromatin organization marks exon-intron structure

Schwartz, S., Meshorer, E., & Ast, G. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1659 · Cited by 638 · see citing works

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

Moran, V. A., Perera, R. J., & Khalil, A. M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks296 · Cited by 637 · see citing works

Aberrant Epigenetic Landscape in Cancer: How Cellular Identity Goes Awry

Berdasco, M., & Esteller, M. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.10.005 · Cited by 623 · see citing works

Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A. B. H., Orlov, Y. L., Sung, W.-K. K., Shahab, A., Kuznetsov, V. A., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.08.004 · Cited by 616 · see citing works

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

Bartke, T., Vermeulen, M., Xhemalce, B., Robson, S. C., Mann, M., & Kouzarides, T. (2010) · Cell · doi:10.1016/j.cell.2010.10.012 · Cited by 611 · see citing works

Facultative Heterochromatin: Is There a Distinctive Molecular Signature?

Trojer, P., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.011 · Cited by 609 · see citing works

QUMA: quantification tool for methylation analysis

Kumaki, Y., Oda, M., & Okano, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn294 · Cited by 606 · see citing works

Genome-scale analysis of aberrant DNA methylation in colorectal cancerPreprint

Hinoue, T., Weisenberger, D. J., Lange, C., Shen, H., Byun, H., Van, D., Malik, S., Pan, F., Noushmehr, H., van, C., et al. (2011) · Genome Research · doi:10.1101/gr.117523.110 · Cited by 604 · see citing works

Next-generation genomics: an integrative approach

Hawkins, R. D., Hon, G. C., & Ren, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2795 · Cited by 591 · see citing works

Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies

Urdinguio, R. G., Sanchez-Mut, J. V., & Esteller, M. (2009) · The Lancet Neurology · doi:10.1016/s1474-4422(09)70262-5 · Cited by 581 · see citing works

Mapping Human Epigenomes

Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550 · see citing works

Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation

Edmunds, J. W., Mahadevan, L. C., & Clayton, A. L. (2008) · The EMBO Journal · doi:10.1038/sj.emboj.7601967 · Cited by 547 · see citing works

A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells

Vedadi, M., Baršytė-Lovejoy, D., Liu, F., Rival‐Gervier, S., Allali‐Hassani, A., Labrie, V., Wigle, T. J., DiMaggio, P. A., Wasney, G. A., Siarheyeva, A., et al. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.599 · Cited by 547 · see citing works

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

West, A. E., & Greenberg, M. E. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005744 · Cited by 532 · see citing works

Decoding the Epigenetic Language of Neuronal Plasticity

Borrelli, E., Nestler, E. J., Allis, C. D., & Sassone‐Corsi, P. (2008) · Neuron · doi:10.1016/j.neuron.2008.10.012 · Cited by 529 · see citing works

Cross talk between microRNA and epigenetic regulation in adult neurogenesis

Szulwach, K. E., Li, X., Smrt, R. D., Li, Y., Luo, Y., Lin, L., Santistevan, N. J., Li, W., Zhao, X., & Jin, P. (2010) · Journal of Cell Biology · doi:10.1083/jcb.200908151 · Cited by 493 · see citing works

Disease variants alter transcription factor levels and methylation of their binding sites

Bonder, M. J., Luijk, R., Zhernakova, D. V., Moed, M., Deelen, P., Vermaat, M., van Iterson, M., van Dijk, F., van Galen, M., Bot, J. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3721 · Cited by 462 · see citing works

Epigenetics in cancer: Targeting chromatin modifications

Ellis, L., Atadja, P. W., & Johnstone, R. W. (2009) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-08-0860 · Cited by 483 · see citing works

Noncoding RNA in development

Amaral, P., & Mattick, J. S. (2008) · Mammalian Genome · doi:10.1007/s00335-008-9136-7 · Cited by 479 · see citing works

