Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
Open accessAbstract
DNA methylation has critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single base-resolution DNA methylome from adult mouse dentate neurons consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in regions of low CpG density, depleted at protein-DNA interaction sites and anticorrelated with gene expression. Functionally, both methylated CpGs (mCpGs) and mCpHs can repress transcription in vitro and are recognized by methyl-CpG binding protein 2 (MeCP2) in neurons in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNA methyltransferase 3A (DNMT3A) for active maintenance in postmitotic neurons. These characteristics of CpH methylation suggest that a substantially expanded proportion of the neuronal genome is under cytosine methylation regulation and provide a new foundation for understanding the role of this key epigenetic modification in the nervous system.
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
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?
Non-CpG methylation is highly concentrated in neurons and glial cells and accumulates in neurons as they mature.
“Non-CpG methylation is highly concentrated in neurons and glial cells61 and accumulates in neurons as they mature.62”
From Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential (2023) · cites this paper as [62]
In neurons, intragenic 5mCH quantitatively modulates gene expression by interacting with MECP2 and recruiting the NCoR corepressor complex to chromatin.
“In neurons, intragenic 5mCH quantitatively modulates gene expression by interacting with MECP2 and recruiting NCoR corepressor complex to chromatin (37–40).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [37]
Independent studies report that MECP2 binds both 5mCA and 5mCG sites with high affinity.
“Independent studies have reported that MECP2 binds to both 5mCA and 5mCG sites with high affinity (37, 39, 40).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [37]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124 · see citing works
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,161 · see citing works
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 · see citing works
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
Law, J. A., & Jacobsen, S. E. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2719 · Cited by 3,868 · 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
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
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
Self-citationHotspots 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 1,545 · see citing works
Astroglia induce neurogenesis from adult neural stem cells
Song, H., Stevens, C. F., & Gage, F. H. (2002) · Nature · doi:10.1038/417039a · Cited by 1,452 · see citing works
Self-citationDNA-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
Lewis, J. D., Meehan, R. R., Henzel, W. J., Maurer-Fogy, I., Jeppesen, P., Klein, F., & Bird, A. (1992) · Cell · doi:10.1016/0092-8674(92)90610-o · Cited by 1,371 · see citing works
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S. E., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J. J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.07.020 · Cited by 1,361 · see citing works
Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain
Guo, J. U., Su, Y., Zhong, C., Ming, G., & Song, H. (2011) · Cell · doi:10.1016/j.cell.2011.03.022 · Cited by 1,355 · see citing works
Self-citationThe Story of Rett Syndrome: From Clinic to Neurobiology
Chahrour, M., & Zoghbi, H. Y. (2007) · Neuron · doi:10.1016/j.neuron.2007.10.001 · Cited by 1,265 · see citing works
Bunz, U. H. F. (2005) · Science · doi:10.1126/science.1111098 · Cited by 1,252 · 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
Dynamic changes in the human methylome during differentiationPreprint
Laurent, L. C., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Sung, K. W. K., Rigoutsos, I., Loring, J. F., et al. (2010) · Genome Research · doi:10.1101/gr.101907.109 · Cited by 1,037 · see citing works
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,022 · see citing works
Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons
Feng, J., Zhou, Y., Campbell, S. L., Le, T., Li, E., Sweatt, J. D., Silva, A. J., & Fan, G. (2010) · Nature Neuroscience · doi:10.1038/nn.2514 · Cited by 1,019 · see citing works
Self-citationRamsahoye, 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
