CpG islands and the regulation of transcription

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836 · see citing works

Long non-coding RNAs: insights into functions

Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654 · 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

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · 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

Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246 · 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

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098 · see citing works

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

Ito, S., D’Alessio, A. C., Taranova, O., Hong, K., Sowers, L. C., & Zhang, Y. (2010) · Nature · doi:10.1038/nature09303 · Cited by 2,542 · 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

Genomic DNA methylation: the mark and its mediators.

Klose, R. J., & Bird, A. P. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.12.008 · Cited by 2,501 · see citing works

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450 · 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

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

Weber, M., Hellmann, I., Stadler, M. B., Ramos, L., Pääbo, S., Rebhan, M., & Schübeler, D. (2007) · Nature Genetics · doi:10.1038/ng1990 · Cited by 2,267 · 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

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

Irizarry, R. A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.298 · Cited by 2,177 · see citing works

Histone demethylation by a family of JmjC domain-containing proteins

Tsukada, Y.-I., Fang, J., Erdjument‐Bromage, H., Warren, M., Borchers, C. H., Tempst, P., & Zhang, Y. (2005) · Nature · doi:10.1038/nature04433 · Cited by 2,171 · see citing works

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works

A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells

Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 1,946 · 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

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

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

Long Noncoding RNAs with Enhancer-like Function in Human Cells

Ørom, U. A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.001 · Cited by 1,721 · see citing works

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

Zhao, J. C., Sun, B. K., Erwin, J. A., Song, J., & Lee, J. T. (2008) · Science · doi:10.1126/science.1163045 · Cited by 1,580 · see citing works

DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument‐Bromage, H., Tempst, P., Lin, S., Allis, C. D., et al. (2007) · Nature · doi:10.1038/nature05987 · Cited by 1,558 · see citing works

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works

Dynamic Regulation of Nucleosome Positioning in the Human Genome

Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,396 · see citing works

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription

Zilberman, D., Gehring, M. A., Tran, R. K., Ballinger, T. J., & Henikoff, S. (2006) · Nature Genetics · doi:10.1038/ng1929 · Cited by 1,369 · 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

Genome-wide analysis of mammalian promoter architecture and evolution

Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1789 · Cited by 1,350 · see citing works

Epigenetic reprogramming in mammals

Morgan, H. D., Santos, F., Green, K., Dean, W., & Reik, W. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi114 · Cited by 1,344 · see citing works

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

Ko, M., Huang, Y., Jankowska, A. M., Pape, U. J., Tahiliani, M., Bandukwala, H. S., An, J., Lamperti, E. D., Koh, K. P., Ganetzky, R. D., et al. (2010) · Nature · doi:10.1038/nature09586 · Cited by 1,294 · 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

c-Myc Regulates Transcriptional Pause Release

Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279 · see citing works

Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer

Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B. E., et al. (2007) · Nature Genetics · doi:10.1038/ng1950 · Cited by 1,226 · see citing works

Molecular basis of base substitution hotspots in Escherichia coli

Coulondre, C., Miller, J. H., Farabaugh, P. J., & Gilbert, W. (1978) · Nature · doi:10.1038/274775a0 · Cited by 1,193 · see citing works

A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling

Wysocka, J., Swigut, T., Xiao, H., Milne, T. A., Kwon, S. Y., Landry, J., Kauer, M., Tackett, A. J., Chait, B. T., Badenhorst, P. W., et al. (2006) · Nature · doi:10.1038/nature04815 · Cited by 1,186 · see citing works

DNA methylation and the frequency of CpG in animal DNA

Bird, A. P. (1980) · Nucleic Acids Research · doi:10.1093/nar/8.7.1499 · Cited by 1,175 · see citing works

Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark

Ruthenburg, A. J., Allis, C. D., & Wysocka, J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2006.12.014 · Cited by 1,147 · see citing works

Controlling the elongation phase of transcription with P-TEFb

Peterlin, B. M., & Price, D. H. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.014 · Cited by 1,144 · see citing works

Epigenetic stem cell signature in cancer

Widschwendter, M., Fiegl, H., Egle, D., Mueller-Holzner, E., Spizzo, G., Marth, C., Weisenberger, D. J., Campan, M., Young, J., Jacobs, I., et al. (2007) · Nature Genetics · doi:10.1038/ng1941 · Cited by 1,143 · see citing works

A stem cell–like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing

Ohm, J. E., McGarvey, K. M., Yu, X., Cheng, L., Schuebel, K. E., Cope, L., Mohammad, H. P., Chen, W., Daniel, V. C., Yu, W., et al. (2007) · Nature Genetics · doi:10.1038/ng1972 · Cited by 1,130 · see citing works

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Ficz, G., Branco, M. R., Seisenberger, S., Santos, F., Krueger, F., Hore, T. A., Marques, C. J., Andrews, S., & Reik, W. (2011) · Nature · doi:10.1038/nature10008 · Cited by 1,123 · see citing works

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095 · see citing works

The non-coding Air RNA is required for silencing autosomal imprinted genes

Sleutels, F., Zwart, R., & Barlow, D. P. (2002) · Nature · doi:10.1038/415810a · Cited by 1,071 · see citing works

