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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA

Sapp, 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

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

Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes

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Viruses in the NucleusPreprint

Lucic, B., de Castro, I. J., & Lušić, M. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039446 · Cited by 24 · see citing works

Systematic Identification of Protein Phosphorylation-Mediated Interactions

Floyd, B. M., Drew, K., & Marcotte, E. M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00750 · Cited by 21 · see citing works

Expansion microscopy allows high resolution single cell analysis of epigenetic readers

Acke, A., Belle, S. V., Louis, B., Vitale, R., Rocha, S., Voet, T., Debyser, Z., & Hofkens, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac521 · Cited by 23 · see citing works

Histone methyltransferase SETD2: An epigenetic driver in clear cell renal cell carcinoma

Yu, M., Qian, K., Wang, G., Xiao, Y., Zhu, Y., & Ju, L. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1114461 · Cited by 23 · see citing works

Epigenomic reprogramming via HRP2-MINA dictates response to proteasome inhibitors in multiple myeloma with t(4;14) translocation

Wang, J., Zhu, X., Dang, L., Jiang, H., Xie, Y., Li, X., Guo, J. R., Wang, Y., Peng, Z., Wang, M., et al. (2022) · Journal of Clinical Investigation · doi:10.1172/jci149526 · Cited by 22 · see citing works

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 LEDGF/p75 Integrase Binding Domain Interactome Contributes to the Survival, Clonogenicity, and Tumorsphere Formation of Docetaxel-Resistant Prostate Cancer Cells

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

Chromatin Transcription Elongation – A Structural Perspective

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The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder

Čermáková, K., Veverka, V., & Hodges, H. C. (2023) · Biochemical Society Transactions · doi:10.1042/bst20220342 · Cited by 17 · see citing works

Structural Transition of the Nucleosome during Transcription Elongation

Kujirai, T., Ehara, H., Sekine, S., & Kurumizaka, H. (2023) · Cells · doi:10.3390/cells12101388 · Cited by 17 · see citing works

Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove

Battista, S., Fedele, M., Secco, L., Ingo, A. M. D., Sgarra, R., & Manfioletti, G. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25168863 · Cited by 17 · see citing works

New connections between ubiquitylation and methylation in the co-transcriptional histone modification network

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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

Nucleosomes unwrapped: Structural perspectives on transcription through chromatin

Farnung, L. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102690 · Cited by 14 · see citing works

H3K36me3 and PSIP1/LEDGF associate with several DNA repair proteins, suggesting their role in efficient DNA repair at actively transcribing loci

Jayakumar, S., Taylor, G. C. A., von Kriegsheim, A., & Pradeepa, M. M. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.11589.4 · Cited by 12 · see citing works

The Nuclear Dense Fine Speckled (DFS) Immunofluorescence Pattern: Not All Roads Lead to DFS70/LEDGFp75

Sanchez-Hernández, E. S., Ortiz-Hernández, G. L., Ochoa, P. T., Reeves, M., Bizzaro, N., Andrade, L. E. C., Mähler, M., & Casiano, C. A. (2023) · Diagnostics · doi:10.3390/diagnostics13020222 · Cited by 13 · see citing works

Crosstalk within and beyond the Polycomb repressive system

Shi, T., Sugishita, H., & Gotoh, Y. (2024) · The Journal of Cell Biology · doi:10.1083/jcb.202311021 · Cited by 12 · see citing works

Dense fine speckled (DFS) immunofluorescence pattern and anti-DFS70 antibodies: Cleaning up the current concepts

Infantino, M. G., Carbone, T., Manfredi, M., Grossi, V., Benucci, M., Casiano, C. A., & Bizzaro, N. (2020) · Clinica Chimica Acta · doi:10.1016/j.cca.2020.07.001 · Cited by 12 · see citing works

Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers

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

Unlike its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival

Belle, S. V., Ashkar, S. E., Čermáková, K., Matthijssens, F., Goossens, S., Canella, A., Hodges, H. C., Christ, F., Rijck, J. D., Vlierberghe, P. V., et al. (2021) · Cells · doi:10.3390/cells10010192 · Cited by 12 · see citing works

Glucocorticoid Receptor Regulates and Interacts with LEDGF/p75 to Promote Docetaxel Resistance in Prostate Cancer Cells

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

Rational 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

Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes

de Fenffe, C. M. D., Govers, J., & Mattiroli, F. (2025) · Biochemistry · doi:10.1021/acs.biochem.5c00114 · 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

Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription

Kaja, A., Adhikari, A., Karmakar, S., Zhang, W., Rothschild, G., Basu, U., Batra, S. K., Davie, J. K., & Bhaumik, S. R. (2021) · Molecular and Cellular Biology · doi:10.1128/mcb.00452-20 · Cited by 10 · see citing works

Role of LEDGF/p75 (PSIP1) in oncogenesis. Insights in molecular mechanism and therapeutic potential

Akele, M. Z., Iervolino, M., Belle, S. V., Christ, F., & Debyser, Z. (2024) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2024.189248 · Cited by 9 · see citing works

Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin

Li, Z., Burgos‐Bravo, F., Xu, K., Li, C., Kwan, K. Y., Tong, A., Shan, Z., Wang, H., Takaku, M., Li, J. H., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01778-8 · Cited by 7 · see citing works

The Emerging Roles of the Stress Epigenetic Reader LEDGF/p75 in Cancer Biology and Therapy Resistance: Mechanisms and Targeting Opportunities

Ortiz-Hernández, G. L., Sanchez-Hernández, E. S., Ochoa, P. T., & Casiano, C. A. (2024) · Cancers · doi:10.3390/cancers16233957 · Cited by 6 · see citing works

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

LEDGF interacts with the NID domain of MeCP2 and modulates MeCP2 condensates

Lesire, S., Lata, R., Hoogvliets, Y., Herrebosch, K., de Velde, P. V., Speleers, A., Christ, F., Belle, S. V., & Debyser, Z. (2024) · Structure · doi:10.1016/j.str.2024.10.016 · Cited by 5 · see citing works

LEDGF/p75 promotes transcriptional pausing through preventing SPT5 phosphorylation

Guo, C., Si, S., Fang, H., Shuai, S., Zhang, Y., Du, X., Duan, B., Wu, J., Yao, H., Ge, Z., et al. (2025) · Science Advances · doi:10.1126/sciadv.adr2131 · Cited by 5 · see citing works

Nsd2 Represses Endogenous Retrovirus MERVL in Embryonic Stem Cells

Gao, T., Chen, F., Zhang, W., Zhao, X., Hu, X., & Lu, X. (2021) · Stem Cells International · doi:10.1155/2021/6663960 · Cited by 5 · see citing works

LEDGF Binds H3R17me2a Promoting De Novo Nucleotide Biosynthesis in SETD2 Mutant Clear Cell Renal Cell Carcinoma

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

Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions

Penzo, C., Özel, I., Martinovic, M., Kuzman, M., Glavas, D., Stanic, M., Reichenbach, T., Müller, T. G., Rheinberger, M., Godarzi, N., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02089-2 · Cited by 6 · see citing works

TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks

Jones, T., Sigauke, R. F., Sanford, L., Taatjes, D. J., Allen, M. A., & Dowell, R. D. (2025) · Genome biology · doi:10.1186/s13059-025-03545-2 · Cited by 4 · see citing works

The SETD2 Methyltransferase Supports Productive HPV31 Replication through the LEDGF/CtIP/Rad51 Pathway

Mac, M., DeVico, B. M., Raspanti, S. M., & Moody, C. A. (2023) · Journal of Virology · doi:10.1128/jvi.00201-23 · Cited by 4 · see citing works

A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networksPreprint

Jones, T., Sigauke, R. F., Sanford, L., Taatjes, D. J., Allen, M. A., & Dowell, R. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.15.585303 · Cited by 4 · see citing works

The 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

Paraspeckle protein NONO regulates active chromatin by allosterically stimulating NSD1

Hsu, C.-I., Mei, S., Demmerle, J., Prakash, A., Ruttenberg, S. M., Sahn, M., & Yu, J.-R. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116247 · Cited by 3 · see citing works

Internal and external normalization of nascent RNA sequencing run-on experiments

Maas, Z. L., & Dowell, R. D. (2024) · BMC Bioinformatics · doi:10.1186/s12859-023-05607-3 · Cited by 3 · see citing works

ZMYND8 Reads H3K36me2 to Activate CEBPE Transcription and Suppress Multiple Myeloma Progression through the Inhibition of Adaptive UPR Pathways

Xu, J., Dong, X., Peng, Y., Yan, J., Xu, P., Li, F., Zhang, S., Chen, L., Meng, X., Wang, K., et al. (2025) · Advanced Science · doi:10.1002/advs.202409219 · Cited by 3 · see citing works

A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox ClustersPreprint

Ortabozkoyun, H., Huang, P., Cho, H., Narendra, V. K., LeRoy, G., Skok, J. A., Tsirigos, A., Mazzoni, E. O., & Reinberg, D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.25.267237 · Cited by 3 · see citing works

Mimicking the Nucleosomal Context in Peptide-Based Binders of a H3K36me Reader Increases Binding Affinity While Altering the Binding Mode

Horn, V., Jongkees, S. A. K., & van Ingen, H. (2020) · Molecules · doi:10.3390/molecules25214951 · Cited by 2 · see citing works

The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylation

Li, J., Li, Z., Yin, J., Wang, Y., Zheng, D., Cai, L., & Wang, G. G. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108423 · Cited by 2 · see citing works

NRF1 Association with AUTS2-Polycomb Mediates Specific Gene Activation in the BrainPreprint

Liu, S., Aldinger, K. A., Cheng, C. V., Kiyama, T., Dave, M., McNamara, H. K., Caraffi, S. G., Ivanovski, I. P., Errichiello, E., Zweier, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.30.437620 · Cited by 2 · see citing works

Chromatin meets condensates: emerging interplays linking nuclear paraspeckles to gene activation

Tu, C.-H., Hsu, C.-I., & Yu, J.-R. (2026) · Epigenetics Reports · doi:10.1080/28361512.2026.2617266 · Cited by 1 · see citing works

