Human DNA methylomes at base resolution show widespread epigenomic differences

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works

Embryonic Stem Cell Lines Derived from Human Blastocysts

Thomson, J. A., Itskovitz‐Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S., & Jones, J. M. (1998) · Science · doi:10.1126/science.282.5391.1145 · Cited by 15,947 · see citing works

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 13,133 · 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

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

The Epigenomics of Cancer

Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515 · 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

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536 · see citing works

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · 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

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278 · see citing works

Linking DNA methylation and histone modification: patterns and paradigms

Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267 · see citing works

The DNA methyltransferases of mammals

Bestor, T. H. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.16.2395 · Cited by 2,045 · see citing works

DNA Modification Mechanisms and Gene Activity During Development

Holliday, R., & Pugh, J. E. (1975) · Science · doi:10.1126/science.187.4173.226 · Cited by 1,973 · see citing works

Stability and flexibility of epigenetic gene regulation in mammalian development

Reik, W. (2007) · Nature · doi:10.1038/nature05918 · Cited by 1,963 · see citing works

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

Bell, A. C., & Felsenfeld, G. (2000) · Nature · doi:10.1038/35013100 · Cited by 1,746 · 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

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

X inactivation, differentiation, and DNA methylation

Riggs, A. D. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000130315 · Cited by 1,343 · see citing works

How Are Alkynes Scrambled?

Bunz, U. H. F. (2005) · Science · doi:10.1126/science.1111098 · Cited by 1,252 · 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

Derivation of human embryonic stem cells in defined conditions

Ludwig, T. E., Levenstein, M. E., Jones, J. M., Berggren, W. T., Mitchen, E. R., Frane, J. L., Crandall, L. J., Daigh, C. A., Conard, K. R., Piekarczyk, M. S., et al. (2006) · Nature Biotechnology · doi:10.1038/nbt1177 · Cited by 1,114 · see citing works

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Ball, M. P., Li, J. B., Gao, Y., Lee, J., LeProust, E. M., Park, I., Xie, B., Daley, G. Q., & Church, G. M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1533 · Cited by 1,087 · see citing works

Characterization of human embryonic stem cell lines by the International Stem Cell Initiative

Initiative, T. I. S. C. (2007) · Nature Biotechnology · doi:10.1038/nbt1318 · Cited by 1,078 · see citing works

Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · 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

Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation

Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A., & Cheng, X. (2007) · Nature · doi:10.1038/nature06146 · Cited by 850 · see citing works

Gene Body-Specific Methylation on the Active X Chromosome

Hellman, A., & Chess, A. J. (2007) · Science · doi:10.1126/science.1136352 · Cited by 732 · see citing works

Feeder-independent culture of human embryonic stem cells

Ludwig, T. E., Bergendahl, V., Levenstein, M. E., Yu, J., Probasco, M. D., & Thomson, J. A. (2006) · Nature Methods · doi:10.1038/nmeth902 · Cited by 681 · see citing works

DNA methyltransferases control telomere length and telomere recombination in mammalian cells

Gonzalo, S., Jaco, I., Fraga, M. F., Chen, T., Li, E., Esteller, M., & Blasco, M. A. (2006) · Nature Cell Biology · doi:10.1038/ncb1386 · Cited by 604 · see citing works

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

Deng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E. M., Antosiewicz‐Bourget, J., Egli, D. M., Maherali, N., Park, I., Yu, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1530 · Cited by 491 · see citing works

The SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation

Johnson, L. M., Bostick, M. L., Zhang, X., Kraft, E., Henderson, I. R., Callis, J., & Jacobsen, S. E. (2007) · Current Biology · doi:10.1016/j.cub.2007.01.009 · Cited by 418 · see citing works

Developmental programming of CpG island methylation profiles in the human genome

Straussman, R., Nejman, D., Roberts, D. N., Steinfeld, I., Blum, B., Benvenisty, N., Simon, I., Zohar Yakhini, B., & Cedar, H. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1594 · Cited by 409 · see citing works

