KRAB Zinc Finger Protein Research Articles

TRIM28, a new molecular marker predicting metastasis and survival in early-stage non-small cell lung cancer

TRIM28 is a universal corepressor for Kruppel-associated box zinc finger proteins. In this study, we demonstrated the expression of TRIM28 gene was significantly higher in cancerous tissues than in noncancerous tissues (P<0.001). TRIM28 knockdown resulted in a decrease in cell proliferation in liquid media as well as in soft agar. The proliferation rate was impaired and the cell cycle progression was inhibited after knockdown of TRIM28 in non-small cell lung cancer cell lines PAa and SK-MES-1. We used real-time polymerase chain reaction to detect circulating cancer cells in 138 non-small cell lung cancer patients. The overall positive detection rate was 30.4% (42 of 138) in peripheral blood of NSCLC patients and was 29.9% (29 of 97) in early-stage patients. In a 70-month follow-up study, 20 of 29 patients (69.0%) in TRIM28 positive group had recurrence and/or metastasis, significantly higher (P=0.004) than in the TRIM28 negative group (25 of 68, 36.8%). In addition, non-small cell lung cancer patients whose circulating cancer cells expressed TRIM28 suffered shorter tumor-specific survival compared with those with absent TRIM28 expression (P<0.001). Results of our study showed that TRIM28 provides a survival advantage to lung cancer cells and may be a new marker to predict metastasis and prognosis in early-stage non-small cell lung cancer patients.

The KRAB Zinc Finger Protein RSL1 Regulates Sex- and Tissue-Specific Promoter Methylation and Dynamic Hormone-Responsive Chromatin Configuration

Over 400 Krüppel-associated box zinc finger proteins (KRAB-ZFPs) are encoded in mammalian genomes. While KRAB-ZFPs strongly repress transcription in vitro, little is known about their biological function or gene targets in vivo. Regulator of sex limitation 1 (Rsl1), one of the first KRAB-Zfp genes assigned a physiological role, accentuates sex-biased liver gene expression, most dramatically for mouse sex-limited protein (Slp), which provides an in vivo reporter of KRAB-ZFP function. Slp is induced in males in the liver and kidney by growth hormone (GH) and androgen, respectively. In the liver but not kidney, the Rsl1 genotype correlates with methylation of a CpG dinucleotide in the Slp promoter that is demethylated at puberty. RSL1 binds 2 kb upstream of the Slp promoter, both in vitro and in vivo, within an enhancer containing response elements for STAT5b. Chromatin immunoprecipitation (ChIP) assays demonstrate that RSL1 recruits KAP1/TRIM28, the corepressor for KRAB action in vitro, to this enhancer. Slp induction requires rapid cycling of STAT5b in chromatin. Remarkably, RSL1 simultaneously binds adjacent to STAT5b with a reciprocal binding pattern that limits hormonal response. These experiments demonstrate a surprisingly dynamic interplay between a hormonal activator, STAT5b, and a KRAB-ZFP repressor and provide unique insights into KRAB-ZFP epigenetic mechanisms.

KAP1 regulates gene networks controlling T‐cell development and responsiveness

Chromatin remodeling at specific genomic loci controls lymphoid differentiation. Here, we investigated the role played in this process by Kruppel-associated box (KRAB)-associated protein 1 (KAP1), the universal cofactor of KRAB-zinc finger proteins (ZFPs), a tetrapod-restricted family of transcriptional repressors. T-cell-specific Kap1-deleted mice displayed a significant expansion of immature thymocytes, imbalances in CD4(+)/CD8(+) cell ratios, and altered responses to TCR and TGFβ stimulation when compared to littermate KAP1 control mice. Transcriptome and chromatin studies revealed that KAP1 binds T-cell-specific cis-acting regulatory elements marked by the H3K9me3 repressive mark and enriched in Ikaros/NuRD complexes. Also, KAP1 directly controls the expression of several genes involved in TCR and cytokine signaling. Among these, regulation of FoxO1 seems to play a major role in this system. Likely responsible for tethering KAP1 to at least part of its genomic targets, a small number of KRAB-ZFPs are selectively expressed in T-lymphoid cells. These results reveal the so far unsuspected yet important role of KAP1-mediated epigenetic regulation in T-lymphocyte differentiation and activation.