Active DNA demethylation: many roads lead to Rome

Wu, S. C., & Zhang, Y. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2950 · Cited by 1,054 · 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 1,011 · see citing works

Divergent transcription from active promoters

Seila, A. C., Calabrese, J. M., Levine, S., Yeo, G. W., Rahl, P., Flynn, R. A., Young, R., & Sharp, P. (2008) · Science · doi:10.1126/science.1162253 · Cited by 923 · see citing works

CpG islands as gene markers in the human genome

Larsen, F., Gundersen, G., Lopez, R., & Prydz, H. (1992) · Genomics · doi:10.1016/0888-7543(92)90024-m · Cited by 922 · 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

Selective Anchoring of TFIID to Nucleosomes by Trimethylation of Histone H3 Lysine 4

Vermeulen, M., Mulder, K. W., Denissov, S., Pijnappel, W. W. M. P., van Schaik, F. M. A., Varier, R. A., Baltissen, M. P. A., Stunnenberg, H. G., Mann, M., & Timmers, H. T. M. (2007) · Cell · doi:10.1016/j.cell.2007.08.016 · Cited by 883 · see citing works

CpG islands – ‘A rough guide’

Illingworth, R. S., & Bird, A. P. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.04.012 · Cited by 881 · see citing works

Tsix, a gene antisense to Xist at the X-inactivation centre

Lee, J. T., Davidow, L. S., & Warshawsky, D. (1999) · Nature Genetics · doi:10.1038/7734 · Cited by 831 · see citing works

The regulated retrotransposon transcriptome of mammalian cells

Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., Schroder, K., Cloonan, N., Steptoe, A. L., Lassmann, T., et al. (2009) · Nature Genetics · doi:10.1038/ng.368 · Cited by 819 · see citing works

Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF

Li, H., Ilin, S., Wang, W., Duncan, E. M., Wysocka, J., Allis, C. D., & Patel, D. J. (2006) · Nature · doi:10.1038/nature04802 · Cited by 816 · see citing works

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M., Arakawa, T., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2136655100 · Cited by 772 · see citing works

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiationPreprint

Dinger, M. E., Amaral, P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B., Askarian-Amiri, M., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 729 · see citing works

A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA

Bird, A. P., Taggart, M. H., Frommer, M., Miller, O. J., & Macleod, D. (1985) · Cell · doi:10.1016/0092-8674(85)90312-5 · Cited by 714 · see citing works

Spl elements protect a CpG island from de novo methylation

Brandeis, M., Frank, D., Keshet, I., Siegfried, Z., Mendelsohn, M. M., Names, A., Temper, V., Razin, A., & Cedar, H. (1994) · Nature · doi:10.1038/371435a0 · Cited by 705 · see citing works

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T. T., Winther, O., da Piedade, I., Krogh, A., Lenhard, B., & Sandelin, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm955 · Cited by 692 · see citing works

The RNA polymerase II core promoter: a key component in the regulation of gene expressionPreprint

Butler, J. E. F., & Kadonaga, J. T. (2002) · Genes & Development · doi:10.1101/gad.1026202 · Cited by 651 · see citing works

Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells

Stock, J. K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A. G., & Pombo, A. (2007) · Nature Cell Biology · doi:10.1038/ncb1663 · Cited by 650 · see citing works

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

Hargreaves, D. C., Horng, T., & Medzhitov, R. M. (2009) · Cell · doi:10.1016/j.cell.2009.05.047 · Cited by 649 · 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

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

Illingworth, R. S., Kerr, A. R. W., DeSousa, D., Jørgensen, H. F., Ellis, P., Stalker, J., Jackson, D. K., Clee, C. M., Plumb, R. W., Rogers, J., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060022 · Cited by 637 · see citing works

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625 · see citing works

DNA Methylation Is the Primary Silencing Mechanism for a Set of Germ Line- and Tumor-Specific Genes with a CpG-Rich Promoter

Smet, C. D., Lurquin, C., Lethé, B., Martelange, V., & Boon, T. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.11.7327 · Cited by 598 · see citing works

Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island.Preprint

Macleod, D., Charlton, J., Mullins, J. J., & Bird, A. P. (1994) · Genes & Development · doi:10.1101/gad.8.19.2282 · Cited by 596 · see citing works

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cellsPreprint

Wu, H., D’Alessio, A. C., Ito, S., Wang, Z., 崔凯荣, Zhao, K., Sun, Y. E., & Zhang, Y. (2011) · Genes & Development · doi:10.1101/gad.2036011 · Cited by 585 · see citing works

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

Ramirez-Carrozzi, V. R., Braas, D., Bhatt, D. M., Cheng, C. S., Hong, C., Doty, K. R., Black, J. C., Hoffmann, A., Carey, M., & Smale, S. T. (2009) · Cell · doi:10.1016/j.cell.2009.04.020 · Cited by 581 · see citing works

Set2 Is a Nucleosomal Histone H3-Selective Methyltransferase That Mediates Transcriptional Repression

