The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Human body epigenome maps reveal noncanonical DNA methylation variation
Open accessAbstract
As part of the Epigenome Roadmap Project, genome-wide maps of DNA methylation and transcriptomes together with genomic DNA sequencing of 18 different primary human tissue types from 4 individuals are presented; analysis reveals widespread differential methylation of CG sites between tissues, and the presence of non-CG methylation in adult tissues. As part of the Epigenome Roadmap project, Joseph Ecker and colleagues provide genome-wide maps of DNA methylation and transcriptomes, in conjunction with genomic DNA sequencing, of 18 different primary human tissue types from four individuals. Analysis of the datasets reveals widespread differential methylation of CG sites between tissues, and methylation at regulatory elements generally has a negative correlation with gene expression as expected. A surprising amount of non-CG methylation is found in a subpopulation of cells in many tissues. Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual’s cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns1,2. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals’ phased genome3, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Intragenic DMRs that stretch for kilobases (large-DMRs) can overlap with tissue defining “signature genes” as well as with predicted super-enhancers, which are clusters of enhancers that function cooperatively (4, 10, 11).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [4]
In the citing paper
“These dynamically methylated CpGs cluster into over 1 million tissue specific differentially methylated regions (DMRs).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [4]
In the citing paper
“direct comparison of whole genome methylome profiles derived from numerous cell types has revealed that under normal physiological conditions 15%-21% of CpGs vary in methylation status between human tissues (4, 5).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [4]
In the citing paper
“These tissue-type specific DMRs are defined by both lineage specific gain and loss of 5mC during embryogenesis.”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [4]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673
Self-citationGREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662
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
X-inactivation profile reveals extensive variability in X-linked gene expression in females
Carrel, L., & Willard, H. F. (2005) · Nature · doi:10.1038/nature03479 · Cited by 2,097
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
Self-citationConserved 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
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
Lister, R., Pelizzola, M., Kida, Y. S., Hawkins, R. D., Nery, J. R., Hon, G. C., Antosiewicz‐Bourget, J., O’Malley, R. C., Castanon, R., Klugman, S. A., et al. (2011) · Nature · doi:10.1038/nature09798 · Cited by 1,595
Self-citationCharting 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
Cited by
Sorted by citations
The diverse roles of DNA methylation in mammalian development and disease
Greenberg, M., & Bourc’his, D. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0159-6 · Cited by 2,272
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
“DMRs upstream of mouse MyoD gene were defined based on human/mouse genome homology (Schultz et al., 2015).”
Landscape of X chromosome inactivation across human tissues
GTEx Consortium, Tukiainen, T., Villani, A.-C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., Aguirre, M., Gauthier, L., Fleharty, M., et al. (2017) · Nature · doi:10.1038/nature24265 · Cited by 1,138
DNA methylation aging clocks: challenges and recommendations
Bell, C. G., Lowe, R., Adams, P. D., Baccarelli, A. A., Beck, S., Bell, J. T., Christensen, B. C., Gladyshev, V. N., Heijmans, B. T., Horvath, S., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1824-y · Cited by 1,025
Zhou, W., Laird, P. W., & Shen, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw967 · Cited by 742
Mapping genome-wide transcription-factor binding sites using DAP-seq
Bartlett, A., O’Malley, R. C., Huang, S. C., Galli, M., Nery, J. R., Gallavotti, A., & Ecker, J. R. (2017) · Nature Protocols · doi:10.1038/nprot.2017.055 · Cited by 721
Self-citationEpigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
Kawakatsu, T., Huang, S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R., Nery, J. R., Barragan, C., He, Y., et al. (2016) · Cell · doi:10.1016/j.cell.2016.06.044 · Cited by 706
Self-citationThe impact of sex on gene expression across human tissues
Oliva, M., Muñoz-Aguirre, M., Kim-Hellmuth, S., Wucher, V., Gewirtz, A. D., Cotter, D. J., Parsana, P., Kasela, S., Balliu, B., Viñuela, A., et al. (2020) · Science · doi:10.1126/science.aba3066 · Cited by 697
Self-citationDynamic 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
