The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants
Open accessAbstract
SUMMARY DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homologue, ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both BAH- and chromo-domains. The structures reveal an aromatic cage within both BAH- and chromo-domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes, and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH- and chromo-domains, and reveals a novel mechanism of interplay between DNA methylation and histone modification.
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.
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
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Jenuwein, T., & Allis, C. D. (2001) · Science · doi:10.1126/science.1063127 · Cited by 9,756
Crystal structure of the nucleosome core particle at 2.8 Å resolution
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. (1997) · Nature · doi:10.1038/38444 · Cited by 9,466
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334
Chen, X., Xiu, M., Xing, J., Yu, S., Min, D., & Guo, F. (2017) · Cellular Physiology and Biochemistry · doi:10.1159/000479439 · Cited by 5,742
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 3,850
Self-citationShotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., Pradhan, S., Nelson, S. F., Pellegrini, M., & Jacobsen, S. E. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,256
Self-citationGateway‐compatible vectors for plant functional genomics and proteomics
Earley, K. W., Haag, J. R., Pontes, O., Opper, K., Juehne, T., Song, K., & Pikaard, C. S. (2006) · The Plant Journal · doi:10.1111/j.1365-313x.2005.02617.x · Cited by 1,790
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S.-P., Allis, C. D., et al. (2007) · Nature · doi:10.1038/nature05987 · Cited by 1,567
UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells
Bostick, M., Kim, J. K., Estève, P.-O., Clark, A., Pradhan, S., & Jacobsen, S. E. (2007) · Science · doi:10.1126/science.1147939 · Cited by 1,455
Self-citationControl of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase
Jackson, J. P., Lindroth, A. M., Cao, X., & Jacobsen, S. E. (2002) · Nature · doi:10.1038/nature731 · Cited by 1,251
Self-citationHhal methyltransferase flips its target base out of the DNA helix
Klimasauskas, S., Kumar, S., Roberts, R. J., & Cheng, X. (1994) · Cell · doi:10.1016/0092-8674(94)90342-5 · Cited by 945
Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation
Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff, S., & Jacobsen, S. E. (2001) · Science · doi:10.1126/science.1059745 · Cited by 938
Self-citationStructure 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 846
Structure of HP1 Chromodomain Bound to a Lysine 9-Methylated Histone H3 Tail
Jacobs, S. A., & Khorasanizadeh, S. (2002) · Science · doi:10.1126/science.1069473 · Cited by 832
Roudier, F., Ahmed, I., Bérard, C., Sarazin, A., Mary-Huard, T., Cortijo, S., Bouyer, D., Caillieux, E., Duvernois-Berthet, E., Al-Shikhley, L., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.103 · Cited by 706
Relationship between nucleosome positioning and DNA methylation
Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., Chen, P.-Y., Stroud, H., Yu, Y., Hetzel, J. A., Kuo, F., Kim, J., Cokus, S. J., et al. (2010) · Nature · doi:10.1038/nature09147 · Cited by 696
Self-citationRecombinant Human DNA (Cytosine-5) Methyltransferase
Pradhan, S., Bacolla, A., Wells, R. D., & Roberts, R. J. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.46.33002 · Cited by 651
Self-citationStructure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation
Song, J., Rechkoblit, O., Bestor, T. H., & Patel, D. J. (2011) · Science · doi:10.1126/science.1195380 · Cited by 471
Self-citationThe SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation
Johnson, L. M., Bostick, M., Zhang, X., Kraft, E., Henderson, I., Callis, J., & Jacobsen, S. E. (2007) · Current Biology · doi:10.1016/j.cub.2007.01.009 · Cited by 418
Self-citationOtani, J., Nankumo, T., Arita, K., Inamoto, S., Ariyoshi, M., & Shirakawa, M. (2009) · EMBO reports · doi:10.1038/embor.2009.218 · Cited by 414
Bestor, T. H., & Ingram, V. M. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.18.5559 · Cited by 366
Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3
Lindroth, A. M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Schubert, D., Patnaik, D., Pradhan, S., Goodrich, J., Schubert, I., et al. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600430 · Cited by 359
Self-citationThe BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier–Gorlin syndrome
Kuo, A. J., Song, J., Cheung, P., Ishibe-Murakami, S., Yamazoe, S., Chen, J. K., Patel, D. J., & Gozani, O. (2012) · Nature · doi:10.1038/nature10956 · Cited by 348
Self-citationStructure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation
Song, J., Teplova, M., Ishibe-Murakami, S., & Patel, D. J. (2012) · Science · doi:10.1126/science.1214453 · Cited by 335
Self-citationBernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., & Jacobsen, S. E. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003156 · Cited by 333
Self-citationJackson, J. P., Johnson, L., Jasencakova, Z., Zhang, X., PerezBurgos, L., Singh, P. B., Cheng, X., Schubert, I., Jenuwein, T., & Jacobsen, S. E. (2004) · Chromosoma · doi:10.1007/s00412-004-0275-7 · Cited by 326
