Structure of H3K36-methylated nucleosome–PWWP complex reveals multivalent cross-gyre binding
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Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here, we report the cryo-electron microscopy structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with an H3K36-methylated nucleosome at 3.2-Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair.
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The LEDGF/p75 PWWP domain binds nucleosomes in vitro carrying a chemical mimic of H3K36me3, and LEDGF/p75 chromatin distribution coincides with H3K36me2 and H3K36me3 marks.
“The LEDGF/p75 PWWP domain can bind nucleosomes in vitro that are modified to carry a chemical mimic of trimethylated lysine at position 36 of the histone H3 tail (H3K36me3)110,111, and spatial distribution of LEDGF/p75 on chromatin coincided with H3K36me2 and H3K36me3 epigenetic marks102.”
From Structure and function of retroviral integrase (2022) · cites this paper as [111]
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Bedwell, G. J., & Engelman, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1207 · Cited by 40 · see citing works
Structures of transcription preinitiation complex engaged with the +1 nucleosome
Wang, H., Schilbach, S., Ninov, M., Urlaub, H., & Cramer, P. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00865-w · Cited by 37 · see citing works
Self-citationStructural basis of transcription reduction by a promoter-proximal +1 nucleosome
Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., & Cramer, P. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.011 · Cited by 48 · see citing works
“Histones preparation and nucleosome reconstitution was performed as described.(52,66) Briefly,X.”
MethodSelf-citationStructures and implications of TBP–nucleosome complexes
Wang, H., Xiong, L., & Cramer, P. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2108859118 · Cited by 36 · see citing works
“PCR products were ethanol-precipitated and purified by anion-exchange chromatography as described (59).”
MethodSelf-citationSapp, N., Burge, N. L., Cox, K. L., Thapa, S., Prakash, P., Balasubramaniam, M., Christensen, D. E., Li, M., Linderberger, J., Kvaratskhelia, M., et al. (2022) · Journal of Virology · doi:10.1128/jvi.01011-22 · Cited by 28 · see citing works
Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure
Lobbia, V. R., Sánchez, M. C. T., & van Ingen, H. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166827 · Cited by 26 · see citing works
Multivalency of nucleosome recognition by LEDGF
Koutná, E., Lux, V., Kouba, T., Škerlová, J., Nováček, J., Srb, P., Hexnerova, R., Šváchová, H., Kukačka, Z., Novák, P., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad674 · Cited by 26 · see citing works
“The recently published cryo-electr on micr oscopy (cryo-EM) structure of the LEDGF / p75 PWWP bound to the H3K36me3 nucleosome re v ealed that the interaction is maintained by a cooperati v e interaction of the PWWP domain with the trimethylated lysine 36 side-chain and both DNA gyres ( 27 ).”
Bröhm, A., Schoch, T., Dukatz, M., Graf, N., Dorscht, F., Mantai, E., Adam, S., Bashtrykov, P., & Jeltsch, A. (2022) · Communications Biology · doi:10.1038/s42003-022-03119-z · Cited by 25 · see citing works
Targeting Epigenetic protein–protein Interactions With small-molecule Inhibitors
Linhares, B. M., Grembecka, J. E., & Cierpicki, T. (2020) · Future Medicinal Chemistry · doi:10.4155/fmc-2020-0082 · Cited by 25 · see citing works
“Recently, the first structure of the LEDGF PWWP domain in complex with H3K36-methylated nucleosome was determined by electron cryomicroscopy and revealed a multivalent binding mode of the PWWP domain, involved in both tri-methyl-lysine recognition and nucleosomal– DNA interactions [60].”