A unique regulatory phase of DNA methylation in the early mammalian embryo
Smith, Z. D., Chan, M. M., Mikkelsen, T. S., Gu, H., Gnirke, A., Regev, A., & Meissner, A. (2012) · Nature · doi:10.1038/nature10960 · Cited by 964 · see citing works
MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system
Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S., & Heintz, N. (2012) · Cell · doi:10.1016/j.cell.2012.11.022 · Cited by 943 · see citing works
Neuronal Activity–Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis
Dengke, K., Jang, M., Guo, J. U., Kitabatake, Y., Chang, M.-L., Pow-anpongkul, N., Flavell, R. A., Lu, B., Ming, G., & Song, H. (2009) · Science · doi:10.1126/science.1166859 · Cited by 929 · see citing works
Self-citationQuantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution
Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) · Science · doi:10.1126/science.1220671 · Cited by 923 · 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
Rethinking how DNA methylation patterns are maintained
Jones, P. A., & Liang, G. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2651 · Cited by 767 · see citing works
Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation
Barreto, G., Schäfer, A., Marhold, J., Stach, D., Swaminathan, S. K., Handa, V., Doederlein, G., Maltry, N., Wu, W., Lyko, F., et al. (2007) · Nature · doi:10.1038/nature05515 · Cited by 753 · see citing works
Relationship between nucleosome positioning and DNA methylation
Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., Chen, P., Stroud, H., Yu, Y., Hetzel, J., Kuo, F., Kim, J., Cokus, S. J., et al. (2010) · Nature · doi:10.1038/nature09147 · Cited by 696 · see citing works
Dynamic DNA methylation across diverse human cell lines and tissuesPreprint
Varley, K. E., Gertz, J., Bowling, K. M., Parker, S. L., Reddy, T. E., Pauli, F., Cross, M. K., Williams, B. A., Stamatoyannopoulos, J. A., Crawford, G. E., et al. (2013) · Genome Research · doi:10.1101/gr.147942.112 · Cited by 693 · see citing works
Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State
Skene, P. J., Illingworth, R. S., Webb, S., Kerr, A. R. W., James, K. D., Turner, D. J., Andrews, R., & Bird, A. P. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.01.030 · Cited by 688 · 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
Self-citationDnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens
LaPlant, Q., Vialou, V., Covington, H. E., Dumitriu, D., Feng, J., Warren, B. L., Maze, I., Dietz, D. M., Watts, E. L., Iñiguez, S. D., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2619 · Cited by 612 · see citing works
Self-citationDnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes
Wu, H., Coskun, V., Tao, J., Xie, W., Ge, W., Yoshikawa, K., Li, E., Zhang, Y., & Sun, Y. E. (2010) · Science · doi:10.1126/science.1190485 · Cited by 604 · see citing works
Epigenetics and the environmental regulation of the genome and its function
Zhang, T.-Y., & Meaney, M. J. (2010) · Annual Review of Psychology · doi:10.1146/annurev.psych.60.110707.163625 · Cited by 565 · see citing works
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
Decoding the Epigenetic Language of Neuronal Plasticity
Borrelli, E., Nestler, E. J., Allis, C. D., & Sassone‐Corsi, P. (2008) · Neuron · doi:10.1016/j.neuron.2008.10.012 · Cited by 529 · see citing works
DNA methylation and memory formation
Day, J. J., & Sweatt, J. D. (2010) · Nature Neuroscience · doi:10.1038/nn.2666 · Cited by 488 · see citing works
The Role of MeCP2 in the Brain
Guy, J., Cheval, H., Selfridge, J., & Bird, A. P. (2011) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-092910-154121 · Cited by 414 · see citing works
Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
Ziller, M. J., Müller, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Boyle, P. J., Epstein, C. B., Bernstein, B., Lengauer, T., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002389 · Cited by 398 · see citing works
Epigenetic regulation of gene expression in physiological and pathological brain processes
Gräff, J., Kim, D., Dobbin, M. M., & Tsai, L.-H. (2011) · Physiological Reviews · doi:10.1152/physrev.00012.2010 · Cited by 373 · see citing works
DNA (cytosine-5)-methyltransferases in mouse cells and tissues. studies with a mechanism-based probe
Yoder, J. A., Soman, N. S., Verdine, G. L., & Bestor, T. H. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1125 · Cited by 359 · 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