Self-citationTranscription 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
Widespread natural variation of DNA methylation within angiosperms
Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M., Kim, K. D., Li, Q., Rohr, N. A., Rambani, A., Burke, J. M., Udall, J. A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1059-0 · Cited by 557
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Luo, C., Keown, C. L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J. R., Sandoval, J. P., et al. (2017) · Science · doi:10.1126/science.aan3351 · Cited by 545
Self-citationGuo, S., Diep, D. H., Plongthongkum, N., Fung, H.-L., Zhang, K., & Zhang, K. (2017) · Nature Genetics · doi:10.1038/ng.3805 · Cited by 528
Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene
Liu, X. S., Wu, H., Krzisch, M., Wu, X., Graef, J. D., Muffat, J., Hnisz, D., Li, C. H., Yuan, B., Xu, C., et al. (2018) · Cell · doi:10.1016/j.cell.2018.01.012 · Cited by 520
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
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature · doi:10.1038/s41586-021-03500-8 · Cited by 398
Self-citationUsing DNA methylation profiling to evaluate biological age and longevity interventions
Petkovich, D. A., Podolskiy, D. I., Lobanov, A. V., Lee, S.-G., Miller, R. A., & Gladyshev, V. N. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.03.016 · Cited by 398
Widespread long-range cis-regulatory elements in the maize genome
Ricci, W. A., Lu, Z., Ji, L., Marand, A. P., Ethridge, C. L., Murphy, N. G., Noshay, J. M., Galli, M., Mejía‐Guerra, M. K., Colomé‐Tatché, M., et al. (2019) · Nature Plants · doi:10.1038/s41477-019-0547-0 · Cited by 383
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
Self-citationEvolution of DNA Methylation across Insects
Bewick, A. J., Vogel, K. J., Moore, A. J., & Schmitz, R. J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw264 · Cited by 364
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Lee, D.-S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J. R., Fitzpatrick, C., O’Connor, C., Dixon, J. R., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0547-z · Cited by 340
Self-citationWidespread adenine N6-methylation of active genes in fungi
Mondo, S. J., Dannebaum, R., Kuo, R. C., Louie, K., Bewick, A. J., LaButti, K. M., Haridas, S., Kuo, A., Salamov, A. A., Ahrendt, S. R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3859 · Cited by 345
On the origin and evolutionary consequences of gene body DNA methylation
Bewick, A. J., Ji, L., Niederhuth, C. E., Willing, E., Hofmeister, B. T., Shi, X., Wang, L., Lu, Z., Rohr, N. A., Hartwig, B., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604666113 · Cited by 322
Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues
Liu, J., Li, K., Cai, J., Zhang, M., Zhang, X., Xiong, X., Meng, H., Xu, X., Huang, Z., Peng, J., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.032 · Cited by 291
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
DNA methylation atlas of the mouse brain at single-cell resolution
Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2021) · Nature · doi:10.1038/s41586-020-03182-8 · Cited by 289
Self-citationXu, L., Liu, Y., Sun, Y., Wang, B., Xiong, Y., Lin, W., Wei, Q., Wang, H., He, W., Wang, B., et al. (2017) · Stem Cell Research & Therapy · doi:10.1186/s13287-017-0716-x · Cited by 284
The how and why of lncRNA function: An innate immune perspective
Robinson, E. K., Covarrubias, S., & Carpenter, S. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.194419 · Cited by 282
Dynamic DNA methylation reconfiguration during seed development and germination
Kawakatsu, T., Nery, J. R., Castanon, R., & Ecker, J. R. (2017) · Genome biology · doi:10.1186/s13059-017-1251-x · Cited by 274
Self-citationBiological 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
Non-CG Methylation in the Human Genome
He, Y., & Ecker, J. R. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025437 · Cited by 280
Self-citationEcker, J. R., Geschwind, D. H., Kriegstein, A. R., Ngai, J., Osten, P., Polioudakis, D., Regev, A., Šestan, N., Wickersham, I. R., & Zeng, H. (2017) · Neuron · doi:10.1016/j.neuron.2017.10.007 · Cited by 258
Self-citationDerivation of consensus inactivation status for X-linked genes from genome-wide studies
Balaton, B. P., Cotton, A. M., & Brown, C. J. (2015) · Biology of Sex Differences · doi:10.1186/s13293-015-0053-7 · Cited by 257
Gilsbach, R., Schwaderer, M., Preißl, S., Grüning, B. A., Kranzhöfer, D., Schneider, P., Nührenberg, T. G., Mulero‐Navarro, S., Weichenhan, D., Braun, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02762-z · Cited by 251
Yuan, M., Yang, B., Rothschild, G., Mann, J. J., Sanford, L. D., Tang, X., Huang, C., Wang, C., & Zhang, W. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01519-z · Cited by 246
“46 DNA methyltransferases (DNMTs) include DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMTL (Fig.”
