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The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
Open accessAbstract
Despite the importance of epigenetic regulation in neurological disorders, little is known about neuronal chromatin. Cerebellar Purkinje neurons have large and euchromatic nuclei, whereas granule cell nuclei are small and have a more typical heterochromatin distribution. While comparing the abundance of 5-methylcytosine in Purkinje and granule cell nuclei, we detected the presence of an unusual DNA nucleotide. Using thin-layer chromatography, high-pressure liquid chromatography, and mass spectrometry, we identified the nucleotide as 5-hydroxymethyl-2'-deoxycytidine (hmdC). hmdC constitutes 0.6% of total nucleotides in Purkinje cells, 0.2% in granule cells, and is not present in cancer cell lines. hmdC is a constituent of nuclear DNA that is highly abundant in the brain, suggesting a role in epigenetic control of neuronal function.
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“5-hydroxymethylcytosine, which is produced by the addition of hydroxyl groups to 5-methylcytosine under the action of the ten-eleven translocation (TET) enzymes (Fig. 2).59,60”
From Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential (2023) · cites this paper as [60]
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“First, neurons have high levels of hydroxymethylcytosine (hmC), a derivative of mC that may have distinct functional roles (Kriaucionis and Heintz, 2009; Mellén et al., 2017).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Kriaucionis and Heintz, 2009
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“This enables FANS purification of target nuclei for assessment of DNA, nascent RNA transcription in the specific cell-type of interest, as well as proteomic analysis of histone modifications or transcription factor binding120,121.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [121]
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Cites
A translational profiling approach for the molecular characterization of CNS cell types
Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Suárez-Fariñas, M., Schwarz, C., Stephan, D. A., Surmeier, D. J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.028 · Cited by 1,134
Self-citationApplication of a translational profiling approach for the comparative analysis of CNS cell types
Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., Bupp, S., Shrestha, P., Shah, R. D., Doughty, M. L., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.029 · Cited by 912
Self-citationValinluck, V. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh739 · Cited by 756
Wyatt, G. R., & Cohen, S. (1953) · Biochemical Journal · doi:10.1042/bj0550774 · Cited by 608
The Colorful History of Active DNA Demethylation
Ooi, S. K. T., & Bestor, T. H. (2008) · Cell · doi:10.1016/j.cell.2008.06.009 · Cited by 537
The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid
Penn, N. W., SUWALSKI, R. T., O'Riley, C., Bojanowski, K., & Yura, R. (1972) · Biochemical Journal · doi:10.1042/bj1260781 · Cited by 280
Gommers-Ampt, J., & Borst, P. (1995) · The FASEB Journal · doi:10.1096/fasebj.9.11.7649402 · Cited by 126
Tardy-Planechaud, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.3.553 · Cited by 88
Oxidative damage to 5-methylcytosine in DNA
Zuo, S., Boorstein, R. J., & Teebor, G. W. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.16.3239 · Cited by 87
Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs
Hayatsu, H., & Shiragami, M. (1979) · Biochemistry · doi:10.1021/bi00571a013 · Cited by 85
Research works printed but not linked: 1
- Ramsahoye B. H., Methods Mol. Biol. 200, 9 (2002).Medline
Cited by
Sorted by citations
DNA methylation and its basic function
Moore, L. D., Le, T., & Fan, G. (2013) · Neuropsychopharmacology · doi:10.1038/npp.2012.112 · Cited by 4,906
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 3,925
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451
Cancer epigenetics: from mechanism to therapy
Dawson, M. A., & Kouzarides, T. (2012) · Cell · doi:10.1016/j.cell.2012.06.013 · Cited by 3,203
A decade of exploring the cancer epigenome—biological and translational implications
Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871
Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.-H., Ito, S., Yang, C., Wang, P., Xiao, M.-T., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2010.12.014 · Cited by 2,875
Epigenetic modifications and human disease
Portela, A., & Esteller, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1685 · Cited by 2,938
The molecular hallmarks of epigenetic control
Allis, C. D., & Jenuwein, T. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.59 · Cited by 2,809
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
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
TET-mediated active DNA demethylation: mechanism, function and beyond
Wu, X., & Zhang, Y. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.33 · Cited by 1,661
TET enzymes, TDG and the dynamics of DNA demethylation
Kohli, R. M., & Zhang, Y. (2013) · Nature · doi:10.1038/nature12750 · Cited by 1,623
Principles and challenges of genome-wide DNA methylation analysis
Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,611
Kulis, M., & Esteller, M. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380866-0.60002-2 · Cited by 1,617
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
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 1,404
Epigenetic Determinants of CancerPreprint
Baylin, S. B., & Jones, P. A. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019505 · Cited by 1,414
“…Gaudet et al. 2003 5-Azacytidine is FDA approved for treatment of myelodysplastic syndrome Discovery of the 5-hydroxymethylcytosine base and the TET1/2/3 enzymes that catalyze this conversion Kaminskas et al. 2005 Kriaucionis and Heintz 2009; Tahiliani et al. 2009 Adapted from You and Jones 2012.”