Strahl, B. D., Grant, P. A., Briggs, S. D., Sun, Z., Bone, J. R., Caldwell, J., Mollah, S., Cook, R. G., Shabanowitz, J., Hunt, D. F., et al. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.5.1298-1306.2002 · Cited by 564 · see citing works

Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

Eskeland, R., Leeb, M., Grimes, G. R., Kress, C., Boyle, S., Sproul, D., Gilbert, N., Fan, Y., Skoultchi, A. I., Wutz, A., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.032 · Cited by 553 · see citing works

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

Illingworth, R. S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R. W., James, K. D., Turner, D. J., Smith, C., Harrison, D. J., Andrews, R., & Bird, A. P. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001134 · Cited by 550 · see citing works

X Chromosome Dosage Compensation: How Mammals Keep the Balance

Payer, B., & Lee, J. T. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091711 · Cited by 519 · 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

Synergism of Xist Rna, DNA Methylation, and Histone Hypoacetylation in Maintaining X Chromosome Inactivation

Csankovszki, G., Nagy, A., & Jaenisch, R. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.153.4.773 · Cited by 494 · see citing works

HMG CoA reductase: A negatively regulated gene with unusual promoter and 5′ untranslated regions

Reynolds, G. A., Basu, S. K., Osborne, T. F., Chin, D. J., Gil, G., Brown, M. S., Goldstein, J. L., & Luskey, K. L. (1984) · Cell · doi:10.1016/0092-8674(84)90549-x · Cited by 492 · see citing works

Alternative chromatin structure at CpG islands

Tazi, J. (1990) · Cell · doi:10.1016/0092-8674(90)90339-g · Cited by 482 · 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

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

Bogdanović, O., & Veenstra, G. J. C. (2009) · Chromosoma · doi:10.1007/s00412-009-0221-9 · Cited by 474 · see citing works

Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells

Lorincz, M. C., Dickerson, D. R., Schmitt, M., & Groudine, M. T. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb840 · Cited by 460 · 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 452 · see citing works

Purification of CpG islands using a methylated DNA binding column

Cross, S. H., Charlton, J. A., Nan, X., & Bird, A. P. (1994) · Nature Genetics · doi:10.1038/ng0394-236 · Cited by 442 · see citing works

Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genesPreprint

Mancini‐DiNardo, D., Steele, S. J., Levorse, J. M., Ingram, R. S., & Tilghman, S. M. (2006) · Genes & Development · doi:10.1101/gad.1416906 · Cited by 421 · see citing works

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

Mendenhall, E. M., Koche, R. P., Truong, T. T., Zhou, V. W., Issac, B., Chi, A. S., Ku, M., & Bernstein, B. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001244 · Cited by 412 · 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

Histone H2A Monoubiquitination Represses Transcription by Inhibiting RNA Polymerase II Transcriptional Elongation

Zhou, W., Zhu, P., Wang, J., Pascual, G., Ohgi, K. A., Lozach, J., Glass, C. K., & Rosenfeld, M. G. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.11.002 · Cited by 407 · see citing works

Mechanisms regulating imprinted genes in clusters

Edwards, C. A., & Ferguson‐Smith, A. C. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.013 · Cited by 406 · see citing works

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

Zhang, Y., Jurkowska, R. Z., Soeroes, S., Rajavelu, A., Dhayalan, A., Bock, I., Rathert, P., Brandt, O., Reinhardt, R., Fischle, W., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq147 · Cited by 405 · see citing works

Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters

Shen, L., Kondo, Y., Guo, Y., Zhang, J., Zhang, L., Ahmed, S., Shu, J., Chen, X., Waterland, R. A., & Issa, J. J. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030181 · Cited by 389 · see citing works

Local DNA hypomethylation activates genes in rice endosperm

Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B. R., Brooks, M. D., & Zilberman, D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009695107 · Cited by 385 · see citing works

Silencing chromatin: comparing modes and mechanisms

Beisel, C., & Paro, R. (2011) · Nature reviews genetics · doi:10.1038/nrg2932 · Cited by 378 · see citing works

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

Kanhere, A., Viiri, K. M., Araújo, C. C., Rasaiyaah, J., Bouwman, R. D., Whyte, W. A., Pereira, C., Brookes, E., Walker, K., Bell, G. W., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.019 · Cited by 370 · see citing works

The RNA polymerase II core promoter — the gateway to transcription

Juven-Gershon, T., Hsu, J.-Y., Theisen, J. W., & Kadonaga, J. T. (2008) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.03.003 · Cited by 367 · 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

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

A Region of the Human HOXD Cluster that Confers Polycomb-Group Responsiveness

Woo, C. J., Kharchenko, P. V., Daheron, L. M., Park, P. J., & Kingston, R. E. (2010) · Cell · doi:10.1016/j.cell.2009.12.022 · Cited by 316 · see citing works

CpG Islands Recruit a Histone H3 Lysine 36 Demethylase

Blackledge, N. P., Zhou, J., Tolstorukov, M. Y., Farcas, A. M., Park, P. J., & Klose, R. J. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.04.009 · Cited by 310 · see citing works

Genetics and epigenetics: stability and plasticity during cellular differentiation

Mohn, F., & Schübeler, D. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.005 · Cited by 299 · see citing works

Methylation of genomes and genes at the invertebrate-vertebrate boundary

Tweedie, S., Charlton, J., Clark, V. H., & Bird, A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.3.1469 · Cited by 293 · see citing works

On the nature of human housekeeping genes

Zhu, J., He, F., Hu, S., & Yu, J. M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.08.004 · Cited by 288 · see citing works

In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells.