BackgroundX-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation
Galupa, R., & Heard, É. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024611 · Cited by 257
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Sabbagh, M. F., Heng, J. S., Luo, C., Castanon, R. G., Nery, J. R., Rattner, A., Goff, L. A., Ecker, J. R., & Nathans, J. (2018) · eLife · doi:10.7554/elife.36187 · Cited by 245
Self-citationActive DNA demethylation at enhancers during the vertebrate phylotypic period
Bogdanović, O., Smits, A. H., de la Calle‐Mustienes, E., Tena, J. J., Ford, E., Williams, R. M., Senanayake, U., Schultz, M. D., Hontelez, S., van Kruijsbergen, I., et al. (2016) · Nature Genetics · doi:10.1038/ng.3522 · Cited by 236
Self-citationOverlooked 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
Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer
Zhang, H., Pandey, S., Travers, M. E., Sun, H., Morton, G. C., Madžo, J., Chung, W., Khowsathit, J., Pérez, Ó. C., Barrero, C. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.051 · Cited by 223
Subtype-specific 3D genome alteration in acute myeloid leukaemia
Xu, J., Song, F., Lyu, H., Kobayashi, M., Zhang, B., Zhao, Z., Hou, Y., Wang, X., Luan, Y., Jia, B., et al. (2022) · Nature · doi:10.1038/s41586-022-05365-x · Cited by 208
Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm
Jeltsch, A., & Jurkowska, R. Z. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw723 · Cited by 219
Guo, W., Zhu, P., Pellegrini, M., Zhang, M. Q., Wang, X., & Ni, Z. (2018) · Bioinformatics · doi:10.1093/bioinformatics/btx595 · Cited by 198
Unique cell-type-specific patterns of DNA methylation in the root meristem
Kawakatsu, T., Stuart, T., Valdes, M., Breakfield, N. W., Schmitz, R. J., Nery, J. R., Urich, M. A., Han, X., Lister, R., Benfey, P. N., et al. (2016) · Nature Plants · doi:10.1038/nplants.2016.58 · Cited by 201
Self-citationOliva, M., Demanelis, K., Lu, Y., Chernoff, M., Jasmine, F., Ahsan, H., Kibriya, M. G., Chen, L., & Pierce, B. L. (2022) · Nature Genetics · doi:10.1038/s41588-022-01248-z · Cited by 202
Korthauer, K. D., Chakraborty, S., Benjamini, Y., & Irizarry, R. A. (2018) · Biostatistics · doi:10.1093/biostatistics/kxy007 · Cited by 192
Wang, J., Zibetti, C., Shang, P., Sripathi, S. R., Zhang, P., Cano, M., Hoang, T., Xia, S., Ji, H., Merbs, S. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03856-y · Cited by 185
Dynamic genome evolution in a model fern
Marchant, D. B., Chen, G. J., Cai, S., Chen, F., Schafran, P., Jenkins, J. W., Shu, S., Plott, C., Webber, J., Lovell, J. T., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01226-7 · Cited by 180
DNA Methylation Signatures of the Plant Chromomethyltransferases
Gouil, Q. A., & Baulcombe, D. C. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006526 · Cited by 184
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
Bewick, A. J., Niederhuth, C. E., Ji, L., Rohr, N. A., Griffin, P. T., Leebens‐Mack, J., & Schmitz, R. J. (2017) · Genome biology · doi:10.1186/s13059-017-1195-1 · Cited by 177
The environment, epigenome, and asthma
Yang, I. V., Lozupone, C., & Schwartz, D. A. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.05.011 · Cited by 177
Escape Artists of the X Chromosome
Balaton, B. P., & Brown, C. J. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.03.007 · Cited by 173
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
Luo, C., Liu, H., Xie, F., Armand, E. J., Siletti, K., Bakken, T. E., Fang, R., Doyle, W. I., Stuart, T., Hodge, R. D., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100107 · Cited by 173
Self-citationThe landscape of DNA methylation amid a perfect storm of autism aetiologies
Ciernia, A. V., & LaSalle, J. M. (2016) · Nature reviews. Neuroscience · doi:10.1038/nrn.2016.41 · Cited by 168