BackgroundChemical inhibitors targeting histone methylation readers
Huang, X., Chen, Y., Xiao, Q., Shang, X., & Liu, Y. (2024) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2024.108614 · Cited by 24 · see citing works
Histone and DNA binding ability studies of the NSD subfamily of PWWP domains
Zhang, M., Yang, Y., Zhou, M., Dong, A., Yan, X., Loppnau, P., Min, J., & Liu, Y. (2021) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2021.07.017 · Cited by 23 · see citing works
Histone code reader SPIN1 is a promising target of cancer therapy
Li, D., Guo, J., & Jia, R. (2021) · Biochimie · doi:10.1016/j.biochi.2021.09.002 · Cited by 23 · see citing works
Weinzapfel, E. N., Fedder-Semmes, K. N., Sun, Z., & Keogh, M. (2024) · Biochemical Journal · doi:10.1042/bcj20230342 · Cited by 23 · see citing works
Structure of histone deacetylase complex Rpd3S bound to nucleosome
(2023) · doi:10.1038/s41594-023-01121-5 · Cited by 20 · see citing works
“Xenopus laevis histones were expressed, purified and assembled into a histone octamer containing the H3K36 C me3 modification as previously reported 26 .”
Self-citationDNMT3B PWWP mutations cause hypermethylation of heterochromatin
Taglini, F., Kafetzopoulos, I., Rolls, W., Musialik, K. I., Lee, H. Y., Zhang, Y., Marenda, M., Kerr, L., Finan, H., Rubio-Ramon, C., et al. (2024) · EMBO Reports · doi:10.1038/s44319-024-00061-5 · Cited by 21 · see citing works
“…PWWP structures found to bind to DNA either in isolation (Protein Data Bank code 6IIT (Tian et al, 2019), 7LH9 (Zhang et al, 2021) https://www.rcsb.org/search? q=rcsb_pubmed_container_identi fi ers.pubmed_id:33556623) or in a modi fi ed nucleosome core particle (LEDGF PDB 6S01, (Wang et al, 2020)).”
Multivalent interactions essential for lentiviral integrase function
Ballandras-Colas, A., Chivukula, V., Gruszka, D. T., Shan, Z., Singh, P. K., Pye, V. E., McLean, R. K., Bedwell, G. J., Li, W., Nans, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29928-8 · Cited by 22 · see citing works
“The N-terminal PWWP domain binds nucleosomes carrying trimethylated histone H3 Lys36 (H3K36me3) (27-29).”
BackgroundStructural Basis of Nucleosome Recognition and Modulation
Sundaram, R., & Vasudevan, D. (2020) · BioEssays · doi:10.1002/bies.201900234 · Cited by 18 · see citing works
Ortiz-Hernández, G. L., Sanchez-Hernández, E. S., Ochoa, P. T., Elix, C. C., Alkashgari, H. R., McMullen, J. R. W., Soto, U., Martinez, S. R., Osterman, C. J. D., Mähler, M., et al. (2021) · Cells · doi:10.3390/cells10102723 · Cited by 19 · see citing works
“H3K36me2, a marker of active chromatin that is recognized by the LEDGF/p75 PWWP domain [25], also co-immunoprecipitated with LEDGF/p75 (Figure 3B).”
BackgroundČermáková, K., Veverka, V., & Hodges, H. C. (2023) · Biochemical Society Transactions · doi:10.1042/bst20220342 · Cited by 17 · see citing works
Zhang, M., Lei, M., Su, Q., Dong, A., Yang, A. W. H., Li, Y., Loppnau, P., Hughes, T. R., Min, J., & Liu, Y. (2021) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2021.194688 · Cited by 17 · see citing works
Retroviral integrase: Structure, mechanism, and inhibition
Passos, D. O., Li, M., Craigie, R., & Lyumkis, D. (2021) · The Enzymes · doi:10.1016/bs.enz.2021.06.007 · Cited by 18 · see citing works
“Since LEDGF is a nuclear factor that binds chromosomal DNA [107-109] through its PWWP domain and HIV-1 IN through its IBD domain, the factor may directly facilitate integration through a bimodal tethering mechanism to bring the PIC to regions characterized by active transcription.”
