Cited by 323Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromatin Remodeling and Cancer

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The KAP1 Corepressor Functions To Coordinate the Assembly of De Novo HP1-Demarcated Microenvironments of Heterochromatin Required for KRAB Zinc Finger Protein-Mediated Transcriptional Repression

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Sripathy, Smitha P., Stevens, Jessica, Schultz, David C.·2006·Molecular and Cellular Biology

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Abstract

KAP1/TIF1beta is proposed to be a universal corepressor protein for the KRAB zinc finger protein (KRAB-zfp) superfamily of transcriptional repressors. To characterize the role of KAP1 and KAP1-interacting proteins in transcriptional repression, we investigated the regulation of stably integrated reporter transgenes by hormone-responsive KRAB and KAP1 repressor proteins. Here, we demonstrate that depletion of endogenous KAP1 levels by small interfering RNA (siRNA) significantly inhibited KRAB-mediated transcriptional repression of a chromatin template. Similarly, reduction in cellular levels of HP1alpha/beta/gamma and SETDB1 by siRNA attenuated KRAB-KAP1 repression. We also found that direct tethering of KAP1 to DNA was sufficient to repress transcription of an integrated transgene. This activity is absolutely dependent upon the interaction of KAP1 with HP1 and on an intact PHD finger and bromodomain of KAP1, suggesting that these domains function cooperatively in transcriptional corepression. The achievement of the repressed state by wild-type KAP1 involves decreased recruitment of RNA polymerase II, reduced levels of histone H3 K9 acetylation and H3K4 methylation, an increase in histone occupancy, enrichment of trimethyl histone H3K9, H3K36, and histone H4K20, and HP1 deposition at proximal regulatory sequences of the transgene. A KAP1 protein containing a mutation of the HP1 binding domain failed to induce any change in the histone modifications associated with DNA sequence…

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“…its ability to recruit KAP1 19 -a scaffold protein that then interacts with several other heterochromatin inducers 20 - comprising the nucleosome remodeling and deacetylation (NuRD) complex 21 , the H3K9 histone methyltransferase SETDB1 22 , and the H3K9 methylation reader HP1 23,24 , among others.”
Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
Yan, X., Williams, M. R., Castillo, A. D. B., Kireev, D., & Hathaway, N. A. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad062 · Cited by 4
KAP1 Positively Modulates Influenza A Virus Replication by Interacting with PB2 and NS1 Proteins in Human Lung Epithelial Cells
Feng, H.-P., Yi, R., Wu, S.-P., Wang, G., Sun, R., Lin, L., Zhu, S., Nie, Z., He, Y.-L., Wang, S., et al. (2022) · Viruses · doi:10.3390/v14040689 · Cited by 4
“The open reading frame of human Kap1 gene was amplified from the cDNA of A549 cells and added Flag tag at C-terminal by primers and cloned into the multiple cloning site (MCS) A of the expression vector pIRES-puromycin which carries the puromycin resistant gene in MCS B site.”
Background
KAP1 is an antiparallel dimer with a natively functional asymmetry
Fonti, G., Marcaida, M., Bryan, L., Traeger, S., Kalantzi, A., Helleboid, P.-Y., Demurtas, D., Tully, M., Grudinin, S., Trono, D., et al. (2019) · bioRxiv · doi:10.1101/553511 · Cited by 4
The KZFP/KAP1 system controls transposable elements-embedded regulatory sequences in adult T cellsPreprint
Marzetta, F., Simó‐Riudalbas, L., Duc, J., Planet, E., Verp, S., Turelli, P., & Trono, D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/523597 · Cited by 5
“These effectors cooperatively induce the formation of heterochromatin thus repress transcription through epigenetic changes (Sripathy et al. 2006).”
