Cited by 407Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related gene regulation

The DOI matches its Crossref record; 45 of the 46 references it cites were found in a registry or an index.

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases

Open access

Horton, John R, Upadhyay, Anup K, Qi, Hank H, Zhang, Xing, Shi, Yang, Cheng, Xiaodong·2010·Nature Structural & Molecular Biology

DOI 10.1038/nsmb.1753PMC PMC2849977

Open this paper in CoChat — free account

Abstract

Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.

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

Crossref · 10.1038/nsmb.1753

Cites

45 of 45 references verified0 citation errors · 0 not checkable

Statistics

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.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,723
Improved methods for building protein models in electron density maps and the location of errors in these models
Jones, T. A., Zou, J.-Y., Cowan, S. W., & Kjeldgaard, M. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767390010224 · Cited by 12,616
Translating the Histone Code
Jenuwein, T., & Allis, C. D. (2001) · Science · doi:10.1126/science.1063127 · Cited by 9,756
The language of covalent histone modifications
Strahl, B. D., & Allis, C. D. (2000) · Nature · doi:10.1038/47412 · Cited by 8,679
Protein production by auto-induction in high-density shaking cultures
Studier, F. W. (2005) · Protein Expression and Purification · doi:10.1016/j.pep.2005.01.016 · Cited by 5,949
Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J. R., Cole, P. A., Casero, R. A., & Shi, Y. (2004) · Cell · doi:10.1016/j.cell.2004.12.012 · Cited by 4,051
Self-citation
Regulation of chromatin structure by site-specific histone H3 methyltransferases
Rea, S., Eisenhaber, F., O'Carroll, D., Strahl, B. D., Sun, Z.-W., Schmid, M., Opravil, S., Mechtler, K., Ponting, C. P., Allis, C. D., et al. (2000) · Nature · doi:10.1038/35020506 · Cited by 2,845 · cited 1×
“Histone lysine modification is a dynamic process established by specific methyltransferases, including SET-domain protein”
Background
The complex language of chromatin regulation during transcription
Berger, S. L. (2007) · Nature · doi:10.1038/nature05915 · Cited by 2,768
Histone demethylation by a family of JmjC domain-containing proteins
Tsukada, Y.-I., Fang, J., Erdjument‐Bromage, H., Warren, M., Borchers, C. H., Tempst, P., & Zhang, Y. (2005) · Nature · doi:10.1038/nature04433 · Cited by 2,171

Flagged first, then by citations

Show all 46 references

1 of the 46 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

Han, Z., Liu, P., Gu, L., Zhang, Y., Chen, S. & Chai, J. Structure basis for histone demethylation by JHDM1. Frontier Science 1, 52–67 (2007).