Adaptive Transgenerational Plasticity in Plants: Case Studies, Mechanisms, and Implications for Natural Populations

Herman, J. J., & Sultan, S. E. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00102 · Cited by 467 · see citing works

Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice

Seki, Y., Yamaji, M., Yabuta, Y., Sano, M., Shigeta, M., Matsui, Y., Saga, Y., Tachibana, M., Shinkai, Y., & Saitou, M. (2007) · Development · doi:10.1242/dev.005611 · Cited by 460 · see citing works

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

Hahn, M. A., Qiu, R., Wu, X., Li, A. X., Zhang, H., Wang, J., Jui, J., Jin, S., Jiang, Y., Pfeifer, G. P., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.011 · Cited by 457 · see citing works

Mechanisms and models of somatic cell reprogramming

Buganim, Y., Faddah, D. A., & Jaenisch, R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3473 · Cited by 453 · see citing works

An Orally Bioavailable Chemical Probe of the Lysine Methyltransferases EZH2 and EZH1

Konze, K. D., Ma, A., Li, F., Baršytė-Lovejoy, D., Parton, T., MacNevin, C. J., Liu, F., Gao, C., Huang, X., Kuznetsova, E., et al. (2013) · ACS Chemical Biology · doi:10.1021/cb400133j · Cited by 450 · see citing works

Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60

Sun, Y., Jiang, X., Xu, Y., Ayrapetov, M. K., Moreau, L. A., Whetstine, J. R., & Price, B. D. (2009) · Nature Cell Biology · doi:10.1038/ncb1982 · Cited by 454 · see citing works

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

Fouse, S. D., Shen, Y., Pellegrini, M. A., Cole, S. W., Meissner, A., Neste, L. V., Jaenisch, R., & Fan, G. (2008) · Cell stem cell · doi:10.1016/j.stem.2007.12.011 · Cited by 447 · see citing works

DNA methylation: An epigenetic mark of cellular memory

Kim, M., & Costello, J. (2017) · Experimental & Molecular Medicine · doi:10.1038/emm.2017.10 · Cited by 450 · see citing works

Epigenetic-Mediated Dysfunction of the Bone Morphogenetic Protein Pathway Inhibits Differentiation of Glioblastoma-Initiating Cells

Lee, J., Son, M. J., Woolard, K., Donin, N. M., Li, A., Cheng, C. H., Kotliarova, S. E., Kotliarov, Y., Walling, J., Ahn, S. J., et al. (2008) · Cancer Cell · doi:10.1016/j.ccr.2007.12.005 · Cited by 429 · see citing works

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

Farlik, M., Sheffield, N. C., Nuzzo, A., Datlinger, P., Schönegger, A., Klughammer, J., & Bock, C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.001 · Cited by 422 · see citing works

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

Shao, Z., Zhang, Y., Yuan, G., Orkin, S. H., & Waxman, D. J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r16 · Cited by 402 · see citing works

Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells

Saitou, M., Kagiwada, S., & Kurimoto, K. (2011) · Development · doi:10.1242/dev.050849 · Cited by 410 · see citing works

A DNA methylation fingerprint of 1628 human samplesPreprint

Fernández, A. F., Assenov, Y., Martín-Subero, J. I., Bálint, B., Siebert, R., Taniguchi, H., Yamamoto, H., Hidalgo, M. M., Tan, A. C., Galm, O., et al. (2011) · Genome Research · doi:10.1101/gr.119867.110 · Cited by 415 · see citing works

Personalized Medicine: Progress and Promise

Chan, I. S., & Ginsburg, G. S. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082410-101446 · Cited by 399 · see citing works

SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability

Li, L., Shi, L., Yang, S., Yan, R., Zhang, D., Yang, J., He, L., Li, W., Yi, X., Sun, L., et al. (2016) · Nature Communications · doi:10.1038/ncomms12235 · Cited by 392 · see citing works

An atlas of dynamic chromatin landscapes in mouse fetal development

Gorkin, D. U., Barozzi, I., Zhao, Y., Zhang, Y., Huang, H., Lee, A. Y., Li, B., Chiou, J., Wildberg, A., Ding, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2093-3 · Cited by 364 · see citing works

Functional Specificity among Ribosomal Proteins Regulates Gene Expression

Komili, S., Farny, N. G., Roth, F. P., & Silver, P. A. (2007) · Cell · doi:10.1016/j.cell.2007.08.037 · Cited by 390 · see citing works

Induced pluripotent stem cells: current progress and potential for regenerative medicine.