Background
A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression
Ecco, G., Rowe, H. M., & Trono, D. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3372-3_25 · Cited by 4
KAP1 in antiviral immunity: dual roles in viral silencing and immune regulation
Xin, R., Garigliany, M.-M., & Li, J. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1618103 · Cited by 2
Activation of endogenous retroviruses during brain development causes neuroinflammationPreprint
Jönsson, M. E., Garza, R., Sharma, Y., Petri, R., Södersten, E., Johansson, J. G., Johansson, P., Atacho, D. A. M., Pircs, K., Madsen, S., et al. (2020) · bioRxiv · doi:10.1101/2020.07.07.191668 · Cited by 3
“…disease, Parkinson’s disease and schizophrenia (Andrews et al., 2000; Douville et al., 2011; Garson et al., 1998; Guo et al., 2018; Karlsson et al., 2001; Li et al., 2015; MacGowan et al., 2007; Perron et al., 1997; Perron et al., 2008; Steele et al., 2005; Sun et al., 2018; Tam et al., 2019b).”
Background
Structure of the tripartite motif of KAP1/TRIM28
Stoll, G., Oda, S., Yu, M., & Modis, Y. (2019) · doi:10.2210/pdb6qaj/pdb · Cited by 3
Precision Medicine, CRISPR, and Genome Engineering
Tsang, S. H. (2017) · Advances in Experimental Medicine and Biology · doi:10.1007/978-3-319-63904-8 · Cited by 3
“For the purpose of studying development, these advances have expedited the generation of valuable null alleles to study gene necessity, epitope tagged alleles to study protein function, and conditional alleles to asses gene function at different times and in different tissues [15].”
BackgroundInfluential
SplitTurboID mapping of dimeric protein phosphatase complex interactomes
Rajkumar, A., Gaudreau-Lapierre, A., Anthony, C. L. F., Nguyen, V., Ooi, S., Campuzano, D., & Trinkle-Mulcahy, L. (2026) · iScience · doi:10.1016/j.isci.2026.115195 · Cited by 2
“29 SplitTurboID can also be exploited to focus on the proximity interactome of a particular 4E where the CTD-tagged actin-binding protein TPRN was paired with an NTD-tagged LifeAct peptide that binds filamentous actin.”
Genome-wide CRISPR-Cas9 screen analyzed by SLIDER identifies network of repressor complexes that regulate TRIM24
Patel, L. R., Stratton, S. A., McLaughlin, M., Krause, P. M., Allton, K. L., Lopez-Rivas, A. R., Barbosa, D., Hart, T., & Barton, M. C. (2022) · iScience · doi:10.1016/j.isci.2023.107126 · Cited by 3
Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppressionPreprint
Wolf, G., Iaco, A. D., Sun, M., Bruno, M., Tinkham, M., Hoang, D., Mitra, A., Ralls, S., Trono, D., & Macfarlan, T. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.17.910679 · Cited by 2
“The KRAB domain binds the corepressor KAP1, which in turn recruits histone modifying enzymes including the NuRD histone deacetylase complex and the H3K9-specific methylase SETDB1 (13, 14), which induces persistent and heritable gene silencing (15).”
Background
Molecular and functional characterization of the role of the histone methyltransferase SETDB1 in malignant melanoma
Umansky, V., Utikal, J., Federico, A., Orouji, E., Larribère, L., & Novák, D. (2020) · doi:10.11588/heidok.00026697 · Cited by 2
“Anticancer research 29: 201-209 Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ, 3rd (2002) SETDB1: a novel KAP-1associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.”
BackgroundInfluential
4.32 Gene Editing Tools
Ede, D., Farhang, N., Stover, J. D., & Bowles, R. D. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803581-8.09290-0 · Cited by 2
DHODH Drives Sunitinib Resistance Via a Non‐Enzymatic Mechanism by Inhibiting TRIM28 Ubiquitination and Consequent VEGFA Activation in RCC
Qian, S., Pu, S., Xu, Z., Ding, Y., Jin, L. L., Li, B., Li, Q., Xi, X., Wang, Z., Xing, J., et al. (2026) · Advanced Science · doi:10.1002/advs.76266 · Cited by 1
“The repressive state is then locked in place through HP1 binding, ensuring stable chromatin compaction and gene silencing [ 43 ].”