Vulnerability of primitive human placental trophoblast to Zika virus
Sheridan, M. A., Yunusov, D., Balaraman, V., Alexenko, A. P., Yabe, S., Verjovski‐Almeida, S., Schust, D. J., Franz, A. W. E., Sadovsky, Y., Ezashi, T., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616097114 · Cited by 164
Spatiotemporal DNA methylome dynamics of the developing mouse fetus
He, Y., Hariharan, M., Gorkin, D. U., Dickel, D. E., Luo, C., Castanon, R., Nery, J. R., Lee, A. Y., Zhao, Y., Huang, H., et al. (2020) · Nature · doi:10.1038/s41586-020-2119-x · Cited by 165
Self-citationEpigenetic drug discovery: breaking through the immune barrier
Tough, D. F., Tak, P. P., Tarakhovsky, A., & Prinjha, R. K. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.185 · Cited by 163
Epigenomic landscapes of retinal rods and cones
Mo, A., Luo, C., Davis, F. P., Mukamel, E. A., Henry, G. L., Nery, J. R., Urich, M. A., Picard, S., Lister, R., Eddy, S. R., et al. (2016) · eLife · doi:10.7554/elife.11613 · Cited by 159
Self-citationLocus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family
Zhou, M., Palanca, A. M. S., & Law, J. A. (2018) · Nature Genetics · doi:10.1038/s41588-018-0115-y · Cited by 157
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS
Luisier, R., Tyzack, G. E., Hall, C. E., Mitchell, J. S., Devine, H. E., Taha, D. M., Malik, B. A., Meyer, I., Greensmith, L., Newcombe, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04373-8 · Cited by 164
McEwen, L. M., Jones, M. J., Lin, D. T. S., Edgar, R. D., Husquin, L. T., MacIsaac, J. L., Ramadori, K. E., Morin, A. M., Rider, C. F., Carlsten, C., et al. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0556-2 · Cited by 147
Single-cell DNA methylation and 3D genome architecture in the human brain
Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R. G., Kenworthy, M., Altshul, J., Valadon, C., Aldridge, A., et al. (2023) · Science · doi:10.1126/science.adf5357 · Cited by 154
Self-citationFirefly genomes illuminate parallel origins of bioluminescence in beetles
Fallon, T. R., Lower, S. E., Chang, C.-H., Bessho‐Uehara, M., Martin, G. J., Bewick, A. J., Behringer, M. G., Debat, H., Wong, I., Day, J. C., et al. (2018) · eLife · doi:10.7554/elife.36495 · Cited by 153
DNA methylation at the crossroads of gene and environment interactions
Law, P. P., & Holland, M. L. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190031 · Cited by 154
Gothe, H. J., Bouwman, B. A. M., Gusmao, E. G., Piccinno, R., Petrosino, G., Sayols, S., Drechsel, O., Minneker, V., Josipović, N., Mizi, A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.015 · Cited by 152
Keller, T. E., Han, P., & Yi, S. V. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv345 · Cited by 148
Diversity of cytosine methylation across the fungal tree of life
Bewick, A. J., Hofmeister, B. T., Powers, R. A., Mondo, S. J., Grigoriev, I. V., James, T. Y., Stajich, J., & Schmitz, R. J. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0810-9 · Cited by 152
Baduel, P., Leduque, B., Ignace, A., Gy, I., Gil, J., Loudet, O., Colot, V., & Quadrana, L. (2021) · Genome biology · doi:10.1186/s13059-021-02348-5 · Cited by 150
Hofmeister, B. T., Lee, K. C., Rohr, N. A., Hall, D. W., & Schmitz, R. J. (2017) · Genome biology · doi:10.1186/s13059-017-1288-x · Cited by 145
Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., et al. (2017) · doi:10.1101/106955 · Cited by 144
Husquin, L. T., Rotival, M., Fagny, M., Quach, H., Zidane, N., McEwen, L. M., MacIsaac, J. L., Kobor, M. S., Aschard, H., Patin, É., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1601-3 · Cited by 149
A spatially resolved multi-omic single-cell atlas of soybean development