BackgroundLessons from the Cancer Genome
Garraway, L. A., & Lander, E. S. (2013) · Cell · doi:10.1016/j.cell.2013.03.002 · Cited by 1,377
Epigenome-wide association studies for common human diseases
Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3000 · Cited by 1,288
The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes
Gu, T., Guo, F., Yang, H., Wu, H.-P., Xu, G., Liu, W., Xie, Z.-G., Shi, L., He, X., Jin, S., et al. (2011) · Nature · doi:10.1038/nature10443 · Cited by 1,144
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 1,160
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
Song, C., Szulwach, K. E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.-H., Zhang, W., Jian, X., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1732 · Cited by 1,094
Role of TET enzymes in DNA methylation, development, and cancer
Rasmussen, K. D., & Helin, K. (2016) · Genes & Development · doi:10.1101/gad.276568.115 · Cited by 1,040
“By comparison, the products of further TET-mediated oxidation, 5fC and 5caC, are observed at ∼10-fold to 100-fold lower levels than 5hmC and often close to or under the detection limit (Kriaucionis and Heintz 2009; Globisch et al. 2010; Szwagierczak et al. 2010; He et al. 2011; Ito et al. 2011; Pfaffeneder et al. 2011…”
BackgroundCTCF: an architectural protein bridging genome topology and function
Ong, C., & Corces, V. G. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3663 · Cited by 1,094
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
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 1,091
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021
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
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 1,050
Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.02.004 · Cited by 973
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
Self-citationDNA Methylation in MammalsPreprint
Li, E., & Zhang, Y. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019133 · Cited by 999
Quantitative 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 951
Quivoron, C., Couronné, L., Della Valle, V., Lopez, C. K., Plo, I., Wagner-Ballon, O., Do Cruzeiro, M., Delhommeau, F., Arnulf, B., Stern, M.-H., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.003 · Cited by 924
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription
Pastor, W. A., Aravind, L., & Rao, A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3589 · Cited by 897
DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation
Cadet, J., & Wagner, J. R. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012559 · Cited by 903
Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells
Fraietta, J. A., Nobles, C. L., Sammons, M. A., Lundh, S., Carty, S. A., Reich, T. J., Cogdill, A. P., Morrissette, J. J. D., DeNizio, J. E., Reddy, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0178-z · Cited by 862
DNA methylation: a historical perspective
Mattei, A. L., Bailly, N., & Meissner, A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.03.010 · Cited by 920
“Published back-to-back, Kriaucionis and Heintz also demonstrated that 5hmC is abundant in neurons, further strengthening the role of 5hmC in the active demethylation pathway [215].”
Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates
Globisch, D., Münzel, M., Müller, M., Michalakis, S., Wagner, M., Koch, S., Brückl, T., Biel, M., & Carell, T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015367 · Cited by 865
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
Popp, C., Dean, W., Feng, S., Cokus, S. J., Andrews, S., Pellegrini, M. A., Jacobsen, S. E., & Reik, W. (2010) · Nature · doi:10.1038/nature08829 · Cited by 895
Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine
Maiti, A., & Drohat, A. C. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.c111.284620 · Cited by 825
5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging
Szulwach, K. E., Li, X., Li, Y., Song, C., Wu, H., Dai, Q., Irier, H. A., Upadhyay, A. K., Gearing, M., Levey, A. I., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2959 · Cited by 843
Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers
Okugawa, Y., Grady, W. M., & Goel, A. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.07.011 · Cited by 782
Cortellino, S., Xu, J., Sannai, M., Moore, R., Caretti, E., Cigliano, A., Le Coz, M., Devarajan, K., Wessels, A., Soprano, D., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.020 · Cited by 809
DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy?
Jin, B., Li, Y., & Robertson, K. D. (2011) · Genes & Cancer · doi:10.1177/1947601910393957 · Cited by 868
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804
Koh, K. P., Yabuuchi, A., Rao, S., Huang, Y., Cunniff, K., Nardone, J., Laiho, A., Tahiliani, M., Sommer, C. A., Mostoslavsky, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.008 · Cited by 776
5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming
Wossidlo, M., Nakamura, T., Lepikhov, K., Marques, C. J., Zakhartchenko, V., Boiani, M., Arand, J., Nakano, T., Reik, W., & Walter, J. (2011) · Nature Communications · doi:10.1038/ncomms1240 · Cited by 793
Uncovering the role of 5-hydroxymethylcytosine in the epigenome
Branco, M. R., Ficz, G., & Reik, W. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3080 · Cited by 766
Rethinking how DNA methylation patterns are maintained
Jones, P. A., & Liang, G. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2651 · Cited by 799
Active DNA Demethylation Mediated by DNA Glycosylases
Zhu, J. (2009) · Annual Review of Genetics · doi:10.1146/annurev-genet-102108-134205 · Cited by 770
Interpreting the language of histone and DNA modifications
Rothbart, S. B., & Strahl, B. D. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.03.001 · Cited by 792
The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing
Huang, Y., Pastor, W. A., Shen, Y., Tahiliani, M., Liu, D. R., & Rao, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008888 · Cited by 731
Epigenetic transgenerational actions of environmental factors in disease etiology
Skinner, M. K., Manikkam, M., & Guerrero‐Bosagna, C. (2010) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2009.12.007 · Cited by 732
Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B., Fouse, S. D., Delaney, A. D., Zhao, Y., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1682 · Cited by 723
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
Morán, S., Arribas, C., & Esteller, M. (2015) · Epigenomics · doi:10.2217/epi.15.114 · Cited by 721
Understanding transgenerational epigenetic inheritance via the gametes in mammals
Daxinger, L., & Whitelaw, E. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3188 · Cited by 728
Structure and Function of Mammalian DNA Methyltransferases
Jurkowska, R. Z., Jurkowski, T. P., & Jeltsch, A. (2010) · ChemBioChem · doi:10.1002/cbic.201000195 · Cited by 725
Iqbal, K., Jin, S., Pfeifer, G. P., & Szabó, P. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014033108 · Cited by 693
Bhutani, N., Burns, D. M., & Blau, H. M. (2011) · Cell · doi:10.1016/j.cell.2011.08.042 · Cited by 727
Histone acetylation: molecular mnemonics on the chromatin
Gräff, J., & Tsai, L.-H. (2013) · Nature Reviews Neuroscience · doi:10.1038/nrn3427 · Cited by 680