BackgroundEnzymology of Mammalian DNA Methyltransferases
Jurkowska, R. Z., & Jeltsch, A. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_4 · Cited by 17 · see citing works
Significance of targeting DNMT3A mutations in AML
Huang, G., Cai, X., & Li, D. (2024) · Annals of Hematology · doi:10.1007/s00277-024-05885-8 · Cited by 18 · see citing works
Structural basis of SIRT7 nucleosome engagement and substrate specificity
Moreno–Yruela, C., Ekundayo, B., Foteva, P. N., Ni, D., Calvino-Sanles, E., Stahlberg, H., & Fierz, B. (2025) · Nature Communications · doi:10.1038/s41467-025-56529-y · Cited by 14 · see citing works
“7) 49 .”
Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex
Markert, J. W., Vos, S. M., & Farnung, L. (2023) · Nature Communications · doi:10.1038/s41467-023-43968-8 · Cited by 15 · see citing works
“This interaction across DNA gyres is reminiscent of the engagement of the LEDGF PWWP domain with the trimethylated H3K36 nucleosome 33 (Supplementary Fig.”
Self-citationPhase separation and histone epigenetics in genome regulation
Harrison, R. E. S., Weng, K., Wang, Y., & Qin, P. (2020) · Current Opinion in Solid State and Materials Science · doi:10.1016/j.cossms.2020.100892 · Cited by 13 · see citing works
“These domains include Chromo domains, Tudor domains, Malignant Brain Tumor (MBT) domains, domains containing the PWWP motif (Pro-Trp-Trp-Pro) [59, 60], PHD finger domains [61, 62], beta-transducin repeats (WD40) [63], bromodomains (BRD) [64, 65], and Ankyrin repeats [66].”
BackgroundDeciphering histone H4 lysine acetylation and methylation via sortase-mediated semisynthesis
Xiao, Y., Zou, K., Yang, J. T., & Wu, M. (2023) · Cell Reports Physical Science · doi:10.1016/j.xcrp.2023.101638 · Cited by 13 · see citing works
Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers
Vann, K. R., Klein, B. J., & Kutateladze, T. G. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.04.003 · Cited by 12 · see citing works
Structures of chromatin modulators in complex with nucleosome
Min, J., & Liu, K. (2021) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2021.02.018 · Cited by 11 · see citing works
Histone modification–driven structural remodeling unleashes DNMT3B in DNA methylation
Cho, C., Huang, H.-H., Jiang, B.-C., Yang, W., Chen, Y., & Yuan, H. S. (2025) · Science Advances · doi:10.1126/sciadv.adu8116 · Cited by 12 · see citing works
“In a cryo-EM structure of the human transcriptional coactivator LEDGF in complex with an H3K36-methylated nucleosome, the PWWP domain displays multivalent binding to the methylated H3 tail and to both gyres of nucleosomal DNA ( 26 ).”
Jayakrishnan, M., Havlová, M., Veverka, V., Regnard, C., & Becker, P. B. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf202 · Cited by 11 · see citing works
“Reader domains for H3K36 methylation include PWWP [ 30 , 31 ], chromo [ 32 , 33 ], and tudor domains [ 34 ].”
Sanchez-Hernández, E. S., Ochoa, P. T., Suzuki, T., Ortiz-Hernández, G. L., Unternaehrer, J., Alkashgari, H. R., Osterman, C. J. D., Martinez, S. R., Chen, Z., Kremsky, I., et al. (2023) · Cells · doi:10.3390/cells12162046 · Cited by 10 · see citing works
“H3K36me2, an active chromatin marker and interacting partner of LEDGF/p75 [38,53,84], was included as a positive control and was also co-immunoprecipitated by the LEDGF/p75 autoantibodies (Figure 6A–C).”