Stein, R., Razin, A., & Cedar, H. (1982) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.79.11.3418 · Cited by 283 · see citing works

X Inactivation in the Mouse Embryo Deficient for Dnmt1: Distinct Effect of Hypomethylation on Imprinted and Random X Inactivation

Sado, T., Fenner, M. H., Tan, S., Tam, P., Shioda, T., & Li, E. (2000) · Developmental Biology · doi:10.1006/dbio.2000.9823 · Cited by 274 · see citing works

Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

Sequeira‐Mendes, J., Díaz‐Uriarte, R., Apedaile, A., Huntley, D. M., Brockdorff, N., & Gómez, M. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000446 · Cited by 261 · see citing works

CpG methylation is targeted to transcription units in an invertebrate genomePreprint

Suzuki, M. M., Kerr, A. R. W., Sousa, D. D., & Bird, A. P. (2007) · Genome Research · doi:10.1101/gr.6163007 · Cited by 256 · see citing works

Xist has properties of the X-chromosome inactivation centre

Herzing, L. B. K., Romer, J. T., Horn, J. M., & Ashworth, A. (1997) · Nature · doi:10.1038/386272a0 · Cited by 253 · see citing works

Initiation of DNA replication at CpG islands in mammalian chromosomes

Delgado, S., Gómez, M., Bird, A., & Antequera, F. (1998) · The EMBO Journal · doi:10.1093/emboj/17.8.2426 · Cited by 242 · see citing works

CpG islands as genomic footprints of promoters that are associated with replication origins

Antequera, F., & Bird, A. P. (1999) · Current Biology · doi:10.1016/s0960-9822(99)80418-7 · Cited by 224 · see citing works

Maize Genome Sequencing by Methylation Filtration

Palmer, L. E., Rabinowicz, P. D., O'Shaughnessy, A. L., Balija, V. S., Nascimento, L. U., Dike, S., de la Bastide, M., Martienssen, R. A., & McCombie, W. R. (2003) · Science · doi:10.1126/science.1091265 · Cited by 216 · see citing works

ING4 Mediates Crosstalk between Histone H3 K4 Trimethylation and H3 Acetylation to Attenuate Cellular Transformation

Hung, T., Binda, O., Glass, K. C., Kuo, A. J., Johnson, K., Chang, H. Y., Simon, M. D., Kutateladze, T. G., & Gozani, O. (2009) · Molecular Cell · doi:10.1016/j.molcel.2008.12.016 · Cited by 201 · see citing works

Methylated and unmethylated DNA compartments in the sea urchin genome

Bird, A. P., Taggart, M. H., & Smith, B. A. (1979) · Cell · doi:10.1016/0092-8674(79)90329-5 · Cited by 196 · see citing works

Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing

Ruike, Y., Imanaka, Y., Sato, F., Shimizu, K., & Tsujimoto, G. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-137 · Cited by 195 · see citing works

Cloning of a Mammalian Transcriptional Activator That Binds Unmethylated CpG Motifs and Shares a CXXC Domain with DNA Methyltransferase, Human Trithorax, and Methyl-CpG Binding Domain Protein 1

Voo, K. S., Carlone, D. L., Jacobsen, B. M., Flodin, A., & Skalnik, D. G. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.6.2108-2121.2000 · Cited by 194 · see citing works

HBO1 HAT Complexes Target Chromatin throughout Gene Coding Regions via Multiple PHD Finger Interactions with Histone H3 Tail

Saksouk, N., Avvakumov, N., Glass, K. C., Hung, T., Doyon, Y., Cayrou, C., Paquet, É. R., Ullah, M., Landry, A.-J., Côté, V., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.007 · Cited by 182 · see citing works

Chromatin, transcript elongation and alternative splicing

Kornblihtt, A. R. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0106-5 · Cited by 173 · see citing works

CpG island chromatin

Blackledge, N. P., & Klose, R. J. (2011) · Epigenetics · doi:10.4161/epi.6.2.13640 · Cited by 163 · see citing works

Polycomb preferentially targets stalled promoters of coding and noncoding transcriptsPreprint

Enderle, D., Beisel, C., Stadler, M. B., Gerstung, M., Athri, P., & Paro, R. (2010) · Genome Research · doi:10.1101/gr.114348.110 · Cited by 156 · see citing works

Roles for Ctk1 and Spt6 in Regulating the Different Methylation States of Histone H3 Lysine 36

Youdell, M., Kizer, K. O., Kisseleva-Romanova, E., Fuchs, S. M., Duro, E., Strahl, B. D., & Mellor, J. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00001-08 · Cited by 154 · see citing works

Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription

Li, B., Jackson, J., Simon, M. D., Fleharty, B., Gogol, M., Seidel, C. W., Workman, J. L., & Shilatifard, A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m808220200 · Cited by 153 · see citing works

Modifications of RNA polymerase II are pivotal in regulating gene expression states

Brookes, E., & Pombo, A. (2009) · EMBO Reports · doi:10.1038/embor.2009.221 · Cited by 152 · see citing works

Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3

van Ingen, H., van Schaik, F. M. A., Wienk, H., Ballering, J., Rehmann, H., Dechesne, A. C., Kruijzer, J. A. W., Liskamp, R. M. J., Timmers, H. T. M., & Boelens, R. (2008) · Structure · doi:10.1016/j.str.2008.04.015 · Cited by 148 · see citing works

Unmethylated CpG islands associated with genes in higher plant DNA

Antequera, F., & Bird, A. P. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb03072.x · Cited by 142 · see citing works

The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islandsPreprint

Takeshima, H., Yamashita, S., Shimazu, T., Niwa, T., & Ushijima, T. (2009) · Genome Research · doi:10.1101/gr.093310.109 · Cited by 135 · see citing works

Global, comparative analysis of tissue-specific promoter CpG methylation

Schilling, E., & Rehli, M. (2007) · Genomics · doi:10.1016/j.ygeno.2007.04.011 · Cited by 134 · see citing works

A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer

Mancini‐DiNardo, D. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg024 · Cited by 131 · see citing works

Contrasting chromatin organization of CpG islands and exons in the human genome

Choi, J. K. (2010) · Genome biology · doi:10.1186/gb-2010-11-7-r70 · Cited by 126 · see citing works

General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells

Gebhard, C., Benner, C. W., Ehrich, M., Schwarzfischer, L., Schilling, E., Klug, M., Dietmaier, W., Thiede, C., Holler, E., Andreesen, R., et al. (2010) · Cancer Research · doi:10.1158/0008-5472.can-09-3406 · Cited by 123 · see citing works

Sequence features that drive human promoter function and tissue specificity.Preprint

Landolin, J., Johnson, D. S., Trinklein, N., Aldred, S. F., Medina, C., Shulha, H., Weng, Z., & Myers, R. (2010) · Genome Research · doi:10.1101/gr.100370.109 · Cited by 114 · see citing works

An Alternative Promoter in the Mouse Major Histocompatibility Complex Class II I-Aβ Gene: Implications for the Origin of CpG Islands

Macleod, D., Ali, R., & Bird, A. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.8.4433 · Cited by 80 · see citing works

Lessons from comparative analysis of X-chromosome inactivation in mammals

Okamoto, I., & Heard, É. (2009) · Chromosome Research · doi:10.1007/s10577-009-9057-7 · Cited by 69 · see citing works

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

Rozenberg, J. M., Shlyakhtenko, A., Glass, K., Rishi, V., Myakishev, M. V., FitzGerald, P. C., & Vinson, C. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-67 · Cited by 62 · see citing works

The JARID2–PRC2 duality: Figure 1.Preprint

Herz, H., & Shilatifard, A. (2010) · Genes & Development · doi:10.1101/gad.1921610 · Cited by 62 · see citing works

Transcription of tissue-specific genes in human preimplantation embryos

Daniels, R., Lowell, S., Bolton, V. N., et al. (1997) · Human Reproduction · doi:10.1093/humrep/12.10.2251 · Cited by 46 · see citing works

Species‐specific organization of CpG island promoters at mammalian homologous genes

Cuadrado, M., Sacristán, M. P., & Antequera, F. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve131 · Cited by 45 · see citing works

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

Jaeger, S. A., Chan, E. T., Berger, M. F., Stottmann, R. W., Hughes, T. R., & Bulyk, M. L. (2010) · Genomics · doi:10.1016/j.ygeno.2010.01.002 · Cited by 42 · see citing works

Transcripts and CpG islands associated with the pro-opiomelanocortin gene and other neurally expressed genes

Gardiner‐Garden, M., & Frommer, M. (1994) · Journal of Molecular Endocrinology · doi:10.1677/jme.0.0120365 · Cited by 42 · see citing works

DNA methylation: roles in mammalian development

Smith, Z. D., & Meissner, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3354 · Cited by 3,045 · see citing works

Transcriptional regulation of macrophage polarization: enabling diversity with identity

Lawrence, T., & Natoli, G. (2011) · Nature Reviews Immunology · doi:10.1038/nri3088 · Cited by 2,284 · 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

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

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

Nuñez, J. K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q., Hung, K. L., Samelson, A. J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.025 · Cited by 760 · see citing works

Intergenerational transmission of trauma effects: putative role of epigenetic mechanisms

Yehuda, R., & Lehrner, A. (2018) · World Psychiatry · doi:10.1002/wps.20568 · Cited by 730 · see citing works

Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion

Yu, Y.-R., Imrichova, H., Wang, H., Chao, T., Xiao, Z., Gao, M., Rincon-Restrepo, M., Franco, F., Genolet, R., Cheng, W.-C., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0793-3 · Cited by 593 · see citing works

EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas

Mohammad, F., Weissmann, S., Leblanc, B., Pandey, D. P., Højfeldt, J. W., Comet, I., Zheng, C., Johansen, J. V., Rapin, N., Porse, B. T., et al. (2017) · Nature Medicine · doi:10.1038/nm.4293 · Cited by 535 · see citing works

Origin and differentiation of human memory CD8 T cells after vaccination

Akondy, R. S., Fitch, M., Edupuganti, S., Yang, S., Kissick, H. T., Li, K. W., Youngblood, B. A., Abdelsamed, H. A., McGuire, D. J., Cohen, K. W., et al. (2017) · Nature · doi:10.1038/nature24633 · Cited by 517 · 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

MYC: Connecting selective transcriptional control to global RNA production

Kress, T. R., Sabò, A., & Amati, B. (2015) · Nature reviews. Cancer · doi:10.1038/nrc3984 · Cited by 521 · see citing works

Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing

Amabile, A., Migliara, A., Capasso, P., Biffi, M., Cittaro, D., Naldini, L., & Lombardo, A. (2016) · Cell · doi:10.1016/j.cell.2016.09.006 · Cited by 516 · see citing works

Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging

Beerman, I., Bock, C., Garrison, B. S., Smith, Z. D., Gu, H., Meissner, A., & Rossi, D. J. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.01.017 · Cited by 485 · see citing works

Gene regulation in the immediate-early response process

Bahrami, S., & Drabløs, F. (2016) · Advances in Biological Regulation · doi:10.1016/j.jbior.2016.05.001 · Cited by 465 · see citing works

Genetics and epigenetics in obesity

Rohde, K., Keller, M., la Cour Poulsen, L., Blüher, M., Kovacs, P., & Böttcher, Y. (2019) · Metabolism · doi:10.1016/j.metabol.2018.10.007 · Cited by 355 · 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

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

The molecular basis of the memory T cell response: differential gene expression and its epigenetic regulation

Weng, N.-P., Araki, Y., & Subedi, K. (2012) · Nature Reviews Immunology · doi:10.1038/nri3173 · Cited by 290 · 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

An epigenetic framework for neurodevelopmental disorders: From pathogenesis to potential therapy

Millan, M. J. (2013) · Neuropharmacology · doi:10.1016/j.neuropharm.2012.11.015 · Cited by 229 · see citing works

The pleiotropic neuroprotective effects of resveratrol in cognitive decline and Alzheimer’s disease pathology: From antioxidant to epigenetic therapy

Griñán-Ferré, C., Bellver-Sanchis, A., Izquierdo, V., Corpas, R., Roig-Soriano, J., Chillón, M., Andres-Lacueva, C., Somogyvári, M., Sőti, C., Sanfeliu, C., et al. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101271 · Cited by 208 · see citing works

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

Smith, Z. D., Shi, J., Gu, H., Donaghey, J., Clement, K., Cacchiarelli, D., Gnirke, A., Michor, F., & Meissner, A. (2017) · Nature · doi:10.1038/nature23891 · Cited by 201 · see citing works

Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets

Dayeh, T. A., Olsson, A. H., Volkov, P., Almgren, P., Rönn, T., & Ling, C. (2013) · Diabetologia · doi:10.1007/s00125-012-2815-7 · Cited by 199 · see citing works

DNA methylation in social insects: how epigenetics can control behavior and longevity

Yan, H., Bonasio, R., Simola, D. F., Liebig, J., Berger, S. L., & Reinberg, D. (2015) · Annual Review of Entomology · doi:10.1146/annurev-ento-010814-020803 · Cited by 183 · see citing works

Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities

Galkin, F., Mamoshina, P., Aliper, A., de Magalhães, J. P., Gladyshev, V. N., & Zhavoronkov, A. (2020) · Ageing Research Reviews · doi:10.1016/j.arr.2020.101050 · Cited by 189 · see citing works

Single-cell DNA methylation profiling: technologies and biological applications

Karemaker, I. D., & Vermeulen, M. (2018) · Trends in Biotechnology · doi:10.1016/j.tibtech.2018.04.002 · Cited by 170 · see citing works

Metabolic Inputs into the Epigenome

Sharma, U., & Rando, O. J. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.02.003 · Cited by 167 · see citing works

Nuclear Tau and Its Potential Role in Alzheimer’s Disease

Bukar Maina, M., Al-Hilaly, Y., & Serpell, L. (2016) · Biomolecules · doi:10.3390/biom6010009 · Cited by 161 · see citing works

Epigenetic Modification of Mitochondrial DNA in the Development of Diabetic Retinopathy

Mishra, M., & Kowluru, R. A. (2015) · Investigative Opthalmology & Visual Science · doi:10.1167/iovs.15-16937 · Cited by 159 · see citing works

Epigenetic dysregulation of SHANK3 in brain tissues from individuals with autism spectrum disorders