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidationPreprint
Wu, H., & Zhang, Y. (2011) · Genes & Development · doi:10.17615/800j-yk16 · Cited by 686
N6-Methyladenine DNA Modification in Drosophila
Zhang, G., Huang, H., Liu, D., Cheng, Y., Liu, X., Zhang, W., Yin, R., Zhang, D., Zhang, P., Liu, J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.018 · Cited by 657
Xu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A. J., Zheng, L., Zhang, H., Huang, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.04.005 · Cited by 647
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 603
The alternative role of DNA methylation in splicing regulation
Lev-Maor, G., Yearim, A., & Ast, G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.002 · Cited by 604
Disruption 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
5-Hydroxymethylcytosine is a predominantly stable DNA modification
Bachman, M., Uribe‐Lewis, S., Yang, X., Williams, M., Murrell, A., & Balasubramanian, S. (2014) · Nature Chemistry · doi:10.1038/nchem.2064 · Cited by 577
Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550
Shock, L. S., Thakkar, P. V., Peterson, E. J., Moran, R. G., & Taylor, S. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012311108 · Cited by 555
Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming
Song, C., Szulwach, K. E., Dai, Q., Fu, Y., Mao, S.-Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.001 · Cited by 562
Understanding the relationship between DNA methylation and histone lysine methylation
Rose, N. R., & Klose, R. J. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.007 · Cited by 576
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
Dawlaty, M. M., Ganz, K., Powell, B. E., Hu, Y.-C., Markoulaki, S., Cheng, A. W., Gao, Q., Kim, J., Choi, S.-W., Page, D. C., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.07.010 · Cited by 508
Naive pluripotency is associated with global DNA hypomethylation
Leitch, H. G., McEwen, K. R., Turp, A., Encheva, V., Carroll, T., Grabole, N., Mansfield, W., Nashun, B., Knezovich, J. G., Smith, A., et al. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2510 · Cited by 516
Differential methylation analysis for BS-seq data under general experimental design
Park, Y., & Wu, H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw026 · Cited by 532
Epigenetic mechanisms in cognition
Day, J. J., & Sweatt, J. D. (2011) · Neuron · doi:10.1016/j.neuron.2011.05.019 · Cited by 510
Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497
DNA methylation and memory formation
Day, J. J., & Sweatt, J. D. (2010) · Nature Neuroscience · doi:10.1038/nn.2666 · Cited by 501
TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS
Deplus, R., Delatte, B., Schwinn, M. K., Defrance, M., Méndez, J., Murphy, N., Dawson, M. A., Volkmar, M., Putmans, P., Calonne, E., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2012.357 · Cited by 508
Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study
Wu, Y., Lin, Z., Li, C., Lin, X. J., Shan, S., Guo, B., Zheng, M.-H., Li, F., Yuan, L., & Li, Z. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01333-7 · Cited by 549
The Discovery of 5‐Formylcytosine in Embryonic Stem Cell DNA
Pfaffeneder, T., Hackner, B., Truß, M., Münzel, M., Müller, M., Deiml, C. A., Hagemeier, C., & Carell, T. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201103899 · Cited by 483
Cancer epigenetics: Moving forward
Nebbioso, A., Tambaro, F. P., Dell’Aversana, C., & Altucci, L. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007362 · Cited by 500
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation
Hashimoto, H., Liu, Y., Upadhyay, A. K., Chang, Y., Howerton, S. B., Vertino, P. M., Zhang, X., & Cheng, X. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks155 · Cited by 473
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA
Fu, Y., Jia, G., Pang, X., Wang, R. N., Wang, X., Li, C. J., Smemo, S., Dai, Q., Bailey, K. A., Nóbrega, M. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms2822 · Cited by 483