Trans-regulation of heterochromatin underlies genetic variation in 3D genome contactsPreprint
Fortin, H. J., Struba, A. Z., & Baker, C. L. (2025) · bioRxiv · doi:10.64898/2025.12.10.693515 · Cited by 1
“Firstly, KZFPs provide DNA-binding specificity to recruit TRIM28, and chromatin modifying enzymes, to form heterochromatin [66,73 – 77].”
Controlling gene expression through five zinc finger domains of ZNF18
Park, S. C., Hwang, Y., Eom, K. S., Cheong, J. S., & Lee, S. J. (2025) · Protein Science · doi:10.1002/pro.70278 · Cited by 2
“…protein 1 (KAP1), which facilitates the assembly of a multi-protein complex including histone methyltransferase, histone deacetylase, and heterochromatin protein 1, leading to a transcriptionally repressive heterochromatin (Groner et al., 2010; Sripathy et al., 2006; Stoll et al., 2022).”
Biomolecular liquid‒liquid phase separation associated with repetitive genomic elements
Asamitsu, S., & Iwasaki, Y. W. (2025) · Polymer Journal · doi:10.1038/s41428-025-01036-6 · Cited by 3
“Unknown SUMO substrates may serve as additional effectors for the organization of functional condensates KAP1 to target ERVs and assemble a repressive chromatin complex including SETDB1 [71 – 73].”
p85β acts as a transcription cofactor and cooperates with BCLAF1 in the nucleus
Wang, P., Mak, V. C. Y., Rao, L., Wu, Q., Zhou, Y., Sharma, R., Kwon, S. C., & Cheung, L. W. T. (2025) · Nature Communications · doi:10.1038/s41467-025-56532-3
ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation
Jones, D. L., Meridew, J., Ducharme, M. T., Lydon, K. L., Choi, K. M., Caporarello, N., Tan, Q., Link, P., Espinosa, A., Xiong, Y.-N., et al. (2020) · bioRxiv · doi:10.1101/2020.07.23.218842 · Cited by 1
The transcriptional repressor Zfp125 modifies hepatic energy metabolism in response to fasting and insulin resistancePreprint
Fernandes, G. W., Bocco, B. M. L. C., Fonseca, T. L., Salas-Lucia, F., Nickel, O., Russo, S. C., Gereben, B., Kettelhut, I., & Bianco, A. (2020) · bioRxiv · doi:10.1101/2020.07.02.185165 · Cited by 1
On the relation of phase separation and Hi-C maps to epigeneticsPreprint
Singh, P. B., & Newman, A. G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/814566 · Cited by 1
Epigenetic regulation of unique genes and repetitive elements by the KRAB zinc finger protein ZFP57Preprint
Shi, H., Strogantsev, R., Takahashi, N., Kazachenka, A., Lorincz, M., Hemberger, M., & Ferguson-Smith, A. (2019) · bioRxiv · doi:10.1101/611400 · Cited by 1
“44 Members of the co-repressor complex include the histone methyltransferase SETDB1 (also known 45 as ESET), heterochromatin protein 1 (HP1), the histone demethylase LSD1, and NuRD histone 46 deacetylase complex [10,11].”
Background
Transposon regulation upon dynamic loss of DNA methylation
Walter, M. (2015) · theses.fr (ABES) · doi:10.70675/275812b8z11e8z4408zbf26zafee926bbb1a
“85 chromoshadow domains and the different KMTs that establish the mark (Chin et al., 2007; Sripathy et al., 2006; Stewart et al., 2005).”
Background
Studying the posttranslational modifications of transcription factor Ikaros and their role in its function
Apostolov, A. (2012) · theses.fr (ABES) · doi:10.70675/23bb8330zf47ez4a62z9f59z2301e60db09f
“These sumo-based interactions lead to KAP1 mediated down-regulation of the transcription and silenced chromatin state (Ivanov et al., 2007; Schultz et al., 2001, 2002; Sripathy et al., 2006; Ryan et al., 1999).”