Sorted by citations

Items 301–400 of 407

Purification, Biochemical Analysis, and Structure Determination of JmjC Lysine Demethylases
Krishnan, S., & Trievel, R. C. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.01.023 · Cited by 7
The emerging roles for histone demethylases in the modulation of signaling pathways
Stefano, L. D., & Dyson, N. J. (2012) · BioMolecular Concepts · doi:10.1515/bmc-2012-0031 · Cited by 6
Chromatin modifiers in neurodevelopment
Rezazadeh, S., Ji, H., & Giulivi, C. (2025) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2025.1551107 · Cited by 7
Origins of Catalysis in Non‐Heme Fe(II)/2‐Oxoglutarate‐Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides
Devadas, S., Thomas, M. G., Rifayee, S. B. J. S., Varada, B., White, W., Sommer, E., Campbell, K. P., Schofield, C. J., & Christov, C. Z. (2024) · Chemistry - A European Journal · doi:10.1002/chem.202403989 · Cited by 5
A Chromatin-Focused siRNA Screen for Regulators of p53-Dependent Transcription
Sammons, M. A., Zhu, J., & Berger, S. L. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.031534 · Cited by 5
Lysine Demethylation in Pathogenesis
Cao, J. P., & Yan, Q. (2023) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-38176-8_1 · Cited by 5
Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis
Walport, L. J., & Schofield, C. J. (2018) · The Chemical Record · doi:10.1002/tcr.201800056 · Cited by 5
Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins
Belle, R., Kamps, J. J. A. G., Poater, J., Kumar., K., V, Pieters, B. J. G. E., Salah, E., Claridge, T. D. W., Paton, R. S., Bickelhaupt, F. M., Kawamura, A., et al. (2022) · Communications Chemistry · doi:10.1038/s42004-022-00640-4 · Cited by 5
Is JmjC Oxygenase Catalysis Limited to Demethylation?
Hopkinson, R. J., Walport, L. J., Münzel, M., Rose, N. R., Smart, T. J., Kawamura, A., Claridge, T. D. W., & Schofield, C. J. (2013) · Angewandte Chemie · doi:10.1002/ange.201303282 · Cited by 5
Lysine Demethylases
García, M. A., Fueyo, R., & Martínez‐Balbás, M. A. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-802389-1.00010-1 · Cited by 5
ZBTB33 (Kaiso) methylated binding sites are associated with primed heterochromatinPreprint
Lin, Q. X. X., Rebbani, K., Jha, S., & Benoukraf, T. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/585653 · Cited by 6
Central carbon metabolism exhibits unique characteristics during the handling of fungal patterns by monocyte-derived dendritic cells
Álvarez, Y., Mancebo, C., Alonso, S., Montero, O., Fernández, N., & Crespo, M. S. (2024) · Redox Biology · doi:10.1016/j.redox.2024.103187 · Cited by 5
Dissecting contributions of catalytic and reader domains in regulation of histone demethylation
Petronikolou, N., Longbotham, J. E., & Fujimori, D. G. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2020.04.015 · Cited by 4
Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3
Anderson, S. E., Longbotham, J. E., O’Kane, P. T., Ugur, F. S., Fujimori, D. G., & Mrksich, M. (2020) · ACS Chemical Biology · doi:10.1021/acschembio.0c00891 · Cited by 4
Surface-based protein domains retrieval methods from a SHREC2021 challenge
Langenfeld, F., Aderinwale, T. W., Christoffer, C. W., Shin, W., Terashi, G., Wang, X., Kihara, D., Benhabiles, H., Hammoudi, K., Cabani, A., et al. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2021.108103 · Cited by 5
The dual functions of KDM7A in HBV replication and immune microenvironment
Yang, D., Tian, R., Deng, R., Xue, B., Liu, S., Wang, L., Li, H., Liu, Q., Wan, M., Tang, S., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.01641-23 · Cited by 4
Identification of family determining residues in J umonji‐C lysine demethylases: A sequence‐based, family wide classification
Slama, P. S. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24986 · Cited by 4
Histone Lysine Methylation, Demethylation, and Hormonal Gene Regulation
Huang, Y., Dennehey, B. K., & Shi, X. (2017) · Wiley eBooks · doi:10.1002/9783527697274.ch3 · Cited by 4
Histone demethylase KDM7A negatively regulates fibrotic macrophage polarization and lung fibrosis progression
Funagura, N., Koga, T., Etoh, K., Hong, S., Ichiyasu, H., Fujijwara, Y., Yasunaga, K.-I., Usuki, S., Noda, A., Sagara, A., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-09610-1 · Cited by 3
Role and mechanism of histone demethylase PHF8 in weightlessness osteoporosis
Ding, Z., Wang, D., Zhang, S., Yang, X., Xu, M., Li, W., Shi, Q., Gao, B., Wang, Y., & Yan, M. (2024) · Experimental Cell Research · doi:10.1016/j.yexcr.2024.114270 · Cited by 3
Helical and β-Turn Conformations in the Peptide Recognition Regions of the VIM1 PHD Finger Abrogate H3K4 Peptide Recognition
Abhishek, S., Deeksha, W., & Rajakumara, E. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00191 · Cited by 3
Kdm7a expression is spatiotemporally regulated in developing Xenopus laevis embryos, and its overexpression influences late retinal development
