Cited by 536Epigenetics and DNA MethylationGenomics and Chromatin DynamicsGenetic Syndromes and Imprinting

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The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

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Weinberg, Daniel N., Papillon-Cavanagh, Simon, Chen, Haifen, Yue, Yuan, Chen, Xiao, Rajagopalan, Kartik N., Horth, Cynthia, McGuire, John T., Xu, Xinjing, Nikbakht, Hamid, Lemiesz, Agata E., Marchione, Dylan M., Marunde, Matthew R., Meiners, Matthew J., Cheek, Marcus A., Keogh, Michael-Christopher, Bareke, Eric, Djedid, Anissa, Harutyunyan, Ashot S., Jabado, Nada, Garcia, Benjamin A., Li, Haitao, Allis, C. David, Majewski, Jacek, Lu, Chao·2019·Nature

DOI 10.1038/s41586-019-1534-3PMC PMC6742567

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Abstract

Enzymes that catalyse CpG methylation in DNA, including the DNA methyltransferases 1 (DNMT1), 3A (DNMT3A) and 3B (DNMT3B), are indispensable for mammalian tissue development and homeostasis 1-4. They are also implicated in human developmental disorders and cancers 5-8, supporting the critical role of DNA methylation in the specification and maintenance of cell fate. Previous studies have suggested that post-translational modifications of histones are involved in specifying patterns of DNA methyltransferase localization and DNA methylation at promoters and actively transcribed gene bodies 9-11. However, the mechanisms that control the establishment and maintenance of intergenic DNA methylation remain poorly understood. Tatton-Brown-Rahman syndrome (TBRS) is a childhood overgrowth disorder that is defined by germline mutations in DNMT3A. TBRS shares clinical features with Sotos syndrome (which is caused by haploinsufficiency of NSD1, a histone methyltransferase that catalyses the dimethylation of histone H3 at K36 (H3K36me2)8,12,13), which suggests that there is a mechanistic link between these two diseases. Here we report that NSD1-mediated H3K36me2 is required for the recruitment of DNMT3A and maintenance of DNA methylation at intergenic regions. Genome-wide analysis shows that the binding and activity of DNMT3A colocalize with H3K36me2 at non-coding regions of euchromatin. Genetic ablation of Nsd1 and its paralogue Nsd2 in mouse cells results in a redistribution of DNMT3A to H3K36me3-modified gene bodies and a reduction in the methylation of intergenic DNA. Blood samples from patients with Sotos syndrome and NSD1-mutant tumours also exhibit hypomethylation of intergenic DNA. The PWWP domain of DNMT3A shows dual recognition of H3K36me2 and H3K36me3 in vitro, with a higher binding affinity towards H3K36me2 that is abrogated by TBRS-derived missense mutations. Together, our study reveals a trans-chromatin regulatory pathway that connects aberrant intergenic CpG methylation to human neoplastic and developmental overgrowth.

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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citation
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Self-citation
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Integrative genomics viewer
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984