Roles of Kruppel-associated Box (KRAB)-associated Co-repressor KAP1 Ser-473 Phosphorylation in DNA Damage Response

The Kruppel-associated box (KRAB)-associated co-repressor KAP1 is an essential nuclear co-repressor for the KRAB zinc finger protein superfamily of transcriptional factors. Ataxia telangiectasia mutated (ATM)-Chk2 and ATM- and Rad3-related (ATR)-Chk1 are two primary kinase signaling cascades activated in response to DNA damage. A growing body of evidence suggests that ATM and ATR phosphorylate KAP1 at Ser-824 in response to DNA damage and regulate KAP1-dependent chromatin condensation, DNA repair, and gene expression. Here, we show that, depending on the type of DNA damage that occurs, KAP1 Ser-473 can be phosphorylated by ATM-Chk2 or ATR-Chk1 kinases. Phosphorylation of KAP1 at Ser-473 attenuated its binding to the heterochromatin protein 1 family proteins and inhibited its transcriptional repression of KRAB-zinc finger protein (KRAB-ZFP) target genes. Moreover, KAP1 Ser-473 phosphorylation induced by DNA damage stimulated KAP1-E2F1 binding. Overexpression of heterochromatin protein 1 significantly inhibited E2F1-KAP1 binding. Elimination of KAP1 Ser-473 phosphorylation increased E2F1-targeted proapoptotic gene expression and E2F1-induced apoptosis in response to DNA damage. Furthermore, loss of phosphorylation of KAP1 Ser-473 led to less BRCA1 focus formation and slower kinetics of loss of γH2AX foci after DNA damage. KAP1 Ser-473 phosphorylation was required for efficient DNA repair and cell survival in response to DNA damage. Our studies reveal novel functions of KAP1 Ser-473 phosphorylation under stress.

Proteins involved in establishment and maintenance of imprinted methylation marks

Epigenetic phenomena are being increasingly recognized to play key roles in normal mammalian development and disease. This is exemplified by the process of genomic imprinting whereby despite identical DNA sequence, the two parental chromosomes are not equivalent and show either maternal- or paternal-specific expression at a subset of genes in the genome. These patterns are set up by differential DNA methylation marking at the imprinting control regions in male and female germ line. In this review, we discuss the specific mechanisms by which these methyl marks are established and then selectively maintained throughout pre-implantation development. Specifically, we discuss the recent findings of a critical role played by a KRAB zinc-finger protein ZFP57 and its co-factor KAP1/TRIM28 in mediating both processes.

The mouse KRAB zinc-finger protein CHATO is required in embryonic-derived tissues to control yolk sac and placenta morphogenesis

Yolk sac and placenta are required to sustain embryonic development in mammals, yet our understanding of the genes and processes that control morphogenesis of these extraembryonic tissues is still limited. The chato mutation disrupts ZFP568, a Krüppel-Associated-Box (KRAB) domain Zinc finger protein, and causes a unique set of extraembryonic malformations, including ruffling of the yolk sac membrane, defective extraembryonic mesoderm morphogenesis and vasculogenesis, failure to close the ectoplacental cavity, and incomplete placental development. Phenotypic analysis of chato embryos indicated that ZFP568 does not control proliferation or differentiation of extraembryonic lineages but rather regulates the morphogenetic events that shape extraembryonic tissues. Analysis of chimeric embryos showed that Zfp568 function is required in embryonic-derived lineages, including the extraembryonic mesoderm. Depleting Zfp568 affects the ability of extraembryonic mesoderm cells to migrate. However, explanted Zfp568 mutant cells could migrate properly when plated on appropriate extracellular matrix conditions. We show that expression of Fibronectin and Indian Hedgehog are reduced in chato mutant yolk sacs. These data suggest that ZFP568 controls the production of secreted factors required to promote morphogenesis of extraembryonic tissues. Our results support previously undescribed roles of the extraembryonic mesoderm in yolk sac morphogenesis and in the closure of the ectoplacental cavity and identify a novel role of ZFP568 in the development of extraembryonic tissues.

Sex-specific Regulation by the RSL KRAB Zinc Finger Proteins Impacts Reproduction, Metabolism, and Evolution.

Sex-specific Regulation by the RSL KRAB Zinc Finger Proteins Impacts Reproduction, Metabolism, and Evolution.