Self-citationATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing
Jacob, Y., Feng, S., LeBlanc, C. A., Bernatavichute, Y. V., Stroud, H., Cokus, S., Johnson, L. M., Pellegrini, M., Jacobsen, S. E., & Michaels, S. D. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1611 · Cited by 324
Self-citationAn Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation
Malagnac, F. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf687 · Cited by 313
EdU, a new thymidine analogue for labelling proliferating cells in the nervous system
Chehrehasa, F., Meedeniya, A. C. B., Dwyer, P., Abrahamsen, G., & Mackay-Sim, A. (2009) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2008.10.006 · Cited by 281
Structural Basis of Silencing: Sir3 BAH Domain in Complex with a Nucleosome at 3.0 Å Resolution
Armache, K.-J., Garlick, J. D., Canzio, D., Narlikar, G. J., & Kingston, R. E. (2011) · Science · doi:10.1126/science.1210915 · Cited by 257
Recognition of Multivalent Histone States Associated with Heterochromatin by UHRF1 Protein
Nady, N., Lemak, A., Walker, J. R., Avvakumov, G. V., Kareta, M. S., Achour, M., Xue, S., Duan, S., Allali-Hassani, A., Zuo, X., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.234104 · Cited by 233
Law, J. A., Ausin, I., Johnson, L. M., Vashisht, A. A., Zhu, J.-K., Wohlschlegel, J. A., & Jacobsen, S. E. (2010) · Current Biology · doi:10.1016/j.cub.2010.03.062 · Cited by 213
Self-citationLaird, C. D., Pleasant, N. D., Clark, A. D., Sneeden, J. L., Hassan, K. M. A., Manley, N. C., Vary, J. C., Morgan, T., Hansen, R. S., & Stöger, R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2536758100 · Cited by 212
Okada, T., Endo, M., Singh, M. B., & Bhalla, P. L. (2005) · The Plant Journal · doi:10.1111/j.1365-313x.2005.02554.x · Cited by 208
Rajakumara, E., Wang, Z., Ma, H., Hu, L., Chen, H., Lin, Y., Guo, R., Wu, F., Li, H., Lan, F., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.07.006 · Cited by 208
Self-citationSelective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA
Jeong, S., Liang, G., Sharma, S., Lin, J. C., Choi, S. H., Han, H., Yoo, C. B., Egger, G., Yang, A. S., & Jones, P. A. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00484-09 · Cited by 192
Role of the Conserved Sir3-BAH Domain in Nucleosome Binding and Silent Chromatin Assembly
Onishi, M., Liou, G.-G., Buchberger, J. R., Walz, T., & Moazed, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.12.004 · Cited by 166
Substrate Specificity and Kinetic Mechanism of Mammalian G9a Histone H3 Methyltransferase
Patnaik, D., Chin, H. G., Estève, P., Benner, J. S., Jacobsen, S. E., & Pradhan, S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409604200 · Cited by 152
Self-citationMaize Chromomethylase Zea methyltransferase2 Is Required for CpNpG Methylation
Papa, C. M., Springer, N. M., Muszynski, M. G., Meeley, R. B., & Kaeppler, S. M. (2001) · The Plant Cell · doi:10.1105/tpc.010064 · Cited by 139
Recombinant Human DNA (Cytosine-5) Methyltransferase
Bacolla, A., Pradhan, S., Roberts, R. J., & Wells, R. D. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.46.33011 · Cited by 131
Self-citationRajakumara, E., Law, J. A., Simanshu, D. K., Voigt, P., Johnson, L. M., Reinberg, D., Patel, D. J., & Jacobsen, S. E. (2011) · Genes & Development · doi:10.1101/gad.1980311 · Cited by 111
Self-citationXie, S., Jakoncic, J., & Qian, C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.11.012 · Cited by 109
Bartee, L. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.10.2127 · Cited by 81
Chang, Y., Horton, J. R., Bedford, M. T., Zhang, X., & Cheng, X. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.018 · Cited by 52
Cited by
DNA methylation pathways and their crosstalk with histone methylation
Du, J., Johnson, L. M., Jacobsen, S. E., & Patel, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4043 · Cited by 1,000
Self-citationGene body DNA methylation in plants
Bewick, A. J., & Schmitz, R. J. (2017) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.12.007 · Cited by 409
Erdmann, R. M., & Picard, C. L. (2020) · PLOS Genetics · doi:10.1371/journal.pgen.1009034 · Cited by 389
Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases
Zhong, X., Du, J., Hale, C. J., Gallego-Bartolome, J., Feng, S., Vashisht, A. A., Chory, J., Wohlschlegel, J. A., Patel, D. J., & Jacobsen, S. E. (2014) · Cell · doi:10.1016/j.cell.2014.03.056 · Cited by 320
Self-citationDynamics of dna methylation and its functions in plant growth and development
Kumar, S., & Mohapatra, T. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.596236 · Cited by 227
Metadata
- Authors
- Du, J., Zhong, X., Bernatavichute, Y. V., Stroud, H., Feng, S., Caro, E., Vashisht, A. A., Terragni, J., Chin, H. G., Tu, A., Hetzel, J., Wohlschlegel, J. A., Pradhan, S., Patel, D. J., & Jacobsen, S. E.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-09
- Volume
- 151
- Issue
- 1
- Pages
- 167-180
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2107314112
- Cited by
- 555
- References
- 49
- FWCI
- 10.92
- Type
- journal article
- Language
- en
- Open access
- bronze
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