Genomic patterns of DNA methylation: targets and function of an epigenetic mark

Weber, M., & Schübeler, D. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.011 · Cited by 387 · see citing works

Characterization of a New Human Diploid Cell Strain, IMR-90

Nichols, W. W., Murphy, D. G., Cristofalo, V. J., Toji, L. H., Greene, A. E., & Dwight, S. (1977) · Science · doi:10.1126/science.841339 · Cited by 368 · see citing works

A human B cell methylome at 100−base pair resolution

Rauch, T. A., Wu, X., Zhong, X., Riggs, A. D., & Pfeifer, G. P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812399106 · Cited by 333 · see citing works

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liverPreprint

Brunner, A. L., Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen, L., Chiao, E. T., et al. (2009) · Genome Research · doi:10.1101/gr.088773.108 · Cited by 283 · see citing works

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activityPreprint

Schmidl, C., Klug, M., Boeld, T. J., Andreesen, R., Hoffmann, P., Edinger, M., & Rehli, M. (2009) · Genome Research · doi:10.1101/gr.091470.109 · Cited by 239 · see citing works

Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpA sites

Gowher, H., & Jeltsch, A. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4710 · Cited by 236 · see citing works

Sp1 binding is inhibited by mCpmCpG methylation

Clark, S. J., Harrison, J., & Molloy, P. L. (1997) · Gene · doi:10.1016/s0378-1119(97)00164-9 · Cited by 204 · see citing works

Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases

Aoki, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.17.3506 · Cited by 182 · see citing works

Site-specific DNA methylation in the neurofibromatosis (NF1) promoter interferes with binding of CREB and SP1 transcription factors

Mancini, D. N., Singh, S. M., Archer, T., & Rodenhiser, D. I. (1999) · Oncogene · doi:10.1038/sj.onc.1202764 · Cited by 133 · see citing works

The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide

Woodcock, D. M., Crowther, P. J., & Diver, W. P. (1987) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(87)91048-5 · Cited by 128 · see citing works

Transcriptional Regulation of Rat Cyclin D1 Gene by CpG Methylation Status in Promoter Region

Kitazawa, S., Kitazawa, R., Kitazawa, R., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.40.28787 · Cited by 82 · see citing works

Modification of Subtelomeric DNA

Steinert, S., Shay, J. W., & Wright, W. E. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.10.4571-4580.2004 · Cited by 72 · see citing works

Inputs and outputs for chromatin-targeted RNAi

Chan, S. W.-L. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2008.05.001 · Cited by 44 · see citing works

Perceptive enzymes

Ferguson‐Smith, A. C., & Greally, J. M. (2007) · Nature · doi:10.1038/449148a · Cited by 44 · see citing works

Identification of endogenous retroviral reading frames in the human genome

Villesen, P., Aagaard, L., Wiuf, C., & Pedersen, F. (2004) · Retrovirology · doi:10.1186/1742-4690-1-32 · Cited by 37 · see citing works

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works

Functions of DNA methylation: islands, start sites, gene bodies and beyond

Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061 · see citing works

DNA methylation and its basic function

Moore, L. D., Le, T., & Fan, G. (2013) · Neuropsychopharmacology · doi:10.1038/npp.2012.112 · Cited by 4,906 · see citing works

A decade of exploring the cancer epigenome—biological and translational implications

Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871 · see citing works

EDC-2: the endocrine society's second scientific statement on endocrine-disrupting chemicals

Gore, A. C., Chappell, V. A., Fenton, S. E., Flaws, J. A., Nadal, A., Prins, G. S., Toppari, J., & Zoeller, R. T. (2015) · Endocrine Reviews · doi:10.1210/er.2015-1010 · Cited by 2,407 · see citing works

Five Years of GWAS Discovery

Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.029 · Cited by 2,425 · see citing works

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378 · 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

Global epigenomic reconfiguration during mammalian brain development

Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science · doi:10.1126/science.1237905 · Cited by 1,830 · see citing works

High density DNA methylation array with single CpG site resolution

Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J. M., Delano, D., Zhang, L., Schroth, G. P., Gunderson, K. L., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.07.007 · Cited by 1,727 · see citing works