KRAB Zinc Finger Protein ZNF382 Is a Proapoptotic Tumor Suppressor That Represses Multiple Oncogenes and Is Commonly Silenced in Multiple Carcinomas

Zinc finger transcription factors are involved broadly in development and tumorigenesis. Here, we report that the little studied zinc finger transcription factor ZNF382 functions as a tumor suppressor in multiple carcinomas. Although broadly expressed in normal tissues, ZNF382 expression was attenuated in multiple carcinoma cell lines due to promoter CpG methylation. ZNF382 was also frequently methylated in multiple primary tumors (nasopharyngeal, esophageal, colon, gastric, and breast). Ectopic expression of ZNF382 in silenced tumor cells significantly inhibited their clonogenicity and proliferation and induced apoptosis. We further found that ZNF382 inhibited NF-kappaB and AP-1 signaling and downregulated the expression of multiple oncogenes including MYC, MITF, HMGA2, and CDK6, as well as the NF-kappaB upstream factors STAT3, STAT5B, ID1, and IKBKE, most likely through heterochromatin silencing. ZNF382 could suppress tumorigenesis through heterochromatin-mediated silencing, as ZNF382 was colocalized and interacted with heterochromatin protein HP1 and further changed the chromatin modifications of ZNF382 target oncogenes. Our data show that ZNF382 is a functional tumor suppressor frequently methylated in multiple carcinomas.

The transcriptional co-repressor TRIM28 is differentially required by KRAB zinc finger proteins during early mammalian embryogenesis

The transcriptional co-repressor TRIM28 is differentially required by KRAB zinc finger proteins during early mammalian embryogenesis

The KRAB Zinc Finger Protein ZFP568 is Required in the Extraembryonic Mesoderm for Yolk Sac and Placental Development

The KRAB Zinc Finger Protein ZFP568 is Required in the Extraembryonic Mesoderm for Yolk Sac and Placental Development

Review for the regulatory functions of KRAB zinc finger proteins in embryonic development and tumorgenesis of higher vertebrates

KRAB-containing zinc-finger proteins (KRAB-ZFPs) first arose in the tetrapod vertebrates, and evolved quickly. Till Homo sapiens, they have become the largest family of transcription factors. Despite the molecular mechanism of transcription regulation by KRAB-ZFPs has been clarified in some degree, the higher-vertebrate-specific biological functions of the KRAB-ZFP family are still largely unknown. This review focused on the important regulatory functions of the KRAB-ZFP in embryonic development and tumorgenesis, which will benefit to the comprehensive understanding of biological roles of KRAB-ZFP in different physiological and pathological states. All of the systematic information will facilitate the further theoretical and applied studies of KRAB-ZFPs.

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1.

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

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 that 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 small interfering RNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes.

A Pair of Mouse KRAB Zinc Finger Proteins Modulates Multiple Indicators of Female Reproduction1

Krüppel-associated box-zinc finger proteins (KRAB-ZFPs) are the largest class of transcriptional regulators in mammals, yet few have been assigned biological roles. Cloning the genes underlying the regulator of sex-limitation (rsl) phenotype, in which the normally male-specific sex-limited protein (SLP) is expressed in female mice, identified two KRAB-ZFPs, Rsl1 and Rsl2, as influencing sexually dimorphic liver gene expression. Combined absence of both repressors in rsl mice leads to increased expression in female liver of major urinary proteins (MUPs) and certain enzymes of steroid metabolism, as well as SLP. We hypothesized that this altered gene expression might affect reproductive physiology in rsl females. Urinary MUP (uMUP) concentration varied with the estrous cycle in both wt and rsl females but was consistently higher in rsl urine. A behavioral odor test revealed that wild-type (wt) males preferred rsl to wt females, possibly due to elevated uMUPs providing greater pheromone presentation. To ascribe activity to Rsl1, Rsl2, or both, the genes were individually expressed as liver-specific transgenes. RSL2 overexpression accentuated uMUP fluctuations across the estrous cycle, whereas RSL1 overexpression did not. In addition, puberty onset, as indicated by vaginal opening (VO), occurred 2 days earlier in rsl females, and excess RSL2, but not RSL1, restored VO timing to wt. Hence, transcriptional repression by RSL in liver modifies female mouse reproduction via targets that likely impact both hormonal and pheromonal cues. The large and rapidly diversifying KRAB-ZFP family may modulate biological processes, including reproduction, to confer individual differences that may isolate populations and ultimately lead to speciation.

