KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA611924 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11286155_1.fastq.gz | Fastqsanger.gz | |||
| SRR11286155_2.fastq.gz | Fastqsanger.gz | |||
| SRR11286156_1.fastq.gz | Fastqsanger.gz | |||
| SRR11286156_2.fastq.gz | Fastqsanger.gz | |||
| SRR11286157_1.fastq.gz | Fastqsanger.gz |
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Project description:We observed changes in protein levels of EZH2, TRIM24, p53, and a substantial number of KRAB-ZF proteins in MCF7 cells upon introducing a peptide fragment containing the KRAB domain.
2020-04-29 | GSE146769 | GEO
Project description:Interactions of KRAB (Krüppel-associated box)-associated protein KAP1 [also known as TRIM28 (tripartite motif containing protein 28)] with DNA-binding KRAB zinc finger (KRAB-ZF) proteins silence many transposable elements during embryogenesis. However, in some cancers, TRIM28 is upregulated and interacts with different partners, many of which are transcription regulators such as EZH2 in MCF7 cells, to form abnormal repressive or activating complexes that lead to misregulation of genes. We ask whether a KRAB domain-the TRIM28 interaction domain present in native binding partners of TRIM28 that mediate repression of transposable elements-could be used as a tool molecule to disrupt aberrant TRIM28 complexes. Expression of KRAB domain containing fragments from a KRAB-ZF protein (ZFP568) in MCF7 cells, without the DNA-binding zinc fingers, inhibited TRIM28-EZH2 interactions and caused degradation of both TRIM28 and EZH2 proteins as well as other components of the EZH2-associated polycomb repressor 2 complex. In consequence, the product of EZH2 enzymatic activity, trimethylation of histone H3 lysine 27 level, was significantly reduced. The expression of a synthetic KRAB domain significantly inhibits the growth of breast cancer cells (MCF7) but has no effect on normal (immortalized) human mammary epithelial cells (MCF10a). Further, we found that TRIM28 is a positive regulator of TRIM24 protein levels, as observed previously in prostate cancer cells, and expression of the KRAB domain also lowered TRIM24 protein. Importantly, reduction of TRIM24 levels, by treatment with either the KRAB domain or a small-molecule degrader targeted to TRIM24, is accompanied by an elevated level of tumor suppressor p53. Taken together, this study reveals a novel mechanism for a TRIM28-associated protein stability network and establishes TRIM28 as a potential therapeutic target in cancers where TRIM28 is elevated. Finally, we discuss a potential mechanism of KRAB-ZF gene expression controlled by a regulatory feedback loop of TRIM28-KRAB.
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Project description:Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are primarily regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated box domain zinc fingers (KRAB-ZNFs), is known to regulate both processes, however exact mechanism and identity of participating KRAB-ZNF genes remains unknown. Here, using a novel reporter system, we first showed that TRIM28/KRAB-ZNFs alter DNA methylation patterns in addition to H3K9me3 to cause gene repression during reprogramming. Next, using several expression datasets, we identified novel KRAB-ZNFs (ZNF114, ZNF483 and ZNF589) in the human genome that regulate pluripotency. Mechanistically, we demonstrated that these KRAB-ZNFs directly alter gene expression of important developmental genes by modulation of H3K9me3 and DNA methylation on their promoters. In summary, TRIM28 employs novel KRAB-ZNFs to evoke epigenetic silencing of its target differentiation genes by H3K9me3 and DNA methylation.
2017-11-30 | GSE97403 | GEO
Project description:Transposable elements (TEs) are subjected to early embryonic repression through sequence-specific recruitment of KRAB zinc finger proteins (KRAB-ZFPs), their cofactor TRIM28 and associated chromatin modifiers. This prevents transposition and modulates TE-induced changes of gene expression in embryonic stem cells (ESCs). It leads to DNA methylation, a self-perpetuating modification considered as responsible for the permanent silencing of TEs after this period. Challenging this view, we reveal here that the KRAB/TRIM28 system keeps mediating a highly dynamic control of TEs and TE-mediated transcriptional influences in adult human cells. Using CD4+ T lymphocytes as an experimental model, we first observed that in these cells many TEs are still bound by TRIM28, the recruitment of which is dynamically regulated upon T cell receptor stimulation. Second, we determined that this transition reflects marked changes in the expression patterns of TE-binding KRAB-ZFPs. Finally, we could demonstrate that TRIM28 depletion induces broad transcriptional alterations in T cells, with de-repression notably of TE-based enhancers leading to the illegitimate activation of nearby genes and breaches of lineage-specific transcriptional restrictions. These data contribute to demonstrate that TEs and their KRAB-ZFP/TRIM28 control system are important regulators of gene expression in adult human cells.