Zhang, X., Luo, Z., Marand, A. P., Yan, H., Jang, H., Bang, S., Mendieta, J. P., Minow, M. A. A., & Schmitz, R. J. (2024) · Cell · doi:10.1016/j.cell.2024.10.050 · Cited by 152
A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development
Yang, Y., Fan, X., Yan, J., Chen, M., Zhu, M., Tang, Y., Liu, S., & Tang, Z. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1203 · Cited by 146
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
Panda, K., Ji, L., Neumann, D. A., Daron, J., Schmitz, R. J., & Slotkin, R. K. (2016) · Genome biology · doi:10.1186/s13059-016-1032-y · Cited by 140
DNA methylation as a transcriptional regulator of the immune system
Morales‐Nebreda, L., McLafferty, F. S., & Singer, B. D. (2018) · Translational research · doi:10.1016/j.trsl.2018.08.001 · Cited by 141
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.-A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J. R., et al. (2023) · Nature · doi:10.1038/s41586-023-06805-y · Cited by 139
Self-citationAccelerated Placental Aging in Early Onset Preeclampsia Pregnancies Identified By DNA Methylation
Mayne, B. T., Leemaqz, S., Smith, A. K., Breen, J., Roberts, C. T., & Bianco‐Miotto, T. (2016) · Epigenomics · doi:10.2217/epi-2016-0103 · Cited by 141
X-chromosome inactivation and escape
Distèche, C. M., & Berletch, J. B. (2015) · Journal of Genetics · doi:10.1007/s12041-015-0574-1 · Cited by 146
Ai, R., Hammaker, D. R., Boyle, D. L., Morgan, R. L., Walsh, A. M., Fan, S., Firestein, G. S., & Wang, W. (2016) · Nature Communications · doi:10.1038/ncomms11849 · Cited by 135
Self-citationHofmeister, B. T., Denkena, J., Colomé‐Tatché, M., Shahryary, Y., Hazarika, R. R., Grimwood, J., Mamidi, S., Jenkins, J. W., Grabowski, P., Sreedasyam, A., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02162-5 · Cited by 134
Tissue-specific 5-hydroxymethylcytosine landscape of the human genome
He, B., Zhang, C., Zhang, X., Fan, Y., Zeng, H., Liu, J., Meng, H., Bai, D., Peng, J., Zhang, Q., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24425-w · Cited by 135
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
BNDF methylation in mothers and newborns is associated with maternal exposure to war trauma
Kertes, D. A., Bhatt, S., Kamin, H. S., Hughes, D. A., Rodney, N. C., & Mulligan, C. J. (2017) · Clinical Epigenetics · doi:10.1186/s13148-017-0367-x · Cited by 131
Klughammer, J., Romanovskaia, D., Nemc, A., Posautz, A., Seid, C. A., Schuster, L. C., Keinath, M. C., Ramos, J. S. L., Kosack, L., Evankow, A. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-34828-y · Cited by 131
Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects
Zhang, X., Marjani, S. L., Hu, Z., Weissman, S. M., Pan, X., & Wu, S. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-1907 · Cited by 122
DNA methylation-based variation between human populations
Kader, F., & Ghai, M. (2016) · Molecular Genetics and Genomics · doi:10.1007/s00438-016-1264-2 · Cited by 126
A Practical Guide to the Measurement and Analysis of DNA Methylation
Singer, B. D. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2019-0150tr · Cited by 130
Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Manzo, M., Wirz, J., Ambrosi, C. M., Villaseñor, R., Roschitzki, B., & Baubec, T. (2017) · The EMBO Journal · doi:10.15252/embj.201797038 · Cited by 128
Applications of Single-Cell DNA Sequencing
Evrony, G. D., Hinch, A. G., & Luo, C. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111320-090436 · Cited by 129
A genomic atlas of systemic interindividual epigenetic variation in humans
Gunasekara, C., Scott, C. A., Laritsky, E., Baker, M. S., MacKay, H., Duryea, J., Kessler, N. J., Hellenthal, G., Wood, A. C., Hodges, K. R., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1708-1 · Cited by 119
DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse
Zhou, W., Hinoue, T., Barnes, B., Mitchell, O. D., Iqbal, W., Lee, S. M., Foy, K. K., Lee, K., Moyer, E. J., VanderArk, A., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100144 · Cited by 116
Predicting the human epigenome from DNA motifs
Whitaker, J. W., Chen, Z., & Wang, W. T. (2014) · Nature Methods · doi:10.1038/nmeth.3065 · Cited by 119
Self-citationReduced DNA methylation patterning and transcriptional connectivity define human skin aging
Bormann, F., Rodríguez‐Paredes, M., Hagemann, S., Manchanda, H., Kristof, B., Gutekunst, J., Raddatz, G., Haas, R. R., Terstegen, L., Wenck, H., et al. (2016) · Aging Cell · doi:10.1111/acel.12470 · Cited by 114
A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers
Smith, B. A., Balanis, N. G., Nanjundiah, A., Sheu, K. M., Tsai, B. L., Zhang, Q., Park, J. W., Thompson, M. J., Huang, J., Witte, O. N., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.062 · Cited by 116
Conserved and divergent gene regulatory programs of the mammalian neocortex
Zemke, N. R., Armand, E. J., Wang, W., Lee, S. Y., Zhou, J., Li, Y. E., Liu, H., Tian, W., Nery, J. R., Castanon, R., et al. (2023) · Nature · doi:10.1038/s41586-023-06819-6 · Cited by 117
Self-citationWang, Q., Yu, G., Ming, X., Xia, W., Xu, X., Zhang, Y., Zhang, W., Li, Y., Huang, C., Xie, H., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0661-y · Cited by 115
A Comparative Analysis of 5-Azacytidine- and Zebularine-Induced DNA Demethylation
Griffin, P. T., Niederhuth, C. E., & Schmitz, R. J. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.030262 · Cited by 110
Epigenetic Mechanisms and Hypertension
Liang, M. (2018) · Hypertension · doi:10.1161/hypertensionaha.118.11171 · Cited by 110
Bs RAD seq: screening DNA methylation in natural populations of non‐model species
Trucchi, E., Mazzarella, A. B., Gilfillan, G. D., Lorenzo, M. T., Schönswetter, P., & Paun, O. (2016) · Molecular Ecology · doi:10.1111/mec.13550 · Cited by 109
Metadata
- Authors
- 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., Lin, S., Lin, Y., Jung, I., Schmitt, A. D., Selvaraj, S., Ren, B., Sejnowski, T. J., Wang, W., & Ecker, J. R.
- Affiliations
- Salk Institute for Biological Studies (US)
- University of California San Diego (US)
- Ludwig Cancer Research (US)
- Stanford University (US)
- Washington University in St. Louis (US)
- Corresponding author
- Ecker, Joseph R.
- ORCID
- Venue
- Nature
- Published
- 2015-06-01
- Volume
- 523
- Issue
- 7559
- Pages
- 212-216
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4499021
- OpenAlex
- W1506411903
- Cited by
- 690
- References
- 30
- Citations by year
- 2026: 30 · 2025: 43 · 2024: 39 · 2023: 61 · 2022: 61 · 2021: 65 · 2020: 80 · 2019: 69 · 2018: 81 · 2017: 63 · 2016: 68 · 2015: 28
- FWCI
- 34.75
- Type
- journal article
- Language
- en
- Update notices
- erratum (2015-11-25)
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Gordon and Betty Moore Foundation
- Mary K. Chapman Foundation
- University of Texas at Austin
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R00HL119617, K99HL119617, F32HL110473)
- National Institute of General Medical Sciences (T32GM008666)
- National Institute of Neurological Disorders and Stroke (R00NS080911, K99NS080911)
- National Institute of Environmental Health Sciences (U01ES017166, R01ES024984)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- DNA methylation, non-CG methylation, tissue-specific methylation, partially methylated domains, allele-specific methylation, X chromosome inactivation escape, gene expression, regulatory elements
- MeSH terms
- Age Factors, Alleles, Chromosome Mapping, Female, Gene Expression Regulation, Humans, Male, Organ Specificity, Genetic Variation, DNA Methylation, Gene Expression Profiling, Epigenesis, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