KAP1 Is Associated With Peritoneal Carcinomatosis in Gastric Cancer

KRAB-associated protein 1 (KAP1) is a universal corepressor for Kruppel-associated box zinc finger proteins. Here we demonstrate the biological function and clinical significance of KAP1 expression in gastric cancer. Knockdown of the KAP1 gene by siRNA transfection was performed to evaluate KAP1 function in gastric cancer cells. Real-time polymerase chain reaction was performed in 91 samples obtained from gastric cancer patients. The proliferation rate was impaired and resistance to anoikis was decreased after knockdown of KAP1 in the gastric cancer cell lines AZ521 and KATO III. Expression of the KAP1 gene was significantly higher in cancerous tissues than in noncancerous tissues (P < .05). Patients with high KAP1 expression showed a higher incidence of peritoneal carcinomatosis (P < .05) and significantly poorer overall survival compared to patients with low KAP1 expression (5-year overall survival rates, 35.4% and 50.5%, respectively; P < .05). Multivariate analysis revealed that high KAP1 expression was an independent prognostic factor (risk ratio, 1.44; 95% confidence interval, 1.03-1.99; P < .05). Intriguingly, high KAP1 expression was also an independent factor for peritoneal carcinomatosis (odds ratio, 4.53; 95% confidence interval, 1.27-18.5; P < .05). KAP1 provides a survival advantage to gastric cancer cells and is an independent factor for peritoneal dissemination in patients with gastric cancer. These results suggest that KAP1 plays an important role in progression to peritoneal carcinomatosis in gastric cancer patients.

Spatial juxtaposition of HIV-1 provirus with PML and KAKA bodies as revealed by 3D Immuno DNA FISH

Various members of tripartite motif (TRIM) protein family display antiviral properties, targeting retroviruses in particular. The potential activity of TRIM19, better known as promyelocytic leukemia protein (PML) against several viruses has been well documented, yet it's role in HIV-1 infection remains elusive. One of the most important cellular partners of HIV-1, P-TEFb kinase complex, composed of CDK9 and CyclinT1 plays a crucial role in regulation of HIV-1 transcription. We have previously demonstrated that both members of P-TEFb interact with PML protein and localize inside the PML Nuclear Bodies (PML NB) [1,2]. In particular, we found that the acetylated and enzymaticaly inactive form of CDK9 binds PML and can be separated with PML in the insoluble chromatin fraction. Our ChIP analysis revealed that acetylated form of CDK9 localizes to the integrated and transcriptionally silent viral genome, thus indicating that PML might have yet unidentified role in regulation of HIV-1 infection and latency [2]. We indeed identified PML protein bound to the silent viral genome in Jurkat cells harboring single integrations of HIV-1 provirus. The distribution of PML protein along the viral genome could be correlated with bimethylated lysine 9 (K9) on Histone 3 (2MetK9 H3), a mark of facultative heterochromatin. Transcriptional activation of the provirus with TNF-α led to a displacement of PML protein from the genome and to a substantial loss of 2MetK9H3 mark. By three-dimensional immuno fluorescent in situ hybridization (3D Immuno DNA FISH) that we developed we visualized the viral genome in close proximity to PML NB and we characterized this position as adjacent. Within the population of cells tested in the silenced state, 40% of the cells showed proximity at the distance of less that 0.6μm. PML NB were recently described to have a close spatial relationship with the so called KAKA foci, characterized by the presence of KAP-1 (or Trim28) and KRAB-Zinc Finger proteins [3] thus prompting us to analyse the relationship of the silent HIV-1 provirus with these nuclear structures. We detected numerous PML and KAKA foci in both Jurkat cells (J-LAT model of latency) and primary human CD4+T lymphocytes, with HIV-1 residing either in close proximity to PML or to KAKA foci (~40% showing less than 0.6μm distance) in J-LAT latency model. Whether this spatial localization of HIV-1 provirus is correlated to silencing of the virus genome or is a general feature of HIV-1 integration and replication remains still to be determined.