2021-06-01 | GSE81872 | GEO
Project description:Transposable elements (TEs) are subjected to early embryonic repression through sequence-specific recruitment of KRAB zinc finger proteins (KRAB-ZFPs), their cofactor TRIM28 and associated chromatin modifiers. This prevents transposition and modulates TE-induced changes of gene expression in embryonic stem cells (ESCs). It leads to DNA methylation, a self-perpetuating modification considered as responsible for the permanent silencing of TEs after this period. Challenging this view, we reveal here that the KRAB/TRIM28 system keeps mediating a highly dynamic control of TEs and TE-mediated transcriptional influences in adult human cells. Using CD4+ T lymphocytes as an experimental model, we first observed that in these cells many TEs are still bound by TRIM28, the recruitment of which is dynamically regulated upon T cell receptor stimulation. Second, we determined that this transition reflects marked changes in the expression patterns of TE-binding KRAB-ZFPs. Finally, we could demonstrate that TRIM28 depletion induces broad transcriptional alterations in T cells, with de-repression notably of TE-based enhancers leading to the illegitimate activation of nearby genes and breaches of lineage-specific transcriptional restrictions. These data contribute to demonstrate that TEs and their KRAB-ZFP/TRIM28 control system are important regulators of gene expression in adult human cells.
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Project description:Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their presumed inactivation by DNA methylation. Analyses of epigentic effectors and marks in KAP1 WT and KD human embryonic stem cells
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Project description:KAP1 is overexpressed in breast cancer. To determine KAP1 regulated genes, we performed microarray analysis of gene expression in KAP1 depleted breast cancer cells MDA-MB-231LN. The transcriptional regulator TRIM28/KAP1 plays an important role in development, stem cell self-renewal, chromatin organization and the DNA damage response. KAP1 is an essential co-repressor for KRAB zinc finger proteins (KRAB-ZNFs). Though KRAB-ZNFs represent the largest family of human transcription factors, their biological functions are largely unknown. Using the conserved zinc fingers linker region (ZnFL) as antigen, we have developed a ZnFL antibody that recognizes multiple KRAB-ZNFs. We showed that KAP1 and many KRAB-ZNFs were overexpressed in human breast cancers and breast cancer cell lines. In addition, an active SUMOylated form of KAP1 was markedly increased in breast cancer cells. Furthermore, KAP1 depletion in breast cancer cell lines reduced cell proliferation and inhibited tumor growth and metastasis of tumor xenografts. Conversely, KAP1 overexpression stimulated cell proliferation and tumor growth. KAP1 knockdown led to down-regulation of genes previously linked to tumor progression and metastasis, including PTGS2/COX2, EREG, CD44, MMP1 and MMP2. Interestingly, KAP1 depletion or genomic deletion led to dramatic down-regulation of multiple KRAB-ZNF proteins due in part to their increased degradation. KAP1-dependent stabilization of KRAB-ZNFs required a direct KRAB-ZNF-KAP1 interaction. These results establish KAP1 as a positive regulator of multiple KRAB-ZNFs and an important factor in the development of breast cancer. 7 total samples were analyzed. Stable sublines of MDA-MB-231LN cells expressing control non-targeting shRNA (Scr, 3 biological replicates) and two different shRNAs against KAP1 (KAP1-3, 2 biological replicates and KAP1-4, 2 biological replicates) from doxycycline-inducible pTRIPZ vector were cultured in the presence of 0.5 ug/ml doxycycline for 7 days to induce shRNA expression. Cells were lysed and total RNA was isolated using mirVana miRNA isolation kit (Ambion) in the WVU Genomics Core Facility.
2014-09-23 | E-GEOD-61639 | biostudies-arrayexpress
Project description:Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their presumed inactivation by DNA methylation.
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Project description:TRIM28 (KAP1 - KRAB-associated protein 1) is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these genetic invaders. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28-sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos. Analyses of transcriptional profiles and chromatin state in TRIM28 WT and KO cells
2012-12-04 | E-GEOD-41903 | biostudies-arrayexpress
Project description:Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger factor (ZNF). However, very few studies have performed genome-wide analyses of ZNF binding patterns and thus it is not clear if the binding code developed in vitro will be useful for identifying target genes of a particular ZNF. We performed genome-wide ChIP-seq for ZNF263, a C2H2 ZNF that contains 9 finger domains, a KRAB repression domain, and a SCAN domain and identified more than 5000 binding sites in K562 cells. Our results suggest that ZNF263 binds to a 24 nt site which differs from the motif predicted by the zinc finger code in several positions. Interestingly, many of the ZNF263 binding sites are located within the transcribed region of the target gene. Although ZNFs containing a KRAB domain are thought to function mainly as transcriptional repressors, many of the ZNF263 target genes are expressed at high levels. To address the biological role of ZNF263, we identified genes whose expression was altered by treatment of cells with ZNF263-specific siRNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of ZNF263 ChIP-seq in K562 cells.
2009-12-03 | E-GEOD-19235 | biostudies-arrayexpress