Background
Retrotransposons and the Mammalian Germline
Adams, I. R. (2017) · Springer eBooks · doi:10.1007/978-3-319-48344-3_1 · Cited by 1
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“KAP1 also binds heterochromatin protein 1 (HP1) for histone methylation, and an inability for KAP1 to bind to HP1 results in a loss of heterochromatin and increased LINE-1 expression [50,66].”
The absence of Trim28 in nephron progenitors results in impaired kidney development and function
Pálházi, B., Paikari, A., Clarén, G., Appenzeller, S., Imdahl, F., Daniel, C., Becker, M., & Gessler, M. (2026) · Development · doi:10.1242/dev.205188
“TRIM28 recruits a number of repressive chromatin factors such as members of the NuRD complex and the heterochromatin-associated protein HP1 (Sripathy et al., 2006).”
A TRIM28-MCM7 regulatory axis sustains DNA replication programs in glioblastoma.
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Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells
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“Firstly, KZFPs provide DNA-binding specificity to recruit TRIM28, and chromatin modifying enzymes, to form heterochromatin [65, 74–78].”
Updates on the role of TRIM proteins in AIDS: molecular mechanisms and potential for interventions
Chen, J., Chen, S., Xu, Y., Wang, X., & Jiang, M. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1742036
Formation and maintenance of genome gigantism
Liu, X., Wang, J., & Huang, Y. (2026) · Trends in Genetics · doi:10.1016/j.tig.2026.01.003
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Ornelas, I. J., Owens, L. A., Álamos, S., Hummel, N. F. C., Zamora, M. G. H., Phan, N., Pattali, R. K., Shih, P. M., & Nuñez, J. K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.10.705154 · Cited by 5
“Two notable exceptions are KRAB and TIF1B (TRIM28/KAP1), which are known physical interactors that establish repressive H3K9me3 and can induce longer-term epigenetic memory 66 .”
Genom-Editierung ohne die DNA-Sequenz zu verändern — geht das?
Schönberg, P. Y., Ding, L., & Buchholz, F. (2023) · BIOspektrum · doi:10.1007/s12268-023-1882-2
In vitro selection of Engineered Transcriptional Repressors for targeted epigenetic silencing and initial evaluation of their specificity profilePreprint
Migliara, A., Cappelluti, M. A., Valsoni, S., Merelli, I., Cittaro, D., & Lombardo, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.30.505942 · Cited by 1
Transcriptional states of retroelement-inserted regions and KRAB zinc finger protein association regulate DNA methylation of retroelements in human male germ cells
Fukuda, K., Makino, Y., Kaneko, S., Okada, Y., Ichiyanagi, K., & Shinkai, Y. (2021) · bioRxiv · doi:10.1101/2021.05.19.444783
“KRAB-ZFPs repress retroelements by recruiting KAP1/TRIM28 (Sripathy et al. 2006) and other repressive epigenetic modifiers (Schultz et al. 2001; Schultz et al. 2002).”
Background
Genomic features of BRDT binding sites in gene units suggest transcriptional partners and specific epigenetic landscapes to regulate transcriptional activity during spermatogenesis
Wang, L., Chepelev, I., Her, Y. R., Manterola, M., Berkovits, B. D., Cui, K.-R., Zhao, K.-J., & Wolgemuth, D. (2019) · bioRxiv · doi:10.1101/822874
Effect of CRISPR-based epigenetic interference on cis-regulatory gene networks
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“This includes heterochromatin protein 1 (HP1), histone deacetylase complex NCOR1, histone methyltransferase SETDB1, and Nucleosome Remodeling Deacetylase (NuRD) co-repressor to transcriptionally silence the target site through chromatin remodeling (Sripathy et al., 2006).”