Conserved role of intragenic DNA methylation in regulating alternative promoters

Maunakea, A. K., Nagarajan, R. P., Bilenky, M., Ballinger, T. J., D’Souza, C., Fouse, S. D., Johnson, B. E., Hong, C., Nielsen, C., Zhao, Y., et al. (2010) · Nature · doi:10.1038/nature09165 · Cited by 1,743 · see citing works

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Pidsley, R., Zotenko, E., Peters, T. J., Lawrence, M. G., Risbridger, G. P., Molloy, P., Van Djik, S., Muhlhausler, B., Stirzaker, C., & Clark, S. J. (2016) · Genome biology · doi:10.1186/s13059-016-1066-1 · Cited by 1,480 · see citing works

Direct detection of DNA methylation during single-molecule, real-time sequencing

Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460 · see citing works

DNA-binding factors shape the mouse methylome at distal regulatory regions

Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383 · see citing works

Conservation and divergence of methylation patterning in plants and animals

Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002720107 · Cited by 1,285 · see citing works

Charting a dynamic DNA methylation landscape of the human genome

Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature · doi:10.1038/nature12433 · Cited by 1,357 · see citing works

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257 · see citing works

Editing DNA Methylation in the Mammalian Genome

Liu, X. S., Wu, H., Ji, X., Stelzer, Y., Wu, X., Czauderna, S., Shu, J., Dadon, D., Young, R. A., & Jaenisch, R. (2016) · Cell · doi:10.1016/j.cell.2016.08.056 · Cited by 1,224 · see citing works

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

Yang, X., Han, H., De Carvalho, D. D., Lay, F. D., Jones, P. A., & Liang, G. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.028 · Cited by 1,199 · 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

Dnmt3a is essential for hematopoietic stem cell differentiation

Challen, G. A., Sun, D., Jeong, M., Luo, M., Jelinek, J., Berg, J. S., Bock, C., Vasanthakumar, A., Gu, H., Xi, Y., et al. (2012) · Nature Genetics · doi:10.1038/ng.1009 · Cited by 1,122 · see citing works

DNA methylation pathways and their crosstalk with histone methylation

Du, J., Johnson, L. M., Jacobsen, S. E., & Patel, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4043 · Cited by 1,000 · see citing works

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

Argelaguet, R., Arnol, D., Bredikhin, D., Deloro, Y., Velten, B., Marioni, J. C., & Stegle, O. (2020) · Genome Biology · doi:10.1186/s13059-020-02015-1 · Cited by 1,091 · see citing works

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065 · see citing works

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

Sandoval, J., Heyn, H., Moran, S., Serra-Musach, J., Pujana, M. A., Bibikova, M., & Esteller, M. (2011) · Epigenetics · doi:10.4161/epi.6.6.16196 · Cited by 990 · see citing works

Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

Bock, C., Kiskinis, E., Verstappen, G., Gu, H., Boulting, G., Smith, Z. D., Ziller, M., Croft, G. F., Amoroso, M. W., Oakley, D. H., et al. (2011) · Cell · doi:10.1016/j.cell.2010.12.032 · Cited by 1,009 · see citing works

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W., & Reik, W. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.001 · Cited by 973 · see citing works

Acute Exercise Remodels Promoter Methylation in Human Skeletal Muscle

Barrès, R., Yan, J., Egan, B., Treebak, J. T., Rasmussen, M., Fritz, T., Caidahl, K., Krook, A., O'Gorman, D. J., & Zierath, J. R. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.01.001 · Cited by 965 · see citing works

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

Pastor, W. A., Aravind, L., & Rao, A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3589 · Cited by 897 · see citing works

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

Bell, J. T., Pai, A. A., Pickrell, J. K., Gaffney, D. J., Pique-Regi, R., Degner, J. F., Gilad, Y., & Pritchard, J. K. (2011) · Genome Biology · doi:10.1186/gb-2011-12-1-r10 · Cited by 838 · see citing works