Self-citationMeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system
Mellén, M., Ayata, P., Dewell, S. B., Kriaučionis, S., & Heintz, N. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-s1-p52 · Cited by 345 · see citing works
Epigenetic choreographers of neurogenesis in the adult mammalian brain
Ma, D. K., Marchetto, M. C., Guo, J. U., Ming, G., Gage, F. H., & Song, H. (2010) · Nature Neuroscience · doi:10.1038/nn.2672 · Cited by 338 · see citing works
Self-citationTomizawa, S.-I., Kobayashi, H., Watanabe, T., Andrews, S., Hata, K., Kelsey, G., & Sasaki, H. (2011) · Development · doi:10.1242/dev.061416 · Cited by 241 · see citing works
Gowher, H., & Jeltsch, A. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4710 · Cited by 236 · see citing works
The Role of DNA Methylation in the Central Nervous System and Neuropsychiatric Disorders
Feng, J., & Fan, G. (2009) · International review of neurobiology · doi:10.1016/s0074-7742(09)89004-1 · Cited by 178 · see citing works
Self-citationPreferential Methylation of Unmethylated DNA by Mammalian de Novo DNA Methyltransferase Dnmt3a
Yokochi, T., & Robertson, K. D. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m106590200 · Cited by 155 · see citing works
A unique family of Mrr-like modification-dependent restriction endonucleases
Zheng, Y., Cohen-Karni, D., Xu, D., Chin, H. G., Wilson, G. G., Pradhan, S., & Roberts, R. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq327 · Cited by 85 · see citing works
Epigenetics in the mature mammalian brain: Effects on behavior and synaptic transmission
Nelson, E. D., & Monteggia, L. M. (2011) · Neurobiology of Learning and Memory · doi:10.1016/j.nlm.2011.02.015 · Cited by 80 · see citing works
Accumulation and loss of asymmetric non-CpG methylation during male germ-cell development
Ichiyanagi, T., Ichiyanagi, K., Miyake, M., & Sasaki, H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1117 · Cited by 80 · see citing works
Distinct Enzymatic Properties of Recombinant Mouse DNA Methyltransferases Dnmt3a and Dnmt3b
Suetake, I. (2003) · The Journal of Biochemistry · doi:10.1093/jb/mvg095 · Cited by 76 · see citing works
“Seq-ing” Insights into the Epigenetics of Neuronal Gene Regulation
Telese, F., Gamliel, A., Skowronska‐Krawczyk, D., García-Bassets, I., & Rosenfeld, M. G. (2013) · Neuron · doi:10.1016/j.neuron.2013.01.034 · Cited by 76 · see citing works
Hu, X. V., Rodrigues, T. M. A., Tao, H., Baker, R. K., Miraglia, L. J., Orth, A. P., Lyons, G. E., Schultz, P. G., & Wu, X. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009025107 · Cited by 74 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.018 · Cited by 739 · 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
Self-citationDisruption of DNA-methylation-dependent long gene repression in Rett syndrome
Gabel, H. W., Kinde, B., Stroud, H., Gilbert, C. S., Harmin, D. A., Kastan, N. R., Hemberg, M., Ebert, D. H., & Greenberg, M. E. (2015) · Nature · doi:10.1038/nature14319 · Cited by 569 · 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
Singewald, N., Schmuckermair, C., Whittle, N., Holmes, A., & Ressler, K. J. (2015) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2014.12.004 · Cited by 390 · see citing works
“However, given the recent finding that methylation can occur outside CpG islands and in CpH (where H= adenine/cytosine/thymine) islands and that these CpH islands can repress (Guo et al., 2014) substantially expands and adds further complexity to how methylation can regulate gene transcription in the central nervous s…”
BackgroundCerebral 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
Epigenetics of Stress-Related Psychiatric Disorders and Gene × Environment Interactions
Klengel, T., & Binder, E. B. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.036 · Cited by 353 · 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
Chen, L., Chen, K., Lavery, L. A., Baker, S. A., Shaw, C. A., Li, W., & Zoghbi, H. Y. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505909112 · Cited by 301 · see citing works
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 · see citing works
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
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
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 · see citing works
“62 It is a rare occurrence in the frontal cortex of human fetuses; however, it increases signi fi cantly during later stages of life.”