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Additional file 12 of Hypoxia induces alterations in tRNA modifications involved in translational control
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Additional file 13 of Hypoxia induces alterations in tRNA modifications involved in translational control
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Additional file 3 of Partial erosion on under-methylated regions and chromatin reprogramming contribute to oncogene activation in IDH mutant gliomas
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Additional file 10 of Hypoxia induces alterations in tRNA modifications involved in translational control
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Additional file 11 of Hypoxia induces alterations in tRNA modifications involved in translational control
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DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development
Ai, K. S., Wu, Y., Liang, G., Kong, H., Yang, X., Li, N., Liu, Z., Dong, Y., Xu, J., Zhang, L., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09003-w
Self-citation
DNA methylation landscapes in human cells and their chromatin determinants
Cui, W., Huang, Z., & Pfeifer, G. P. (2025) · Ageing and Cancer Research & Treatment · doi:10.70401/acrt.2025.0007
Additional file 3 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer
Song, P., Li, Y., Wang, F., Pu, L., Bao, L., Gao, H., Zhu, C., Wang, M., & Tao, L. (2022) · Figshare · doi:10.6084/m9.figshare.21443528
Additional file 8 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600414
Additional file 4 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer
Song, P., Li, Y., Wang, F., Pu, L., Bao, L., Gao, H., Zhu, C., Wang, M., & Tao, L. (2022) · Figshare · doi:10.6084/m9.figshare.21443531
Additional file 7 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600411
Additional file 5 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer
Song, P., Li, Y., Wang, F., Pu, L., Bao, L., Gao, H., Zhu, C., Wang, M., & Tao, L. (2022) · Figshare · doi:10.6084/m9.figshare.21443534
Additional file 2 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600387
Additional file 4 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600396
Additional file 1 of CircMAPK1 induces cell pyroptosis in sepsis-induced lung injury by mediating KDM2B mRNA decay to epigenetically regulate WNK1
Li, M., Lu, H., Ruan, C., Ke, Q., Hu, L., Li, Z., & Liu, X. (2024) · Figshare · doi:10.6084/m9.figshare.27071746
Additional file 6 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600405
Additional file 2 of Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome
Khoury, L. Y. E., Pan, X., Hlady, R. A., Wagner, R. T., Shaikh, S., Wang, L., Humphreys, M. R., Castle, E. P., Stanton, M. L., Ho, T. H., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26585937
Additional file 5 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600402
Additional file 3 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600390
Additional file 1 of Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome
Khoury, L. Y. E., Pan, X., Hlady, R. A., Wagner, R. T., Shaikh, S., Wang, L., Humphreys, M. R., Castle, E. P., Stanton, M. L., Ho, T. H., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26585934
Additional file 1 of Partial erosion on under-methylated regions and chromatin reprogramming contribute to oncogene activation in IDH mutant gliomas
Wang, X., Dai, L., Liu, Y., Li, C., Fan, D., Zhou, Y., Li, P., Kong, Q., & Su, J. (2023) · Figshare · doi:10.6084/m9.figshare.22721486
Additional file 9 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600417
Additional file 3 of Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation
Zheng, Y., Ziman, B., Ho, A. S., Sinha, U. K., Xu, L.-Y., Li, E., Koeffler, H. P., Berman, B. P., & Lin, D.-C. (2023) · Figshare · doi:10.6084/m9.figshare.24030888
Additional file 2 of CircMAPK1 induces cell pyroptosis in sepsis-induced lung injury by mediating KDM2B mRNA decay to epigenetically regulate WNK1
Li, M., Lu, H., Ruan, C., Ke, Q., Hu, L., Li, Z., & Liu, X. (2024) · Figshare · doi:10.6084/m9.figshare.27071752
Additional file 1 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer
Song, P., Li, Y., Wang, F., Pu, L., Bao, L., Gao, H., Zhu, C., Wang, M., & Tao, L. (2022) · Figshare · doi:10.6084/m9.figshare.21443522
Additional file 1 of Hypoxia induces alterations in tRNA modifications involved in translational control
Guo, H., Xia, L., Wang, W., Xu, W., Shen, X., Wu, X., He, T., Jiang, X., Xu, Y., Zhao, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22600378
Additional file 1 of Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation
Zheng, Y., Ziman, B., Ho, A. S., Sinha, U. K., Xu, L.-Y., Li, E., Koeffler, H. P., Berman, B. P., & Lin, D.-C. (2023) · Figshare · doi:10.6084/m9.figshare.24030882
Additional file 1 of Polygenic risk score model for renal cell carcinoma in the Korean population and relationship with lifestyle-associated factors
Hong, J. Y., Han, J. H., Jeong, S. H., Kwak, C., Kim, H. H., & Jeong, C. W. (2024) · Figshare · doi:10.6084/m9.figshare.24979546
Convergent DNA methylation abnormalities at enhancers and bivalent promoters in human growth disorders
Wheeler, M. E. S., Takahashi, Y., Lee, J., Perez, C. T., Chen, X., Lee, Y., Pope, Z. S., Lu, D., Seldin, M., Marazzi, I., et al. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00650-1 · Cited by 1
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The role of NSD1 gene expression in cancer pathogenesis: Opportunities for personalized therapeutics
Dara, M., Dianatpour, M., Azarpira, N., & Pourjafar, S. (2026) · Human Gene · doi:10.1016/j.humgen.2026.201535
The conserved N-terminal SANT1-binding domain (SBD) of EZH2 regulates PRC2 activityPreprint
Patriotis, A. L., Soto‐Feliciano, Y. M., Barrows, D., Khan, L. F., Leboeuf, M., Lund, P. J., Marunde, M. R., Djomo, A., Keogh, M., Carroll, T. S., et al. (2026) · Genes & Development · doi:10.1101/gad.353070.125
Self-citation
Nucleosome spacing regulates linker methylation by DNMT3A2/3B3
Xie, X., Liu, M., Chua, G. N. L., Zhou, X. E., Dykstra, M. L., Liu, S., Jones, P. A., & Worden, E. J. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.01.030 · Cited by 1
Pathology of Methylation, Demethylation, and Methylated DNA Binding Machinery
Земляная, О. А., Strelnikov, V. V., & Zaletaev, D. V. (2026) · Molecular Biology · doi:10.1134/s0026893325700566