Martini, D., Digregorio, M., Voto, I. A. P., Morabito, G., Degl’Innocenti, A., Giudetti, G., Giannaccini, M., & Andreazzoli, M. (2023) · Developmental Dynamics · doi:10.1002/dvdy.670 · Cited by 3
Transcription factor Olig2 is a major downstream effector of histone demethylase Phf8 during oligodendroglial development
Kremp, M., Aberle, T., Sock, E., Bohl, B., Hillgärtner, S., Winkler, J., & Wegner, M. (2024) · Glia · doi:10.1002/glia.24538 · Cited by 3
Histone Methyltransferases: Opportunities in Cancer Drug Discovery
Chesworth, R., Wigle, T. J., Kuntz, K. W., Smith, J. J., & Richon, V. M. (2013) · Springer eBooks · doi:10.1007/978-3-642-38404-2_9 · Cited by 3
Overview of Epigenetic Signatures and Their Regulation by Epigenetic Modification Enzymes
Ganai, S. A. (2020) · Springer eBooks · doi:10.1007/978-981-15-8179-3_1 · Cited by 3
Histone Recognition by Tandem Modules and Modulation by Multiple PTMs
Li, H., Zhao, S., & Patel, D. J. (2015) · Springer eBooks · doi:10.1007/978-3-319-18102-8_7 · Cited by 3
HER3 promotes triple-negative breast cancer progression by upregulating PHF8 via miR-34b-5p-dependent mechanism
Lyu, H., Tan, C., Wu, Y., Larsen, M. E., Yu, Q., Kang, G., Wood, C. E., Tang, S., & Liu, B. (2025) · Cell Death and Disease · doi:10.1038/s41419-025-08115-9 · Cited by 2
KDM7A and KDM1A inhibition suppresses tumour promoting pathways in prostate cancer
Jeyapalan, J. N., Metzler, V. M., de Brot, S., Woodcock, C. L., Harris, A. E., Lothion‐Roy, J. H., Nilsson, E. M., Ntekim, A., Toss, M. S., Persson, J. L., et al. (2026) · Molecular Oncology · doi:10.1002/1878-0261.70238 · Cited by 2
Beyond Histone Demethylation: Mechanisms of N -Alkyl Consecutive Oxidations by the Non-Heme Fe(II)/2-Oxoglutarate Oxygenase KDM6B
Rifayee, S. B. J. S., Devadas, S., Thomas, M. G., Varada, B., Sommer, E., Talaba, C., Schofield, C. J., & Christov, C. Z. (2026) · JACS Au · doi:10.1021/jacsau.6c00575 · Cited by 4
Genome mining with hypothetical proteins
Kenney, G. E. (2025) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2025.04.004 · Cited by 1
Inhibitors of Jumonji C-Domain Histone Demethylases
Staller, P. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800206-3.00020-3 · Cited by 1
Molecular Technology for Controlling Epigenetics: Regulation of Histone Acetylation and Methylation by Small Molecules
Itoh, Y., & Suzuki, T. (2016) · Journal of Synthetic Organic Chemistry Japan · doi:10.5059/yukigoseikyokaishi.74.441 · Cited by 1
DNA and Histone Modifications in Cancer Therapy
Suzuki, T. (2017) · Cancer drug discovery and develogment/Cancer drug discovery and development · doi:10.1007/978-3-319-59786-7_20 · Cited by 1
The Role of Protein Lysine Methylation in the Regulation of Protein Function: Looking Beyond the Histone Code
Adhikary, H., Bakos, O., & Biggar, K. K. (2019) · RNA technologies · doi:10.1007/978-3-030-14792-1_18 · Cited by 1
High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations
Qu, H., Glessner, J., Qu, J., Liu, Y., Watson, D. J., Chang, X., Saeidian, A. H., Qiu, H., Mentch, F. D., Connolly, J. J., et al. (2023) · Translational research · doi:10.1016/j.trsl.2023.11.004 · Cited by 1
Histone modifications
Morse, R. H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-814809-9.00002-0 · Cited by 1
Interaction Between PHF8 and a Segment of KDM2A, Which Is Controlled by the Phosphorylation Status at a Specific Serine in an Intrinsically Disordered Region of KDM2A, Regulates rRNA Transcription and Cell Proliferation in a Breast Cancer Cell Line
Okamoto, K., Mihara, Y., Ogasawara, S., Murakami, T., Ohmori, S., Mori, T., Umata, T., Kawasaki, Y., Hirano, K., Yano, H., et al. (2025) · Biomolecules · doi:10.3390/biom15050661 · Cited by 1
The Histone Demethylase PHF8 and Neural Development*
Guo, X., Shen, Y., Bei, L. I. U., Chang, Y., & Duan, X. (2011) · PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS · doi:10.3724/sp.j.1206.2010.00390 · Cited by 1
Novel Targets in the Treatment of Neuroendocrine Tumors: RBP2
Maggi, E. C., & Crabtree, J. S. (2017) · International Journal of Endocrine Oncology · doi:10.2217/ije-2016-0022 · Cited by 1
Inhibitors of JmjC-Containing Histone Demethylases
Wright, M., Brennan, P. E., & Kawamura, A. (2019) · Topics in medicinal chemistry · doi:10.1007/7355_2019_75 · Cited by 1
Study of the expression of genes associated with post-translational changes in histones in the internal thoracic artery and the saphenous vein grafts used in coronary artery bypass grafting procedure
Kałużna, S., Nawrocki, M. J., Bryl, R., Stefańska, K., Jemielity, M., Mozdziak, P. E., Nowicki, M. O., & Perek, B. (2020) · Medical Journal of Cell Biology · doi:10.2478/acb-2020-0024 · Cited by 1
Discovery of a Highly Selective Cell‐Active Inhibitor of the Histone Lysine Demethylases KDM2/7
Gerken, P. A., Wolstenhulme, J. R., Tumber, A., Hatch, S. B., Zhang, Y., Müller, S., Chandler, S. A., Mair, B., Li, F., Nijman, S. M. B., et al. (2017) · Angewandte Chemie · doi:10.1002/ange.201706788 · Cited by 1