Characterization of Hepatoma-Derived Growth Factor-Related Protein 2 Interactions with Heterochromatin

Wistner, S. C., MacDonald, I. A., Stanley, K. A., & Hathaway, N. A. (2023) · Cells · doi:10.3390/cells12020325 · Cited by 1 · see citing works

Dietary compounds as inhibitors of DNA methyltransferases

Rasmi, Y., Khan, J., Ghoshal, K., & Daeihassani, B. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-824412-8.00008-4 · Cited by 1 · see citing works

LEDGF Interacts with the NID of MeCP2 and Modulates MeCP2 CondensatesPreprint

Lesire, S., Lata, R., Hoogvliets, Y., Herrebosch, K., de Velde, P. V., Speleers, A., Christ, F., Belle, S. V., & Debyser, Z. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.24.590897 · Cited by 1 · see citing works

The 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

Co-targeting menin and LSD1 dismantles oncogenic programs and restores differentiation in MLL-rearranged AMLPreprint

Tayari, M. M., Santos, H. G. D., Beckedorff, F., Totiger, T. M., Mookhtiar, A. K., Kingham, A. L., Lavezzo, G. M., Martín, G. M., Huang, H.-T., Karaca, E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.13.681683 · Cited by 1 · see citing works

Chromatin and transcription

Morse, R. H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-814809-9.00009-3

Mechanistic insights into the phosphorylation-regulated a disordered protein interaction module

Zang, Y., Ni, Y., Li, X., Yang, Z., Fu, Z., & Zhang, S. (2025) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2025.2460748

Additional file 1 of Internal and external normalization of nascent RNA sequencing run-on experiments

Maas, Z. L., & Dowell, R. D. (2024) · Figshare · doi:10.6084/m9.figshare.26666902

Additional file 2 of Internal and external normalization of nascent RNA sequencing run-on experiments

Maas, Z. L., & Dowell, R. D. (2024) · Figshare · doi:10.6084/m9.figshare.26666905

Unified function of FACT in mammalian chromatin replication and transcription, dissolving and restoring nucleosomes to counteract genome aggregationPreprint

Frater, R., Jensen, R. R., Ollé-López, J., Flury, V., van den Berg, J., Bournonville, A. L., Alcaraz, N., Wang, S., Richter, H. J., Yang, M. G., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.25.707725

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

Identification of specific phylogenetic properties of HIV-1 M and O integrases

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Maintenance of nucleosome organization through replication and transcription counteracts aberrant coalescence of active chromatin

Frater, R. C. M., Jensen, R. R., Ollé-López, J., Flury, V., van den Berg, J., Humbert, J., Bournonville, A. L., Alcaraz, N., Wang, S., Richter, H. J., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.07.028

DPF3a 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

Processed HIV-1 integration site datasets from Jurkat and HEK293T cells with host factors (LEDGF/p75 and CPSF6) perturbations

Singh, P. (2026) · Harvard Dataverse · doi:10.7910/dvn/udt6uc

Retroviral_integration_sites_distribution_across_gene_length.R

Singh, P. (2023) · Harvard Dataverse · doi:10.7910/dvn/au3kyv

Processed HIV-1 integration site datasets from Jurkat cells with capsid mutants

Singh, P. (2026) · Harvard Dataverse · doi:10.7910/dvn/xrkmnr

BindingDB Entry 50022853: Rational fragment-based design of compounds targeting the PWWP domain of the HRP family.

BindingDB (2026) · UC San Diego · doi:10.7270/q2s75n55

LEDGF and HDGF2 destabilize nucleosomes and facilitate reassembly

Joshi, J., McCauley, M. J., Morse, M., Shan, Z., Jing, T., Becker, N. A., Rouzina, I. F., Maher, L. J., Lyumkis, D., & Williams, M. C. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2023.11.1437

Ledgf/P75 Decreases Nucleosome Accessibility

Cox, K. L., Gibson, M. D., Kvaratskhelia, M., & Poirier, M. G. (2019) · Biophysical Journal · doi:10.1016/j.bpj.2018.11.418

Nucleosome chaperone activity of LEDGF and HDGF2 characterized with single molecule force spectroscopy

Joshi, J., McCauley, M. J., Becker, N. A., Morse, M., Rouzina, I. F., Maher, L. J., Lyumkis, D., & Williams, M. C. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2022.11.617

BPS2025 - LEDGF preferentially remodels histone-DNA interactions in methylated nucleosomes

Joshi, J., McCauley, M. J., Morse, M., Shan, Z., Jing, T., Becker, N. A., Rouzina, I. F., Maher, L. J., Lyumkis, D., & Williams, M. C. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2024.11.277

DNA Binding Domains and Nuclear Localization Signal of LEDGF: Contribution of two Helix-Turn-Helix (HTH)-like Domains and a Stretch of 58 Amino Acids of the N-terminal to the Trans-activation Potential of LEDGF

Singh, D. P., Kubo, E., Takamura, Y., Shinohara, T., Kumar, A., Chylack, L. T., & Fatma, N. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.10.054 · Cited by 67 · see citing works