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806 · see citing works

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804 · see citing works

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

Koh, K. P., Yabuuchi, A., Rao, S., Huang, Y., Cunniff, K., Nardone, J., Laiho, A., Tahiliani, M., Sommer, C. A., Mostoslavsky, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.008 · Cited by 776 · see citing works

Genome Architecture: Domain Organization of Interphase Chromosomes

Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.001 · Cited by 725 · see citing works

Non-coding RNAs as regulators of gene expression and epigenetics

Kaikkonen, M. U., Lam, M. T. Y., & Glass, C. K. (2011) · Cardiovascular Research · doi:10.1093/cvr/cvr097 · Cited by 764 · see citing works

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

Hangauer, M. J., Vaughn, I. W., & McManus, M. T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003569 · Cited by 738 · see citing works

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Clark, S. J., Argelaguet, R., Kapourani, C.-A., Stubbs, T. M., Lee, H. J., Alda-Catalinas, C., Krueger, F., Sanguinetti, G., Kelsey, G., Marioni, J. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03149-4 · Cited by 657 · see citing works

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

Lyko, F., Foret, S., Kucharski, R., Wolf, S., Falckenhayn, C., & Maleszka, R. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000506 · Cited by 727 · see citing works

The transcriptional landscape of age in human peripheral blood

Peters, M. J., Joehanes, R., Pilling, L. C., Schurmann, C., Conneely, K. N., Powell, J., Reinmaa, E., Sutphin, G. L., Zhernakova, A., Schramm, K., et al. (2015) · Nature Communications · doi:10.1038/ncomms9570 · Cited by 725 · see citing works

Dynamic DNA methylation: In the right place at the right time

Luo, C., Hajkova, P., & Ecker, J. R. (2018) · Science · doi:10.1126/science.aat6806 · Cited by 668 · see citing works

Transcription factors as readers and effectors of DNA methylation

Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649 · see citing works

Uterine fibroids

Bulun, S. E. (2013) · New England Journal of Medicine · doi:10.1056/nejmra1209993 · Cited by 703 · see citing works

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

Guo, J. U., Su, Y., Shin, J. H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3607 · Cited by 714 · see citing works

Human body epigenome maps reveal noncanonical DNA methylation variation

Schultz, M. D., He, Y., Whitaker, J. W., Hariharan, M., Mukamel, E. A., Leung, D., Rajagopal, N., Nery, J. R., Urich, M. A., Chen, H., et al. (2015) · Nature · doi:10.1038/nature14465 · Cited by 690 · see citing works

Neuronal activity modifies the DNA methylation landscape in the adult brain

Guo, J. U., Ma, D. K., Mo, H., Ball, M. P., Jang, M.-H., Bonaguidi, M. A., Balazer, J. A., Eaves, H. L., Xie, B., Ford, E., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2900 · Cited by 669 · see citing works

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

Wu, H., D’Alessio, A. C., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Eve Sun, Y., & Zhang, Y. (2011) · Nature · doi:10.1038/nature09934 · Cited by 646 · see citing works

Tobacco-smoking-related differential DNA methylation: 27K discovery and replication

Breitling, L. P., Yang, R., Korn, B., Burwinkel, B., & Brenner, H. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.003 · Cited by 640 · see citing works

Widespread plasticity in CTCF occupancy linked to DNA methylation

Wang, H., Maurano, M. T., Qu, H., Varley, K. E., Gertz, J., Pauli, F., Lee, K., Canfield, T., Weaver, M., Sandstrom, R., et al. (2012) · Genome Research · doi:10.1101/gr.136101.111 · Cited by 588 · see citing works

The ageing haematopoietic stem cell compartment

Geiger, H., de Haan, G., & Florian, M. C. (2013) · Nature Reviews Immunology · doi:10.1038/nri3433 · Cited by 604 · see citing works

Evaluation of the Infinium Methylation 450K technology

Dedeurwaerder, S., Defrance, M., Calonne, E., Denis, H., Sotiriou, C., & Fuks, F. (2011) · Epigenomics · doi:10.2217/epi.11.105 · Cited by 569 · see citing works