The Evolution of Tyramides in Male Fungus-Growing Ants (Formicidae: Myrmicinae: Attini: Attina)
Luo, A. R., Hassler, M. F., Jones, T. H., Meer, R. Κ. V., & Adams, R. M. M. (2022) · Journal of Chemical Ecology · doi:10.1007/s10886-022-01382-2 · Cited by 1
Co-evolutionary analysis suggests a role for TLR9 in papillomavirus restrictionPreprint
King, K. M., Larsen, B. B., Gryseels, S., Richet, C., Kraberger, S. J., Jackson, R., Worobey, M., Harrison, J. S., Varsani, A., & Doorslaer, K. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.17.440006 · Cited by 1
JmjC ‐domain‐Containing Histone Demethylases
Højrup, C., Coleman, O. D., Bukowski, J., Clausen, R. P., & Kawamura, A. (2019) · Methods and principles in medicinal chemistry · doi:10.1002/9783527809257.ch11 · Cited by 1
Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistancePreprint
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2023) · Research Square · doi:10.21203/rs.3.rs-3138103/v1 · Cited by 1
Arc: a therapeutic hub for Alzheimer’s diseasePreprint
VanDongen, A. M. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.16.632170 · Cited by 1
Molecular mechanisms of enhanced expression of the chemokine interleukin 8 (CXCL8) in cystic fibrosis (CF) airway epithelial cells
Poghosyan, A. (2014) · Nottingham ePrints (University of Nottingham)
Regulators of chromatin and transcription in Drosophila
Crona, F. (2013) · DiVA (Stockholm University)
Crystallography-Based Mechanistic Insights into Epigenetic Regulation
Zhao, S., & Li, H. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801080-8.00007-7
Fragment-Based Approaches to Epigenetic Targets
Chung, C., & Bamborough, P. (2015) · Royal Society of Chemistry eBooks · doi:10.1039/9781782620938-00238
Epigenetic Readers Interpreting the Lysine Methylome—Biological Roles and Drug Discovery
Wagner, T., Robaa, D., Sippl, W., & Jung, M. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-802208-5.00011-4
Chemical Biology of Histone Modifications
Rose, N. R., Schofield, C. J., & Heightman, T. D. (2010) · Royal Society of Chemistry eBooks · doi:10.1039/9781849732178-00151
Stochastic Activation of Enhancers in the Innate Immune Response by the Histone Demethylase JMJD2D
Chandwani, R. (2025) · Digital Commons - RU (Rockefeller University) · doi:10.48496/rywh-tv54
Loss of the Histone Demethylase Phf8 Is Compatible With Development but Confers Resilience to Anxiety and Depression
Walsh, R. M. (2016) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Probing the Charge and Conformational Requirements of JmjC Demethylases
Langley, G. W., Brinkø, A., Münzel, M., Walport, L. J., Schofield, C. J., & Hopkinson, R. J. (2017) · The FASEB Journal · doi:10.1096/fasebj.31.1_supplement.767.1
Characterisation of the cellular response to defective translational termination
Ploumakis, A. (2018) · University of Birmingham Institutional Research Archive (University of Birmingham)
APOC2 accelerates colorectal cancer progression via modulating lipid metabolism and transcriptional activity of PHF8Preprint
Chen, J., Xiao, C. W., Wang, Y., Song, G., Wang, X., Liu, X., Chen, J., Lu, H., Kuai, J., Qin, X., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/680967
[The Role of Histone Demethylase in Osteogenic and Chondrogenic Differentiation of Mesenchymal Stem Cells: A Literature Review].
Sui, H., & Zhang, T. (2021) · PubMed Central · doi:10.12182/20210560202
Non‐canonical bivalent H3K4me3K9me3 recognition by Spindlin1/C11orf84 complex
Du, Y., & Qian, C. (2022) · BioEssays · doi:10.1002/bies.202100229
Faculty Opinions recommendation of ChromID identifies the protein interactome at chromatin marks.
Tiwari, V. K., & Mariappan, A. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737462814.793573114
Outline of epigenetics
Ganguly, S., Paul, B., & Tollefsbol, T. O. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823577-5.00014-3
Comprehensive analysis identified and validated BRD4, CHD1, and KDM7A as potential biomarkers for osteoarthritisPreprint
Li, Y., Zhang, J., Meng, L., Shang, M., Huo, R., Li, J., Zhang, C., Fan, F., Cheng, Y., Liu, Q., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2312000/v1
Epigenetic regulation: Histone modifying enzymes as targets for novel therapeutics
Dietrich, N., & Archer, T. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824010-6.00067-8
Glucose-Sensing JMJD1A Facilitates Glucose Metabolism and Lipid Storage During AdipogenesisPreprint
Ariyanto, E. F., Zhang, J., Yang, C., Ito, R., Xie, S., Yang, C., Suzuki, T., Komatsu, T., Sagae, H., Jin, H., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4849131
Histone Demethylases
Kales, S. C., & Simeonov, A. M. (2024) · Royal Society of Chemistry eBooks · doi:10.1039/9781837674916-00383
Drug Discovery for Chromatin Readers, Writers, Erasers, Remodelers and Epitranscriptomic Targets
(2024) · Royal Society of Chemistry eBooks · doi:10.1039/9781837674916-part3
Fe ion coordination direction and refresh mechanism in off-line αKG-dependent hydroxylase