Amabile, G., & Meissner, A. (2009) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2008.12.003 · Cited by 408 · see citing works

RNA regulation of epigenetic processes

Mattick, J. S., Amaral, P., Dinger, M. E., Mercer, T. R., & Mehler, M. F. (2009) · BioEssays · doi:10.1002/bies.080099 · Cited by 381 · see citing works

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

Gal‐Yam, E. N., Egger, G., Iniguez, L., Holster, H., Einarsson, S. O., Zhang, X., Lin, J., Liang, G., Jones, P. A., & Tanay, A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806437105 · Cited by 380 · see citing works

UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9

Liu, X., Gao, Q., Li, P., Zhao, Q., Zhang, J., Li, J., Koseki, H., & Wong, J. (2013) · Nature Communications · doi:10.1038/ncomms2562 · Cited by 377 · see citing works

Finding the fifth base: Genome-wide sequencing of cytosine methylationPreprint

Lister, R., & Ecker, J. R. (2009) · Genome Research · doi:10.1101/gr.083451.108 · Cited by 377 · see citing works

Quantitative Proteomic Analysis of Histone Modifications

Huang, H., Lin, S., Garcia, B. A., & Zhao, Y. (2015) · Chemical Reviews · doi:10.1021/cr500491u · Cited by 372 · see citing works

Epigenetic modifications in pluripotent and differentiated cells

Meissner, A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1684 · Cited by 373 · see citing works

Genome-wide approaches to studying chromatin modifications

Schones, D. E., & Zhao, K. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2270 · Cited by 370 · see citing works

The SNAG domain of Snail1 functions as a molecular hook for recruiting lysine‐specific demethylase 1

Lin, Y., Wu, Y., Li, J., Dong, C., Ye, X., Chi, Y., Evers, B. M., & Zhou, B. P. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.63 · Cited by 362 · see citing works

The functional role of long non-coding RNAs and epigenetics

Cao, J. (2014) · Biological Procedures Online · doi:10.1186/1480-9222-16-11 · Cited by 359 · see citing works

Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells

Fiskus, W. C., Wang, Y., Sreekumar, A., Buckley, K. M., Shi, H., Jillella, A., Üstün, C., Rao, R., Fernandez, P., Chen, J., et al. (2009) · Blood · doi:10.1182/blood-2009-03-213496 · Cited by 357 · see citing works

Raman Spectroscopy for Chemical Biology Research

Dodo, K., Fujita, K., & Sodeoka, M. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c05359 · Cited by 333 · see citing works

Diet induced epigenetic changes and their implications for health

McKay, J. A., & Mathers, J. C. (2011) · Acta Physiologica · doi:10.1111/j.1748-1716.2011.02278.x · Cited by 339 · see citing works

ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a

Gao, X., Tate, P. H., Hu, P., Tjian, R., Skarnes, W. C., & Wang, Z. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801802105 · Cited by 336 · see citing works

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

Kulis, M., Merkel, A., Heath, S. C., Queirós, A. C., Schuyler, R. P., Castellano, G., Beekman, R., Raineri, E., Esteve‐Codina, A., Clot, G., et al. (2015) · Nature Genetics · doi:10.1038/ng.3291 · Cited by 329 · see citing works