BackgroundRizzardi, L. F., Hickey, P. F., Rodriguez DiBlasi, V., Tryggvadóttir, R., Callahan, C. M., Idrizi, A., Hansen, K. D., & Feinberg, A. P. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0297-8 · Cited by 146 · see citing works
Neuropathology of suicide: Recent findings and future directions
Lutz, P.-E., Mechawar, N., & Turecki, G. (2017) · Molecular Psychiatry · doi:10.1038/mp.2017.141 · Cited by 158 · see citing works
Mellén, M., Ayata, P., & Heintz, N. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708044114 · Cited by 151 · see citing works
Hing, B., Sathyaputri, L., & Potash, J. B. (2018) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32616 · Cited by 137 · see citing works
DNA methylation in the gene body influences MeCP2-mediated gene repression
Kinde, B., Wu, D. Y., Greenberg, M. E., & Gabel, H. W. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618737114 · Cited by 118 · see citing works
At the frontier of epigenetics of brain sex differences
McCarthy, M. M., & Nugent, B. M. (2015) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2015.00221 · Cited by 123 · see citing works
Evolving insights on how cytosine methylation affects protein-DNA binding
Dantas Machado, A. C., Zhou, T., Rao, S., Goel, P., Rastogi, C., Lazarovici, A., Bussemaker, H. J., & Rohs, R. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu040 · Cited by 124 · see citing works
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
Analytical tools and current challenges in the modern era of neuroepigenomics
Maze, I., Shen, L., Zhang, B., Garcia, B. A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C. D., & Nestler, E. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3816 · Cited by 100 · 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
Genetic and epigenetic factors associated with depression: an updated overview
Alshaya, D. S. (2022) · Saudi Journal of Biological Sciences · doi:10.1016/j.sjbs.2022.103311 · Cited by 81 · see citing works
DNA Methylation and Its Implications and Accessibility for Neuropsychiatric Therapeutics
Day, J. J., Kennedy, A. J., & Sweatt, J. D. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124527 · Cited by 78 · see citing works
Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Luo, C., Lee, Q. Y., Wapinski, O., Castanon, R., Nery, J. R., Mall, M., Kareta, M. S., Cullen, S. M., Goodell, M. A., Chang, H. Y., et al. (2019) · eLife · doi:10.7554/elife.40197 · Cited by 76 · see citing works
Zhou, J., Li, M., Wang, X., He, Y., Xia, Y., Sweeney, J. A., Kopp, R. F., Liu, C., & Chen, C. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.674273 · Cited by 56 · see citing works
Epigenetic reprogramming in mice and humans: From fertilization to primordial germ cell development
Singh, A., Rappolee, D. A., & Ruden, D. M. (2023) · Cells · doi:10.3390/cells12141874 · Cited by 50 · see citing works
Colquitt, B. M., Markenscoff-Papadimitriou, E., Duffié, R., & Lomvardas, S. (2014) · Neuron · doi:10.1016/j.neuron.2014.07.013 · Cited by 38 · see citing works
DNA Epigenetics in Addiction Susceptibility
Kaplan, G., Xu, H., Abreu, K., & Feng, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.806685 · Cited by 34 · see citing works
Moving pharmacoepigenetics tools for depression toward clinical use
Hack, L. M., Fries, G. R., Eyre, H. A., Bousman, C. A., Singh, A. B., Quevedo, J., John, V. P., Baune, B. T., & Dunlop, B. W. (2019) · Journal of Affective Disorders · doi:10.1016/j.jad.2019.02.009 · Cited by 33 · see citing works
- Authors
- Guo, J. U., Su, Y., Shin, J. H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., Zhu, H., Chang, Q., Gao, Y., Ming, G.-L., & Song, H.
- Affiliations
- Johns Hopkins University (US)
- University of Wisconsin–Madison (US)
- University of California, Los Angeles (US)
- Corresponding author
- Song, Hongjun
- ORCID
- Venue
- Nature Neuroscience
- Published
- 2013-12-22
- Volume
- 17
- Issue
- 2
- Pages
- 215-222
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC3970219
- OpenAlex
- W2170356111
- Cited by
- 714
- References
- 57
- Citations by year
- 2026: 25 · 2025: 29 · 2024: 29 · 2023: 44 · 2022: 52 · 2021: 56 · 2020: 56 · 2019: 62 · 2018: 77 · 2017: 92 · 2016: 80 · 2015: 77 · 2014: 35
- FWCI
- 28.64
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Funders
- Johns Hopkins University
- National Institute on Aging (R01AG024984)
- National Institute of Mental Health (R21MH087874, R33MH087874, MH087874)
- National Institute of General Medical Sciences (R01GM076102)
- National Institute of Neurological Disorders and Stroke (NS 048271, R01NS047344, NS 047344, R01NS048271, NS072924, R37NS047344, R21NS072924, R56NS047344)
- National Institute of Environmental Health Sciences (R21ES021957, ES021957)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD066560, R01HD069184, R21HD066560, HD064743, R01HD064743, P30HD003352, HD069184)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- methylome, dentate gyrus neurons, MeCP2, DNMT3A, transcriptional repression, neuronal maturation, epigenetic regulation, mouse brain, human brain
- MeSH terms
- DNA Methyltransferase 3A, Animals, Brain, Embryo, Mammalian, Humans, Male, Mice, Inbred C57BL, Nerve Tissue Proteins, Neurons, RNA, Messenger, Gene Expression, Genome, CpG Islands, DNA Methylation, Electrophoretic Mobility Shift Assay, Chromatin Immunoprecipitation, Mice, Methyl-CpG-Binding Protein 2, Epigenomics
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