BackgroundRational fragment-based design of compounds targeting the PWWP domain of the HRP family
Vantieghem, T., Aslam, N. A., Osipov, E. M., Akele, M. Z., Belle, S. V., Beelen, S., Drexler, M., Paulovcakova, T., Lux, V., Fearon, D., et al. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116960 · Cited by 10 · see citing works
Molecular Mechanism of LEDGF/p75 Dimerization
Lux, V., Brouns, T., Čermáková, K., Srb, P., Fábry, M., Mádlíková, M., Hořejší, M., Kukačka, Z., Novák, P., Kugler, M., et al. (2020) · Structure · doi:10.1016/j.str.2020.08.012 · Cited by 10 · see citing works
DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics
Wedd, L., Kucharski, R., & Maleszka, R. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_7 · Cited by 10 · see citing works
Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer
Dhahri, H., Saintilnord, W. N., Chandler, D., & Fondufe‐Mittendorf, Y. N. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25126788 · Cited by 9 · see citing works
Using human disease mutations to understand de novo DNA methyltransferase function
Rolls, W., Wilson, M. D., & Sproul, D. (2024) · Biochemical Society Transactions · doi:10.1042/bst20231017 · Cited by 9 · see citing works
Catching Nucleosome by Its Decorated Tails Determines Its Functional States
Sehrawat, P., Shobhawat, R., & Kumar, A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.903923 · Cited by 9 · see citing works
“Except for Pdp1, all the proteins containing PWWP domains bind specifically to the H3K36 methylation, suggesting its role as the H3K36 methylation sensor (Vezzoli et al., 2010; van Nuland et al., 2013; Wang et al., 2020).”
BackgroundZhang, Y., Guo, W., Feng, Y., Yang, L., Lin, H., Zhou, P., Zhao, K., Jiang, L., Yao, B., & Feng, N. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.08.023 · Cited by 9 · see citing works
“The PWWP domain reads the H3K36me3 mark, which is an important regulatory mode in epigenetics[39].”
BackgroundApproaches to Study Native Chromatin-Modifying Complex Activities and Functions
Galloy, M., Lachance, C., Cheng, X., Distéfano‐Gagné, F., Côté, J., & Fradet‐Turcotte, A. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.729338 · Cited by 9 · see citing works
“Indeed, many histone PTMs are regulated by crosstalk between histone modifications, a phenomenon that can induce secondary effects when histone modifiers are depleted or knocked out (McGinty et al., 2008; Lalonde et al., 2014; Jacquet et al., 2016; Wojcik et al., 2018; Zhang and Kutateladze, 2019).”
BackgroundAdvances in inhibitor development targeting the PWWP domain
Huang, Y., Li, Y., & Min, J. (2024) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2024.01.007 · Cited by 8 · see citing works
Kawai, T., Kinoshita, S., Takayama, Y., Ohnishi, E., Kamura, H., Kojima, K., Kikuchi, H., Terao, M., Sugawara, T., Migita, O., et al. (2024) · Genetics in Medicine Open · doi:10.1016/j.gimo.2024.101838 · Cited by 7 · see citing works
“43 These genes could be involved in pathological conditions as direct targets of Nsd2 loss-of-function variants.”
Su, R., Wang, Q., Hu, Q., Wendurige, Li, K., Wang, C., & Tao, L. (2025) · Biomolecules · doi:10.3390/biom15020282 · Cited by 7 · see citing works
“Given that HDGF family members possess a highly conserved PWWP structural domain [23], we hypothesize that HDGF has a similar function in regulating DDR.”
H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function
Li, J., Bergmann, L., de Almeida, A. R., Webb, K. M., Gogol, M., Voigt, P., Liu, Y., Liang, H., & Smolle, M. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac077 · Cited by 7 · see citing works
Structure and function of IWS1 in transcription elongation
Syau, D., Steinruecke, F., Roth, S., Schmid, E., Adelman, K., Walter, J. C., & Farnung, L. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag357 · Cited by 5 · see citing works
“Of note, we included LEDGF in the preparation because of its known interaction with IWS1 and nucleosomes [ 19 , 25 , 59 , 60 ].”
InfluentialSelf-citationInhibitors targeting the PWWP domain-containing proteins
Huang, Y., Li, B., Wu, Z., Liu, K., & Min, J. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116965 · Cited by 6 · see citing works
Zou, K., Yang, J., Gao, Y., Feng, F., & Wu, M. (2024) · Chemical Science · doi:10.1039/d4sc05886k · Cited by 6 · see citing works
Dias, J. K., & D’Arcy, S. (2025) · Biochemical Society Transactions · doi:10.1042/bst20230721 · Cited by 6 · see citing works
“Positioning sequence models are crucial in making high-resolution structural work possible due to higher nucleosome stability [15,21,47–49] although the W601 does have a similar unwrapping energy to native yeast nucleosomes [50].”
The Impact of Lens Epithelium-Derived Growth Factor p75 Dimerization on Its Tethering Function
Brouns, T., Lux, V., Belle, S. V., Christ, F., Veverka, V., & Debyser, Z. (2024) · Cells · doi:10.3390/cells13030227 · Cited by 5 · see citing works
Modulation of the functional interfaces between retroviral intasomes and the human nucleosome
Mauro, E., Lapaillerie, D., Tumiotto, C., Charlier, C., Martins, F. G., Sousa, S. F., Métifiot, M., Weigel, P., Yamatsugu, K., Kanai, M., et al. (2023) · mBio · doi:10.1128/mbio.01083-23 · Cited by 5 · see citing works
MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation
Watson, J. A., Alexander-Howden, B., Hall, T. S., Wear, M. A., McGhie, F., Clifford, G., Wapenaar, H., Zou, J., Bird, A. P., & Wilson, M. D. (2026) · Nature Communications · doi:10.1038/s41467-026-71741-0 · Cited by 4 · see citing works
Zhang, Y., Zhou, Y., Zhang, Y., Lv, J., Shen, Y., Zhang, D., Liu, B., Zhao, W., Ju, J., Zhu, Q., et al. (2025) · Advanced Science · doi:10.1002/advs.202416809 · Cited by 4 · see citing works
Jayakrishnan, M., Havlová, M., Veverka, V., Regnard, C., & Becker, P. B. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae449 · Cited by 4 · see citing works
RetractedThe role of chromatin in retroviral preintegration complex function
Sapp, N., Prakash, P., Chakraborty, R., Balasubramaniam, M., & Dash, C. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.110440 · Cited by 3 · see citing works
“4), binds to methylated histones and the C-terminal IN-binding domain (110, 113–115, 219, 257).”
PWWP3A deficiency accelerates testicular senescence in aged mice
Chen, Z., Liu, C., Qu, W., Han, Y., Zhu, X., Li, Z., Ma, D., Huang, M., Gong, W., Sun, Q., et al. (2024) · Andrology · doi:10.1111/andr.13774 · Cited by 3 · see citing works
Structure of the complete S. cerevisiae Rpd3S-nucleosome complexPreprint
Markert, J. W., Vos, S. M., & Farnung, L. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.03.551877 · Cited by 3 · see citing works
Self-citationThe structural basis for de novo DNA methylation in chromatinPreprint
Xie, X., Liu, M., Zhou, X. E., Dykstra, M. L., Jones, P. A., & Worden, E. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.19.629503 · Cited by 3 · see citing works
Chromatin Regulatory Targets for Anticancer Therapeutics
Barta, P. A., Carter, T. R., & Erb, M. A. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.5c00231 · Cited by 2 · see citing works
Horn, V., Jongkees, S. A. K., & van Ingen, H. (2020) · Molecules · doi:10.3390/molecules25214951 · Cited by 2 · see citing works
“(a) Structure of PSIP1PWWP bound to nucleosomes with trimethylated H3 tail residue K36 (H3K36me3), illustrating the electrostatic interactions of positively charged surface residues on the PWWP domain with both gyres of nucleosomal DNA [36,38].”