Background
Rôle du médiateur et des cohésines dans la réparation des dommages oxydatifs de l'ADN
Lebraud, E. (2018) · theses.fr (ABES) · doi:10.70675/a2b027cdza460z4df2zb7bcz644b30f238b5
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Genome and epigenome engineering CRISPR toolkit for probing in vivo cis-regulatory interactions in the chicken embryo
Williams, R. M., Senanayake, U., Artibani, M., Taylor, G., Wells, D., Ahmed, A., & Sauka-Spengler, T. (2017) · bioRxiv · doi:10.1101/135525
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With or Without them: Essential Roles of Cofactors in ES Cells
Ma, H. (2012) · Journal of Stem Cell Research & Therapy · doi:10.4172/2157-7633.s10-006
“Other than MLV, TRIM28 also represses other retroviruses, including those that harbour PBS sequences different from MLV, such as visna, spuma, and the Mason-Pfizer monkey virus [105], and endogenous retroviruses (ERVs) that are active in the mammalian genome [106].”
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Kurisaki, A., Seki, Y., & Intoh, A. (2011) · InTech eBooks · doi:10.5772/14212
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Xie, L.-Y. (2025) · Journal of Clinical Personalized Medicine · doi:10.12677/jcpm.2025.42303
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Goes, C. P. (2019) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.42.2020.tde-12022020-153318
DETERMINATION OF THE CONSENSUS TARGET SEQUENCES RECOGNIZED BY ZNFO, A NOVEL OOCYTE-SPECIFIC ZINC FINGER TRANSCRIPTION FACTOR IN CATTLE
Zhang, M. (2018) · The Research Repository @ WVU (West Virginia University) · doi:10.33915/etd.7286
Transcriptional silencing of endogenous retroviruses by the novel lysine methyltransferase co-repressor hnRNP K
Thompson, P. J. (2015) · cIRcle (University of British Columbia) · doi:10.14288/1.0221305

Authors: Sripathy, S. P., Stevens, J., & Schultz, D. C.
Affiliations: Case Comprehensive Cancer Center (US)
ORCID: Sripathy, Smitha P.
Schultz, David C.
Venue: Molecular and Cellular Biology
Publisher: Informa UK Limited
Published: 2006-11-01
Volume: 26
Issue: 22
Pages: 8623-8638
ISSN: 0270-7306 (ISSN-L)
1098-5549
DOI: 10.1128/mcb.00487-06
PMC: PMC1636786
OpenAlex: W2105073128
Cited by: 323
References: 70
Citations by year: 2026: 9 · 2025: 10 · 2024: 20 · 2023: 15 · 2022: 14 · 2021: 21 · 2020: 24 · 2019: 14 · 2018: 14 · 2017: 14 · 2016: 15 · 2015: 19 · 2014: 13 · 2013: 12 · 2012: 20
FWCI: 6.11
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Molecular and Cellular Biology (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Case Comprehensive Cancer Center, Case Western Reserve University
National Cancer Institute (K01CA099093, CA-99093)
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: KRAB zinc finger proteins, transcriptional repression, heterochromatin, HP1 proteins, SETDB1, PHD finger, bromodomain, histone modifications, H3K9 trimethylation, H3K4 methylation, nuclear compartmentalization, chromatin templates, RNA polymerase II recruitment
MeSH terms: Tripartite Motif-Containing Protein 28, Chromobox Protein Homolog 5, Cell Line, Chromatin, DNA-Binding Proteins, Heterochromatin, Histones, Hormones, Humans, Histone-Lysine N-Methyltransferase, Protein Methyltransferases, Repressor Proteins, RNA Polymerase II, Transcription Factors, Transcription, Genetic, Transfection, Genes, Reporter, Integrases, Saccharomyces cerevisiae Proteins, RNA, Small Interfering

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The KAP1 Corepressor Functions To Coordinate the Assembly of De Novo HP1-Demarcated Microenvironments of Heterochromatin Required for KRAB Zinc Finger Protein-Mediated Transcriptional Repression

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