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

Maunakea, A. K., Chepelev, I., Cui, K., & Zhao, K. (2013) · Cell Research · doi:10.1038/cr.2013.110 · Cited by 552 · see citing works

High‐resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome

Iacovoni, J. S., Caron, P., Lassadi, I., Nicolas, E., Massip, L., Trouche, D., & Legube, G. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.38 · Cited by 515 · see citing works

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

Guo, H., Zhu, P., Wu, X., Li, X., Wen, L., & Tang, F. (2013) · Genome Research · doi:10.1101/gr.161679.113 · Cited by 518 · see citing works

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

Xie, W., Barr, C. L., Kim, A., Yue, F., Lee, A. Y., Eubanks, J., Dempster, E. L., & Ren, B. (2012) · Cell · doi:10.1016/j.cell.2011.12.035 · Cited by 543 · see citing works

Stress-induced perinatal and transgenerational epigenetic programming of brain development and mental health

Babenko, O., Kovalchuk, I., & Metz, G. A. S. (2015) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2014.11.013 · Cited by 513 · see citing works

Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion

Dayeh, T., Volkov, P., Salö, S., Hall, E., Nilsson, E., Olsson, A. H., Kirkpatrick, C. L., Wollheim, C. B., Eliasson, L., Rönn, T., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004160 · Cited by 523 · see citing works

Factors underlying variable DNA methylation in a human community cohort

Lam, L. L., Emberly, E., Fraser, H. B., Neumann, S. M., Chen, E., Miller, G. E., & Kobor, M. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121249109 · Cited by 476 · see citing works

The Ensembl Regulatory Build

Zerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429 · see citing works

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

Kelly, T. K., Liu, Y., Lay, F. D., Liang, G., Berman, B. P., & Jones, P. A. (2012) · Genome Research · doi:10.1101/gr.143008.112 · Cited by 455 · see citing works

Annotating non-coding regions of the genome.

Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464 · see citing works

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

Gutierrez-Arcelus, M., Lappalainen, T., Montgomery, S. B., Buil, A., Ongen, H., Yurovsky, A., Bryois, J., Giger, T., Romano, L., Planchon, A., et al. (2013) · eLife · doi:10.7554/elife.00523 · Cited by 440 · see citing works

De novo DNA methylation: a germ cell perspective

Smallwood, S. A., & Kelsey, G. (2012) · Trends in Genetics · doi:10.1016/j.tig.2011.09.004 · Cited by 448 · see citing works

Aging and epigenetic drift: a vicious cycle

Issa, J.-P. (2014) · Journal of Clinical Investigation · doi:10.1172/jci69735 · Cited by 419 · see citing works

CpG and non-CpG methylation in epigenetic gene regulation and brain function

Jang, H., Shin, W., Lee, J., & Do, J. (2017) · Genes · doi:10.3390/genes8060148 · Cited by 427 · see citing works

Epigenetics across the human lifespan

Kanherkar, R. R., Bhatia-Dey, N., & Csoka, A. B. (2014) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2014.00049 · Cited by 407 · see citing works

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411 · see citing works

DNA methylation loss in late-replicating domains is linked to mitotic cell division

Zhou, W., Dinh, H. Q., Ramjan, Z., Weisenberger, D. J., Nicolet, C. M., Shen, H., Laird, P. W., & Berman, B. P. (2018) · Nature Genetics · doi:10.1038/s41588-018-0073-4 · Cited by 405 · see citing works

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

Shoemaker, R., Deng, J., Wang, W., & Zhang, K. (2010) · Genome Research · doi:10.1101/gr.104695.109 · Cited by 380 · see citing works

Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements

Grundberg, E., Meduri, E., Sandling, J. K., Hedman, Å. K., Keildson, S., Buil, A., Busche, S., Yuan, W., Nisbet, J., Sekowska, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.004 · Cited by 370 · see citing works

Towards a comprehensive catalogue of validated and target-linked human enhancers

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

Luo, C., Lancaster, M. A., Castanon, R., Nery, J. R., Knoblich, J. A., & Ecker, J. R. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.12.001 · Cited by 370 · see citing works