The HP1α–CAF1–SetDB1‐containing complex provides H3K9me1 for Suv39‐mediated K9me3 in pericentric heterochromatin

Trimethylation of lysine 9 in histone H3 (H3K9me3) enrichment is a characteristic of pericentric heterochromatin. The hypothesis of a stepwise mechanism to establish and maintain this mark during DNA replication suggests that newly synthesized histone H3 goes through an intermediate methylation state to become a substrate for the histone methyltransferase Suppressor of variegation 39 (Suv39H1/H2). How this intermediate methylation state is achieved and how it is targeted to the correct place at the right time is not yet known. Here, we show that the histone H3K9 methyltransferase SetDB1 associates with the specific heterochromatin protein 1alpha (HP1alpha)-chromatin assembly factor 1 (CAF1) chaperone complex. This complex monomethylates K9 on non-nucleosomal histone H3. Therefore, the heterochromatic HP1alpha-CAF1-SetDB1 complex probably provides H3K9me1 for subsequent trimethylation by Suv39H1/H2 in pericentric regions. The connection of CAF1 with DNA replication, HP1alpha with heterochromatin formation and SetDB1 for H3K9me1 suggests a highly coordinated mechanism to ensure the propagation of H3K9me3 in pericentric heterochromatin during DNA replication.

Regulator of sex-limitation KRAB zinc finger proteins modulate sex-dependent and -independent liver metabolism

Krüppel-related zinc finger proteins (KRAB-zfps) comprise the largest mammalian transcription factor family, but their specific functions are largely unknown. Two KRAB-zfps, regulator of sex-limitation (Rsl) 1 and Rsl2, repress expression of the mouse sex-limited protein (Slp) gene, the hallmark of Rsl activity, as well as some other male-predominant liver genes. This phenotype suggests Rsl modifies sex-specific transcription. The scope of Rsl control was determined by expression profiling of liver RNA from wild-type (wt), rsl, and transgenic mice with hepatic overexpression of Rsl1 or Rsl2. About 7.5% of the liver transcriptome was Rsl-responsive. More genes in males than females were affected by the loss of Rsl (e.g., in rsl mice), whereas Rsl overexpression altered more transcripts in females than males. Rsl dramatically repressed some female-predominant genes, but most were modestly (1.25- to 2-fold) influenced. In males, most Rsl-responsive genes unexpectedly expressed at lower levels in rsl than wt, suggesting not all are direct targets of Rsl repression. Gene Ontology analysis showed Rsl targets enriched in pathways of cholesterol, steroid, and lipid metabolism, linking Rsl to energy balance. In accord with this, blood glucose levels were less in male rsl than wt mice, and less responsive to fasting and refeeding. rsl mice were also leaner than wt, consistent with their hepatic regulation of phosphoenolpyruvate carboxykinase 1 and stearoyl-Coenzyme A desaturase 1. Altogether, Rsl's effect on sexually dimorphic and metabolically sensitive liver gene expression suggests a role for KRAB-zfps as broad genetic modulators of individual adaptation.

Regulation of Episomal Gene Expression by KRAB/KAP1-Mediated Histone Modifications

KAP1 is an essential cofactor of KRAB zinc finger proteins, a family of vertebrate-specific epigenetic repressors of largely unknown functions encoded in the hundreds by the mouse and human genomes. So far, KRAB/KAP1-mediated gene regulation has been studied within the environment of chromosomal DNA. Here we demonstrate that KRAB/KAP1 regulation is fully functional within the context of episomal DNA, such as adeno-associated viral and nonintegrated lentiviral vectors, and is correlated with histone modifications typically associated with this epigenetic regulator.

KRAB zinc-finger proteins localise to novel KAP1-containing foci that are adjacent to PML nuclear bodies

The KRAB-zinc finger proteins (KRAB-ZFPs) represent a very large, but poorly understood, family of transcriptional regulators in mammals. They are thought to repress transcription via their interaction with KRAB-associated protein 1 (KAP1), which then assembles a complex of chromatin modifiers to lay down histone marks that are associated with inactive chromatin. Studies of KRAB-ZFP/KAP1-mediated gene silencing, using reporter constructs and ectopically expressed proteins, have shown colocalisation of both KAP1 and repressed reporter target genes to domains of constitutive heterochromatin in the nucleus. However, we show here that although KAP1 does indeed become recruited to pericentric heterochromatin during differentiation of mouse embryonic stem (ES) cells, endogenous KRAB-ZFPs do not. Rather, KRAB-ZFPs and KAP1 relocalise to novel nucleoplasmic foci that we have termed KRAB- and KAP1-associated (KAKA) foci. HP1s can also concentrate in these foci and there is a close spatial relationship between KAKA nuclear foci and PML nuclear bodies. Finally, we reveal differential requirements for the recruitment of KAP1 to pericentric heterochromatin and KAKA foci, and suggest that KAKA foci may contain sumoylated KAP1 - the form of the protein that is active in transcriptional repression.