Authors: Weinberg, D. N., Papillon-Cavanagh, S., Chen, H., Yue, Y., Chen, X., Rajagopalan, K. N., Horth, C., McGuire, J. T., Xu, X., Nikbakht, H., Lemiesz, A. E., Marchione, D. M., Marunde, M. R., Meiners, M. J., Cheek, M. A., Keogh, M.-C., Bareke, E., Djedid, A., Harutyunyan, A. S., Jabado, N., Garcia, B. A., Li, H., Allis, C. D., Majewski, J., & Lu, C.
Affiliations: Rockefeller University (US)
Center for Life Sciences (CN)
Columbia University Irving Medical Center (US)
McGill University (CA)
University of Pennsylvania (US)
McGill University Health Centre (CA)
Corresponding author: Allis, C. David
Majewski, Jacek
ORCID: Weinberg, Daniel N.
Chen, Xiao
Rajagopalan, Kartik N.
Horth, Cynthia
Xu, Xinjing
Nikbakht, Hamid
Marchione, Dylan M.
Marunde, Matthew R.
Meiners, Matthew J.
Cheek, Marcus A.
Keogh, Michael-Christopher
Bareke, Eric
Djedid, Anissa
Harutyunyan, Ashot S.
Jabado, Nada
Garcia, Benjamin A.
Li, Haitao
Allis, C. David
Majewski, Jacek
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-09-04
Volume: 573
Issue: 7773
Pages: 281-286
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1534-3
PMC: PMC6742567
OpenAlex: W2972254987
Cited by: 524
References: 47
Citations by year: 2026: 48 · 2025: 66 · 2024: 85 · 2023: 79 · 2022: 95 · 2021: 97 · 2020: 46 · 2019: 7
FWCI: 20.43
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Cancer Institute (P01CA196539, R00CA212257, F30CA224971, P30CA013696)
National Institute of General Medical Sciences (T32GM008275, R44GM117683, R44GM116584, T32GM007739)
National Institute of Environmental Health Sciences (P30ES013508)
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: H3K36me3, DNMT3A, DNA methylation, intergenic regions, CpG methylation, NSD1, NSD2, PWWP domain, histone modifications, Sotos syndrome, Tatton-Brown-Rahman syndrome, overgrowth disorder, histone methyltransferase
MeSH terms: Protein Domains, DNA Methyltransferase 3A, Animals, Cell Line, DNA (Cytosine-5-)-Methyltransferases, Growth Disorders, Histones, Humans, Protein Binding, DNA Methylation, Protein Transport, DNA, Intergenic, Mice, Genome-Wide Association Study, Sotos Syndrome

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The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

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