BackgroundPWWP2A/B: Prominent players in the proteomic landscape
Ponne, S., Chinnadurai, R. K., Kumar, R., Mohanty, A. K., Brilhante, R. S. N., Nhung, T. T. T., & Baluchamy, S. (2025) · Gene · doi:10.1016/j.gene.2025.149245 · Cited by 2 · see citing works
NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization
Li, Z., & Fei, J. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26104874 · Cited by 2 · see citing works
Vantieghem, T., Osipov, E. M., Beelen, S., & Strelkov, S. V. (2025) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x25006302 · Cited by 2 · see citing works
Kim, S. H., Enwerem-Lackland, I., Williams, N. L., Fisher, R., Plaisier, C. L., & Haynes, K. A. (2026) · npj Systems Biology and Applications · doi:10.1038/s41540-026-00781-5 · Cited by 1 · see citing works
The NPAC-LSD2 complex in nucleosome demethylation
Caroli, J., & Mattevi, A. (2023) · The Enzymes · doi:10.1016/bs.enz.2023.03.003 · Cited by 1 · see citing works
Recognition of histone methylation and DNA by the PWWP domain: Mechanism and function
Fang, Y., Mangipudy, V. S., Jia, S., Lü, C., & Chen, X. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-823376-4.00008-2 · Cited by 1 · see citing works
Structural basis of thymidine-rich DNA recognition by Drosophila P75 PWWP domain
Jin, Z., Meng, Z., Liu, Y., Li, C., Zhang, X., Yin, Y., Gao, G., Dou, K., & Huang, Y. (2025) · Communications Biology · doi:10.1038/s42003-025-07895-2 · Cited by 1 · see citing works
Intact Nucleosomal Context Enables Chromodomain Reader MRG15 to Distinguish H3K36me3 from - Me2Preprint
Faulkner, S., Couturier, A. M., Josephson, B., Watts, T., Davis, B. G., & Esashi, F. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.30.070136 · Cited by 1 · see citing works
Sapp, N., Burge, N. L., Cox, K. L., Thapa, S., Prakash, P., Balasubramaniam, M., Christenson, D., Li, M., Linderberger, J., Kvaratskhelia, M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.16.480507 · Cited by 1 · see citing works
Kawai, T., Kinoshita, S., Takayama, Y., Onishi, E., Kamura, H., Kojima, K., Kikuchi, H., Terao, M., Sugawara, T., Migita, O., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.06.522834 · Cited by 1 · see citing works
“NSD2 is reportedly located near TSS but avoids it,(33) and involved in transcription.(34) These genes could be involved in pathological conditions as direct targets of Nsd2 loss-of-function variants.”
BackgroundThe role of LEDGF in transcription is exploited by HIV-1 to position integrationPreprint
Pathak, R., Esnault, C., Radhakrishnan, R., Singh, P. K., Zhang, H., Dale, R., Anand, A., Bedwell, G. J., Engelman, A., Rabi, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.29.601340 · Cited by 1 · see citing works
H3.3 De Novo Mutations Alter Lysine 36 Methylation via Distinct MechanismsPreprint
Morcos, S. M., Sarvan, S., Saettone, A., Wong, C. J., Vo, S., Milo, A., Bayoumy, O. H., Angireddy, R., Burke, G. L., Greenblatt, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.09.674984 · Cited by 1 · see citing works
H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeller functionPreprint
Li, J., Bergmann, L., de Almeida, A. R., Webb, K. M., Gogol, M., Voigt, P., Liu, Y., Liang, H., & Smolle, M. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.26.432832
Toward Understanding Pharmacological Modulation of DNA Methylation
Horton, J. R. (2024) · Royal Society of Chemistry eBooks · doi:10.1039/9781837674916-00193
Drug Discovery for Chromatin Readers, Writers, Erasers, Remodelers and Epitranscriptomic Targets
(2024) · Royal Society of Chemistry eBooks · doi:10.1039/9781837674916-part3
Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?