The epigenetics of aging and neurodegeneration

Lardenoije, R., Iatrou, A., Kenis, G., Kompotis, K., Steinbusch, H. W. M., Mastroeni, D., Coleman, P., Lemere, C. A., Hof, P. R., van den Hove, D. L. A., et al. (2015) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2015.05.002 · Cited by 381 · see citing works

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

Halder, R., Hennion, M., Vidal, R. O., Shomroni, O., Rahman, R.-U., Rajput, A., Centeno, T. P., van Bebber, F., Capece, V., Vizcaino, J. C. G., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4194 · Cited by 358 · see citing works

Senescent cells harbour features of the cancer epigenome

Cruickshanks, H. A., McBryan, T., Nelson, D. M., VanderKraats, N. D., Shah, P. P., van Tuyn, J., Singh Rai, T., Brock, C., Donahue, G., Dunican, D. S., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2879 · Cited by 358 · see citing works

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.011 · Cited by 365 · see citing works

Structural insight into autoinhibition and histone H3-induced activation of DNMT3A

Guo, X., Wang, L., Li, J., Ding, Z., Xiao, J., Yin, X., He, S., Shi, P., Dong, L., Li, G., et al. (2015) · Nature · doi:10.1038/nature13899 · Cited by 361 · see citing works

DNA methylation presents distinct binding sites for human transcription factors

Hu, S., Wan, J., Su, Y., Song, Q., Zeng, Y., Nguyen, H. N., Shin, J., Cox, E., Rho, H. S., Woodard, C., et al. (2013) · eLife · doi:10.7554/elife.00726 · Cited by 349 · see citing works

Sensitivity of transcription factors to DNA methylation

Héberlé, É., & Bardet, A. F. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190033 · Cited by 347 · see citing works

Transcriptional and Epigenetic Control of T Helper Cell Specification: Molecular Mechanisms Underlying Commitment and Plasticity

Kanno, Y., Vahedi, G., Hirahara, K., Singleton, K., & O'Shea, J. J. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-075058 · Cited by 342 · see citing works

Highly scalable generation of DNA methylation profiles in single cells

Mulqueen, R. M., Pokholok, D., Norberg, S. J., Torkenczy, K. A., Fields, A. J., Sun, D., Sinnamon, J. R., Shendure, J., Trapnell, C., O'Roak, B. J., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4112 · Cited by 289 · see citing works

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

Fortin, J.-P., & Hansen, K. D. (2015) · Genome Biology · doi:10.1186/s13059-015-0741-y · Cited by 333 · see citing works

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

Landan, G., Cohen, N. M., Mukamel, Z., Bar, A., Molchadsky, A., Brosh, R., Horn-Saban, S., Zalcenstein, D. A., Goldfinger, N., Zundelevich, A., et al. (2012) · Nature Genetics · doi:10.1038/ng.2442 · Cited by 305 · see citing works

Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus

Suderman, M., McGowan, P. O., Sasaki, A., Huang, T. C. T., Hallett, M. T., Meaney, M. J., Turecki, G., & Szyf, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121260109 · Cited by 327 · see citing works

The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells

Provençal, N., Suderman, M. J., Guillemin, C., Massart, R., Ruggiero, A., Wang, D., Bennett, A. J., Pierre, P. J., Friedman, D. P., Côté, S. M., et al. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.1470-12.2012 · Cited by 312 · see citing works

Simultaneous profiling of transcriptome and DNA methylome from a single cell

Hu, Y., Huang, K., An, Q., Du, G., Hu, G., Xue, J., Zhu, X., Wang, C.-Y., Xue, Z., & Fan, G. (2016) · Genome Biology · doi:10.1186/s13059-016-0950-z · Cited by 300 · see citing works

The role of bisphenol A in shaping the brain, epigenome and behavior

Wolstenholme, J. T., Rissman, E. F., & Connelly, J. J. (2011) · Hormones and Behavior · doi:10.1016/j.yhbeh.2010.10.001 · Cited by 309 · see citing works