Fang, Y., Gong, W., & Yang, L. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.140942
Are Epigenetic Mechanisms Involved in Axonal Regeneration
Lindner, R. (2013)
The Functions and Importance of CH···O Bonds in SET Domain Methyltransferases.
Horowitz, S. A. (2013) · Deep Blue (University of Michigan)
Additional file 2 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.25347205
Additional file 12 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688998
Additional file 10 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688992
Additional file 8 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688986
Additional file 5 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688977
Additional file 11 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688995
Additional file 4 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688974
Additional file 7 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688983
Additional file 9 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688989
Additional file 3 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688971
Additional file 6 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.26688980
Additional file 1 of Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance
Correa, R. L., Kutnjak, D., Ambrós, S., Bustos, M., & Elena, S. F. (2024) · Figshare · doi:10.6084/m9.figshare.25347176
KDM7B-mediated demethylation of RNF113A regulates small cell lung cancer sensitivity to alkylation damagePreprint
Ahmad, T., Yang, X., Foucher, A., Ren, L., Tsao, N., Flores, N. M., Wan, J., Belmudes, L., Dubiez, E., Bhowmik, M. C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.03.697470
Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis
Artés, M. H., Iacobucci, S., Barallobre, M. J., Carballeira, P., Garcia‐Cajide, M., Pérez‐Venteo, A., Padilla, N., Viegas, B., Díaz-Vásquez, A., Nacht, A. S., et al. (2026) · EMBO Reports · doi:10.1038/s44319-026-00713-8
Catalytic Mechanisms of Non‐Heme Fe(II) and 2‐Oxoglutarate‐Dependent Enzymes: A Computational Perspective
Christov, C. Z., Karabencheva‐Christova, T. G., Devadas, S., Bathir, J. S. R. S., Krishnan, A., & Thomas, M. G. (2026) · Encyclopedia of Inorganic and Bioinorganic Chemistry · doi:10.1002/9781119951438.eibc2895
NOTCH1 Nuclear Interactome Reveals Key Regulators of Its Transcriptional Activity and Oncogenic Function
Yatim, A. (2013) · theses.fr (ABES) · doi:10.70675/4494c948zfc48z4bd5zaea7z9653c047186d
Dynamiques épigénétiques du macrosatellite D4Z4 par la protéine SMCHD1 dans deux pathologies rares : exploitation du modèle IPSCs
Dion, C. (2018) · theses.fr (ABES) · doi:10.70675/3efa9215z51a5z4c60z89a8zcb82f128e3aa
Méthylation de H3K27 : régulation et rôle dans le cartilage articulaire
Allas, L. (2019) · theses.fr (ABES) · doi:10.70675/0b801552z0546z4765za411z263c0baf83ef
Role of the cardioprotective protein, Carabin, and its nuclear partners, MLL3 and CHD8, in gene regulation during cardiac hypertrophy
Pane, R. (2020) · theses.fr (ABES) · doi:10.70675/ac6dec71z3eb4z4528zb0e5zbec83e9e3cd7
Metabolic imprint induces histone hypermethylation during Chlamydia trachomatis infection
Charendoff, C. I. (2021) · doi:10.70675/e68c5753z858bz4d57z88e6z3a1d79eb3134
Regulation of heterochromatin by a pluripotency-associated long non coding RNA in mouse embryonic stem cells and in oocytes : implications for early embryogenesis
Bernard, L. D. (2021) · theses.fr (ABES) · doi:10.70675/05f4f7dbz61a7z4676za4a0za42de848cbcd
From molecular to functional diversity : a genome wide in vivo study of the Drosophila melanogaster neurons, glia and macrophages
Sakr, R. (2021) · theses.fr (ABES) · doi:10.70675/723d2d54zfcecz48f3zbaeazdee458dd9b64
The role of PHD fingers in chromatin signaling
Morrison, E. A., & Musselman, C. A. (2016) · Elsevier eBooks · doi:10.1016/b978-0-443-19001-8.00010-6
Lysine demethylases
García, M. A., Fueyo, R., & Martínez‐Balbás, M. A. (2016) · Elsevier eBooks · doi:10.1016/b978-0-443-19001-8.00013-1
Neuronal activity-regulated histone demethylase KDM7A controls hippocampal gene expression and behavior
Paraíso‐Luna, J., Niñerola, S., Scandaglia, M., López-Gómez, M. C., Martín-González, A., & Barco, Á. (2026) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2026.102957
BindingDB Entry 50047300: Recent Progress in Histone Demethylase Inhibitors.
BindingDB (2017) · UC San Diego · doi:10.7270/q2mp5559
BindingDB Entry 50040497: Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.
BindingDB (2013) · UC San Diego · doi:10.7270/q2jh3n9s
BindingDB Entry 7449: An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells.
BindingDB (2016) · UC San Diego · doi:10.7270/q2cf9nxw
BindingDB Entry 50034383: Lysine demethylases inhibitors.
BindingDB (2012) · UC San Diego · doi:10.7270/q2d50nfr
BindingDB Entry 50043097: Quantitative analysis of histone demethylase probes using fluorescence polarization.
BindingDB (2014) · UC San Diego · doi:10.7270/q2vm4dnk