SUZUKI, H., Okumura, H., & Itoh, S. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0259337
Association of the PWWP ‐domain protein HUA2 and the H3K36 methylation in flowering time control
Xie, Q., Li, Z., Zhao, W., Dong, A., Ruan, Y., & Shen, W. (2025) · The Plant Journal · doi:10.1111/tpj.70461
Genome-wide identification and characterization of SET domain family genes in Neopyropia yezoensis
Tang, X., Wang, J., Zhu, X., Qin, H., Bian, K., Meng, C., & Mao, Y. (2026) · BMC Genomics · doi:10.1186/s12864-026-12530-3
“These domains facilitate the recruitment of chromatin-modifying complexes and establish transcriptionally active chromatin states [36, 37].”
Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration
Pathak, R., Esnault, C., Radhakrishnan, R., Singh, P. K., Zhang, H., Dale, R., Anand, A., Mitra, A., Bedwell, G. J., Engelman, A., et al. (2026) · mBio · doi:10.1128/mbio.00090-26 · Cited by 2 · see citing works
“This result was unexpected because of reports that the PWWP domain is important for the association of LEDGF with chromatin (23, 26, 31, 33).”
Identification of specific phylogenetic properties of HIV-1 M and O integrases
Toccafondi, E. (2022) · theses.fr (ABES) · doi:10.70675/2facab6ezc20az472dz8350z9fb6e718e1d4 · Cited by 1 · see citing works
High-Affinity Nanobody Against the LEDGF PWWP Domain Inhibits Chromatin Binding In Vitro
Vantieghem, T., Jansen, S., Akele, M. Z., Maele, P. V., Noppen, S., Schols, D., Dewilde, M., Debyser, Z., & Strelkov, S. V. (2026) · Biomolecules · doi:10.3390/biom16050716
De novo design of proteinaceous binders targeting the LEDGF PWWP domain
Vantieghem, T., Delepine, J., Noppen, S., Beelen, S., Drexler, M., Holková, J., Houser, J., Veverka, V., Schols, D., & Strelkov, S. V. (2026) · Protein Science · doi:10.1002/pro.70726
“Of note, past cryo-EM studies (Koutn (cid:1) a et al., 2023; Wang et al., 2020) identified positively charged residues involved in DNA engagement upon binding to the nucleosome (Figure S1), namely Lys73, Arg74, and Lys75 (forming the so-called R74 groove), as well as Lys14, Lys16, Lys39, and Lys56.”
InfluentialDPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesisPreprint
Yu, M., Xue, J., Zhang, Q., Pan, Y., Hao, M., Hu, M., Liu, M., Feng, Y., Yao, Y., Peng, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.25.746968
BindingDB Entry 50022700: Inhibitors targeting the PWWP domain-containing proteins.
BindingDB (2026) · UC San Diego · doi:10.7270/q29028k3
BindingDB (2026) · UC San Diego · doi:10.7270/q2s75n55
- Authors
- Wang, H., Farnung, L., Dienemann, C., & Cramer, P.
- Affiliations
- Max Planck Institute for Biophysical Chemistry (DE)
- Corresponding author
- Cramer, Patrick
- Venue
- Nature Structural & Molecular Biology
- Published
- 2019-12-09
- Volume
- 27
- Issue
- 1
- Pages
- 8-13
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC6955156
- OpenAlex
- W2994082096
- Cited by
- 93
- References
- 75
- Citations by year
- 2026: 10 · 2025: 15 · 2024: 20 · 2023: 13 · 2022: 12 · 2021: 14 · 2020: 9
- FWCI
- 2.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- H3K36 methylation, nucleosome, PWWP domain, LEDGF, multivalent binding, chromatin regulation, transcriptional coactivator, cryo-EM structure
- MeSH terms
- Protein Domains, Amino Acid Sequence, DNA, Histones, Humans, Methylation, Models, Molecular, Nucleosomes, Protein Binding, Protein Conformation, Transcription Factors, Sequence Alignment, Cryoelectron Microscopy, Adaptor Proteins, Signal Transducing
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