Zhu, L., Wang, X., Li, X.-L., Towers, A., Cao, X., Wang, P., Bowman, R., Yang, H., Goldstein, J., Li, Y.-J., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddt547 · Cited by 147 · see citing works

Tracing dynamic changes of DNA methylation at single cell resolution

Stelzer, Y., Shivalila, C. S., Soldner, F., Markoulaki, S., & Jaenisch, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.046 · Cited by 141 · see citing works

Widespread DNA hypomethylation and differential gene expression in Turner syndrome

Trolle, C., Nielsen, M. M., Skakkebæk, A., Lamy, P., Vang, S., Hedegaard, J., Nordentoft, I., Ørntoft, T. F., Pedersen, J. S., & Gravholt, C. H. (2016) · Scientific Reports · doi:10.1038/srep34220 · Cited by 149 · see citing works

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

Ngan, C. Y., Wong, C. H., Tjong, H., Wang, W., Goldfeder, R. L., Choi, C., He, H., Gong, L., Lin, J., Urban, B., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0581-x · Cited by 140 · see citing works

<i>Dnmt3a</i> restrains mast cell inflammatory responses

Leoni, C., Montagner, S., Rinaldi, A., Bertoni, F., Polletti, S., Balestrieri, C., & Monticelli, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616420114 · Cited by 138 · see citing works

Lead (Pb) and neurodevelopment: A review on exposure and biomarkers of effect (BDNF, HDL) and susceptibility

Gundacker, C., Forsthuber, M., Szigeti, T., Kakucs, R., Mustieles, V., Fernandez, M. F., Bengtsen, E., Vogel, U., Hougaard, K. S., & Saber, A. T. (2021) · International Journal of Hygiene and Environmental Health · doi:10.1016/j.ijheh.2021.113855 · Cited by 135 · see citing works

DNA methylation: Insights into human evolution

Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J., & Marques-Bonet, T. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005661 · Cited by 128 · see citing works

Artificial light at night: melatonin as a mediator between the environment and epigenome

Haim, A., & Zubidat, A. E. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0121 · Cited by 133 · see citing works

Identification of a CpG Island Methylator Phenotype in Adrenocortical Carcinomas

Barreau, O., Assié, G., Wilmot-Roussel, H., Ragazzon, B., Baudry, C., Perlemoine, K., René-Corail, F., Bertagna, X., Dousset, B., Hamzaoui, N., et al. (2013) · The Journal of Clinical Endocrinology &amp; Metabolism · doi:10.1210/jc.2012-2993 · Cited by 132 · see citing works

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

Kozlenkov, A., Li, J., Apontes, P., Hurd, Y. L., Byne, W. M., Koonin, E. V., Wegner, M., Mukamel, E. A., & Dracheva, S. (2018) · Science Advances · doi:10.1126/sciadv.aau6190 · Cited by 103 · see citing works

Childhood adversity and epigenetic regulation of glucocorticoid signaling genes: Associations in children and adults

Tyrka, A. R., Ridout, K. K., & Parade, S. H. (2016) · Development and Psychopathology · doi:10.1017/s0954579416000870 · Cited by 119 · see citing works

The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes

Gabriele, M., Lopez Tobon, A., D'Agostino, G., & Testa, G. (2018) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2017.12.013 · Cited by 103 · see citing works

Genetics and epigenetics of atopic dermatitis: an updated systematic review

Martin, M. J., Estravís, M., García-Sánchez, A., Dávila, I., Isidoro-García, M., & Sanz, C. (2020) · Genes · doi:10.3390/genes11040442 · Cited by 99 · see citing works

Differential Methylation of the Oxytocin Receptor Gene in Patients with Anorexia Nervosa: A Pilot Study

Kim, Y.-R., Kim, J.-H., Kim, M. J., & Treasure, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088673 · Cited by 97 · see citing works

Epigenetics, Development, and Psychopathology

O'Donnell, K. J., & Meaney, M. J. (2020) · Annual Review of Clinical Psychology · doi:10.1146/annurev-clinpsy-050718-095530 · Cited by 94 · see citing works

Short-term gain, long-term pain: the senescence life cycle and cancer

Chan, A. S. L., & Narita, M. (2019) · Genes &amp; Development · doi:10.1101/gad.320937.118 · Cited by 80 · see citing works

Molecular basis for chromatin binding and regulation of MLL5

Ali, M., Rincón-Arano, H., Zhao, W., Rothbart, S. B., Tong, Q., Parkhurst, S. M., Strahl, B. D., Deng, L.-W., Groudine, M., & Kutateladze, T. G. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310156110 · Cited by 84 · see citing works

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

Krebs, A. R., Dessus-Babus, S., Burger, L., & Schübeler, D. (2014) · eLife · doi:10.7554/elife.04094 · Cited by 81 · see citing works

Epigenetic mechanisms in irritable bowel syndrome

Mahurkar-Joshi, S., & Chang, L. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.00805 · Cited by 59 · see citing works

VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system

So, J., Mabe, N. W., Englinger, B., Chow, K.-H., Moyer, S. M., Yerrum, S., Trissal, M. C., Marques, J. G., Kwon, J. J., Shim, B., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.158755 · Cited by 45 · see citing works