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

Tung, J., Barreiro, L. B., Johnson, Z. P., Hansen, K. D., Michopoulos, V., Toufexis, D., Michelini, K., Wilson, M. E., & Gilad, Y. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202734109 · Cited by 277 · see citing works

Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification

Dapas, M., & Dunaif, A. (2022) · Endocrine Reviews · doi:10.1210/endrev/bnac001 · Cited by 300 · see citing works

Genomic imprinting and parent-of-origin effects on complex traits

Lawson, H. A., Cheverud, J. M., & Wolf, J. B. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3543 · Cited by 262 · see citing works

Role of DNA Methylation in Modulating Transcription Factor Occupancy

Maurano, M. T., Wang, H., John, S., Shafer, A., Canfield, T., Lee, K., & Stamatoyannopoulos, J. A. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.024 · Cited by 281 · see citing works

Biological embedding of experience: a primer on epigenetics

Aristizabal, M. J., Anreiter, I., Halldorsdottir, T., Odgers, C. L., McDade, T. W., Goldenberg, A., Mostafavi, S., Kobor, M. S., Binder, E. B., Sokolowski, M. B., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1820838116 · Cited by 268 · see citing works

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

Hashimoto, H., Wang, D., Horton, J. R., Zhang, X., Corces, V. G., & Cheng, X. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.004 · Cited by 268 · see citing works

Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms

Li, P., Marshall, L., Oh, G., Jakubowski, J. L., Groot, D., He, Y., Wang, T., Petronis, A., & Labrie, V. (2019) · Nature Communications · doi:10.1038/s41467-019-10101-7 · Cited by 234 · see citing works

The effects of early life stress on the epigenome: From the womb to adulthood and even before

Provençal, N., & Binder, E. B. (2015) · Experimental Neurology · doi:10.1016/j.expneurol.2014.09.001 · Cited by 255 · see citing works

DNA methylation status predicts cell type‐specific enhancer activity

Wiench, M., John, S., Baek, S., Johnson, T. A., Sung, M., Escobar, T., Simmons, C. A., Pearce, K. H., Biddie, S. C., Sabo, P. J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.210 · Cited by 245 · see citing works

Epigenetic Epidemiology of Common Complex Disease: Prospects for Prediction, Prevention, and Treatment

Relton, C. L., & Davey Smith, G. (2010) · PLoS Medicine · doi:10.1371/journal.pmed.1000356 · Cited by 254 · see citing works

Overlooked roles of DNA damage and maternal age in generating human germline mutations

Gao, Z., Moorjani, P., Sasani, T. A., Pedersen, B. S., Quinlan, A. R., Jorde, L. B., Amster, G., & Przeworski, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1901259116 · Cited by 229 · see citing works

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

Kinde, B., Gabel, H. W., Gilbert, C. S., Griffith, E. C., & Greenberg, M. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1411269112 · Cited by 236 · see citing works

Nongenetic inheritance and transgenerational epigenetics

Szyf, M. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.12.004 · Cited by 238 · see citing works

Genetic and Environmental Impacts on DNA Methylation Levels in Twins

Yet, I., Tsai, P.-C., Castillo-Fernandez, J. E., Carnero-Montoro, E., & Bell, J. T. (2016) · Epigenomics · doi:10.2217/epi.15.90 · Cited by 36 · see citing works

[Tobacco and DNA methylation: the case for epigenetic alterations].

Bouzigon, E., & Barouki, R. (2021) · PubMed

DNA methylation in osteoarthritic chondrocytes: a new molecular target.

Roach, H., & Aigner, T. (2007) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2006.07.002 · Cited by 92 · see citing works

Early Nutritional Influences on Human Developmental Epigenetics

Waterland, R. A. (2015) · Journal of Nutritional Science and Vitaminology · doi:10.3177/jnsv.61.s82

Changes of DNA methylation of Isoetes sinensis under Pb and Cd stress

Ding, G., Guo, D.-D., Guan, Y., et al. (2018) · Environmental Science and Pollution Research · doi:10.1007/s11356-018-3864-3 · Cited by 19 · see citing works