DNA Methylation, Its Mediators and Genome Integrity

Meng, H., Cao, Y., Qin, J., Song, X., Zhang, Q., Shi, Y. S., & Cao, L. (2015) · International Journal of Biological Sciences · doi:10.7150/ijbs.11218 · Cited by 327 · see citing works

GlcNAcylation of histone H2B facilitates its monoubiquitination

Fujiki, R., Hashiba, W., Sekine, H., Yokoyama, A., Chikanishi, T., Ito, S., Imai, Y., Kim, J., He, H. H., Igarashi, K., et al. (2011) · Nature · doi:10.1038/nature10656 · Cited by 329 · see citing works

Malleability, plasticity, and individuality: How children learn and develop in context¹

Cantor, P., Osher, D., Berg, J., Steyer, L., & Rose, T. (2019) · Applied Developmental Science · doi:10.1080/10888691.2017.1398649 · Cited by 328 · see citing works

Epigenetics of endometriosis

Guo, S.-W. (2009) · Molecular Human Reproduction · doi:10.1093/molehr/gap064 · Cited by 328 · see citing works

H3K27 Demethylases, at Long Last

Swigut, T., & Wysocka, J. (2007) · Cell · doi:10.1016/j.cell.2007.09.026 · Cited by 327 · see citing works

MYCN and the epigenome

He, S., Liu, Z., Oh, D., & Thiele, C. J. (2013) · Frontiers in Oncology · doi:10.3389/fonc.2013.00001 · Cited by 327 · see citing works

Epigenetic variation during the adult lifespan: cross‐sectional and longitudinal data on monozygotic twin pairs

Talens, R. P., Christensen, K., Putter, H., Willemsen, G. A. H. M., Christiansen, L., Kremer, D., Suchiman, H. E. D., Slagboom, P. E., Boomsma, D. I., & Heijmans, B. T. (2012) · Aging Cell · doi:10.1111/j.1474-9726.2012.00835.x · Cited by 326 · see citing works

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

Wu, M., Wang, P. F., Lee, J. S., Martin‐Brown, S., Florens, L. A., Washburn, M. P., & Shilatifard, A. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00976-08 · Cited by 324 · see citing works

Physical exercise as an epigenetic modulator of brain plasticity and cognition

Fernandes, J., Arida, R. M., & Gómez‐Pinilla, F. (2017) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2017.06.012 · Cited by 326 · see citing works

Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during T Helper Cell Differentiation

Wei, L., Vahedi, G., Sun, H., Watford, W. T., Takatori, H., Ramos, H. L., Takahashi, H., Liang, J. Z., Gutierrez-Cruz, G., Zang, C., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.003 · Cited by 322 · see citing works

Inhibitors of Protein Methyltransferases and Demethylases

Kanıskan, H. Ü., Martini, M. L., & Jin, J. J. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00801 · Cited by 320 · see citing works

Non-coding RNAs, epigenetics and complexity

Costa, F. F. (2007) · Gene · doi:10.1016/j.gene.2007.12.008 · Cited by 319 · see citing works

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

Li, Y., Zhu, J., Tian, G., Li, N., Li, Q., Ye, M., Zheng, H., Yu, J., Wu, H., Sun, J., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000533 · Cited by 318 · see citing works

Genome-wide approaches to studying chromatin modifications

Schones, D. E., & Zhao, K. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2270 · Cited by 370 · see citing works

Analyses of Genome-Wide Histone Modifications in the Mammalian Genome

Tian, S., Slager, S. L., Gaonkar, K. S., & Yan, H. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00010-9 · Cited by 1 · see citing works

Editorial

Bartolomei, M. S., & Bickmore, W. A. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi118 · Cited by 2 · see citing works

The functional genome: epigenetics and epigenomics

Reddy, T. E. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-800684-9.00017-4

Grand challenge in chromatin epigenomics: everything, everywhere, all at once

Dent, S. (2023) · Frontiers in Epigenetics and Epigenomics · doi:10.3389/freae.2023.1195690 · Cited by 2 · see citing works