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
Stroud, H., Feng, S., Kinney, S. R. M., Pradhan, S., & Jacobsen, S. E. (2011) · Genome biology · doi:10.1186/gb-2011-12-6-r54 · Cited by 490
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Hájková, P., Jeffries, S. J., Lee, C. G. L., Miller, N. G. A., Jackson, S. P., & Surani, M. A. (2010) · Science · doi:10.1126/science.1187945 · Cited by 473
Habibi, E., Brinkman, A. B., Arand, J., Kroeze, L. I., Kerstens, H. H. D., Matarese, F., Lepikhov, K., Gut, M., Heath, I. B., Hubner, N. C., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.06.002 · Cited by 485
PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos
Nakamura, T., Liu, Y.-J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., & Nakano, T. (2012) · Nature · doi:10.1038/nature11093 · Cited by 466
IDH1andIDH2Mutations in Tumorigenesis: Mechanistic Insights and Clinical Perspectives
Yang, H., Ye, D., Guan, K., & Xiong, Y. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-1773 · Cited by 477
Epigenetic regulation of brain region-specific microglia clearance activity
Ayata, P., Badimon, A., Strasburger, H. J., Duff, M. K., Montgomery, S. E., Loh, Y.-H. E., Ebert, A., Pimenova, A. A., Ramirez, B. R., Chan, A. T., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0192-3 · Cited by 460
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Nestler, E. J. (2013) · Neuropharmacology · doi:10.1016/j.neuropharm.2013.04.004 · Cited by 474
Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis
Hahn, M. A., Qiu, R., Wu, X., Li, A. X., Zhang, H., Wang, J., Jui, J., Jin, S., Jiang, Y., Pfeifer, G. P., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.011 · Cited by 455
Yıldırım, Ö., Li, R., Hung, J., Chen, P. B., Dong, X., Ee, L.-S., Weng, Z., Rando, O. J., & Fazzio, T. G. (2011) · Cell · doi:10.1016/j.cell.2011.11.054 · Cited by 463
Epigenetic mechanisms in neurological disease
Jakovcevski, M., & Akbarian, S. (2012) · Nature Medicine · doi:10.1038/nm.2828 · Cited by 450
Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation
Hu, L., Li, Z., Cheng, J., Rao, Q., Gong, W., Liu, M., Shi, Y. G., Zhu, J., Wang, P., & Xu, Y. (2013) · Cell · doi:10.1016/j.cell.2013.11.020 · Cited by 467
Jin, S., Jiang, Y., Qiu, R., Rauch, T. A., Wang, Y., Schackert, G., Krex, D., Lü, Q., & Pfeifer, G. P. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-2023 · Cited by 449
Epitranscriptome sequencing technologies: decoding RNA modifications
Li, X., Xiong, X., & Yi, C. (2017) · Nature Methods · doi:10.1038/nmeth.4110 · Cited by 447
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Rudenko, A., Dawlaty, M. M., Seo, J., Cheng, A. W., Meng, J., Le, T. T., Faull, K. F., Jaenisch, R., & Tsai, L. (2013) · Neuron · doi:10.1016/j.neuron.2013.08.003 · Cited by 450
Metadata
- Authors
- Kriaucionis, S., & Heintz, N.
- Affiliations
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
- Howard Hughes Medical Institute (US)
- Corresponding author
- Heintz, Nathaniel
- ORCID
- Heintz, Nathaniel
- Venue
- Science
- Published
- 2009-05-15
- Volume
- 324
- Issue
- 5929
- Pages
- 929-930
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3263819
- OpenAlex
- W2152451432
- Cited by
- 2,700
- References
- 14
- Citations by year
- 2026: 53 · 2025: 69 · 2024: 84 · 2023: 93 · 2022: 112 · 2021: 137 · 2020: 107 · 2019: 150 · 2018: 190 · 2017: 218 · 2016: 236 · 2015: 220 · 2014: 259 · 2013: 252 · 2012: 202
- FWCI
- 69.99
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- 5-hydroxymethylcytosine, Purkinje cells, cerebellar granule cells, DNA methylation, epigenetic regulation, brain DNA, nucleotide composition
- MeSH terms
- Animals, Brain Chemistry, Cell Line, Cerebellum, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Cytosine, Deoxycytidine, DNA, DNA Damage, Humans, Purkinje Cells, Mass Spectrometry, 5-Methylcytosine, Mice
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