DNA methylation in epigenetic inheritance of metabolic diseases through the male germ line

Illum, L. R. H., Bak, S. T., Lund, S., & Nielsen, A. L. (2018) · Journal of Molecular Endocrinology · doi:10.1530/jme-17-0189 · Cited by 51 · see citing works

Analyzing Circulating Tumor Cells One at a Time

Ortiz, V., & Yu, M. (2018) · Trends in Cell Biology · doi:10.1016/j.tcb.2018.05.004 · Cited by 48 · see citing works

A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue

van den Oord, E. J. C. G., Clark, S. L., Xie, L. Y., Shabalin, A. A., Dozmorov, M. G., Kumar, G., Swedish Schizophrenia Consortium, Vladimirov, V. I., Magnusson, P. K. E., & Aberg, K. A. (2016) · Schizophrenia Bulletin · doi:10.1093/schbul/sbv182 · Cited by 47 · see citing works

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

Ford, E., Grimmer, M. R., Stolzenburg, S., Bogdanovic, O., Mendoza, A. D., Farnham, P. J., Blancafort, P., & Lister, R. (2017) · doi:10.1101/170506 · Cited by 45 · see citing works

Mammalian cells acquire epigenetic hallmarks of human cancer during immortalization

Tommasi, S., Zheng, A., Weninger, A., Bates, S. E., Li, X. A., Wu, X., Hollstein, M., & Besaratinia, A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1051 · Cited by 45 · see citing works

Do short, frequent DNA sequence motifs mould the epigenome

Quante, T., & Bird, A. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.31 · Cited by 40 · see citing works

Nitric oxide controls shoot meristem activity via regulation of DNA methylation

Zeng, J., Zhao, X., Liang, Z., Hidalgo, I., Gebert, M., Fan, P., Wenzl, C., Gornik, S. G., & Lohmann, J. U. (2023) · Nature Communications · doi:10.1038/s41467-023-43705-1 · Cited by 36 · see citing works

Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes

Ehrlich, K. C., Baribault, C., & Ehrlich, M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218394 · Cited by 35 · see citing works

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

Laan, L., Klar, J., Sobol, M., Hoeber, J., Shahsavani, M., Kele, M., Fatima, A., Zakaria, M., Annerén, G., Falk, A., et al. (2020) · Clinical Epigenetics · doi:10.1186/s13148-019-0803-1 · Cited by 33 · see citing works

Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

Ridinger-Saison, M., Boeva, V., Rimmelé, P., Kulakovskiy, I., Gallais, I., Levavasseur, B., Paccard, C., Legoix-Né, P., Morlé, F., Nicolas, A., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks659 · Cited by 28 · see citing works

Demethylation of ITGAV accelerates osteogenic differentiation in a blast-induced heterotopic ossification in vitro cell culture model

Logan, N. J., Camman, M., Williams, G., & Higgins, C. A. (2018) · Bone · doi:10.1016/j.bone.2018.09.008 · Cited by 21 · see citing works

Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif

Ru, W., Koga, T., Wang, X., Guo, Q., Gearhart, M. D., Zhao, S., Murphy, M., Kawakami, H., Corcoran, D., Zhang, J., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102607 · Cited by 20 · see citing works

Histone methyltransferase KMT2A: developmental regulation to oncogenic transformation

Ogino, J., & Dou, Y. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107791 · Cited by 21 · see citing works

Effects of Cellular Methylation on Transgene Expression and Site-Specific Integration of Adeno-Associated Virus

Chanda, D., Hensel, J., Higgs, J., Grover, R., Kaza, N., & Ponnazhagan, S. (2017) · Genes · doi:10.3390/genes8090232 · Cited by 19 · see citing works

Sp1-activated FGFR2 is involved in early-life exposure to nickel-induced craniosynostosis by regulating the ERK1/2 signaling pathway

Weng, Z., Xu, C., Chen, X., Yan, Q., Fu, Z., Jiao, J., Xu, J., Liu, Q., Wang, D., Liang, J., et al. (2024) · Environment International · doi:10.1016/j.envint.2024.108477 · Cited by 5 · see citing works

DNA sequence and structural properties as predictors of human and mouse promoters

Akan, P., & Deloukas, P. (2007) · Gene · doi:10.1016/j.gene.2007.12.011 · Cited by 47 · see citing works

CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A., & Vingron, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp682 · Cited by 48 · see citing works

Profiling ascidian promoters as the primordial type of vertebrate promoter

Okamura, K., Yamashita, R., Takimoto, N., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s3-s7 · Cited by 14 · see citing works

Functional Analysis of Promoter CPG-Methylation using a CpG-Free Luciferase Reporter Vector

Klug, M., & Rehli, M. (2006) · Epigenetics · doi:10.4161/epi.1.3.3327 · Cited by 249 · see citing works

Methylation of CpG dinucleotides in the open reading frame of a testicular germ cell-specific intronless gene, Tact1/Actl7b, represses its expression in somatic cells

Hisano, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg670 · Cited by 55 · see citing works