Authors: Horton, J. R., Upadhyay, A. K., Qi, H. H., Zhang, X., Shi, Y., & Cheng, X.
Affiliations: Emory University (US)
Boston Children's Hospital (US)
Corresponding author: Cheng, Xiaodong
ORCID: Horton, John R
Upadhyay, Anup K
Qi, Hank H
Zhang, Xing
Shi, Yang
Cheng, Xiaodong
Venue: Nature Structural & Molecular Biology
Publisher: Springer Science and Business Media LLC
Published: 2009-12-20
Volume: 17
Issue: 1
Pages: 38-43
ISSN: 1545-9985 (ISSN-L)
1545-9993
DOI: 10.1038/nsmb.1753
PMC: PMC2849977
OpenAlex: W2132614547
Cited by: 389
References: 46
Citations by year: 2026: 10 · 2025: 14 · 2024: 22 · 2023: 12 · 2022: 13 · 2021: 24 · 2020: 22 · 2019: 27 · 2018: 18 · 2017: 19 · 2016: 30 · 2015: 27 · 2014: 27 · 2013: 28 · 2012: 26
FWCI: 12.25
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Structural & Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Public Health Service (NCI118487)
National Institute of General Medical Sciences (GM058012, R01GM058012, R01GM068680, GM06860)
National Institute of Diabetes and Digestive and Kidney Diseases (R56DK082678, DK082678)
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 › Molecular Biology › Cancer-related gene regulation
Keywords: PHF8, plant homeodomain, histone lysine demethylation, H3K4me3, H3K9me2, H3K27me2, substrate specificity, protein conformation, histone modifications, transcriptional activation, histone reader proteins
MeSH terms: Histones, Humans, Models, Molecular, Oxidoreductases, N-Demethylating, Protein Binding, Protein Conformation, Substrate Specificity, Transcription Factors, Protein Structure, Tertiary, F-Box Proteins, Histone Demethylases, Jumonji Domain-Containing Histone Demethylases

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

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks