KRAB-containing Zinc Finger Protein Research Articles

ZNF383, a novel KRAB-containing zinc finger protein, suppresses MAPK signaling pathway

Mitogen-activated protein kinases (MAPKs) are major components of pathways controlling embryogenesis, cell differentiation, cell proliferation, and cell death. One of the most explored functions of MAPK signaling is the regulation of gene expression by direct or indirect phosphorylation and subsequent activation of transcription factors. In this article, we isolated a novel KRAB-related zinc finger gene named ZNF383 from an early embryo heart cDNA library. The cDNA of ZNF383 is 2220 bp, encoding a protein of 475 amino acids. The protein is conserved in evolution across different species. Northern blot analysis indicates that a 2.2 kb transcript specific for ZNF383 is detected in most of the examined human adult and embryonic tissues with a higher level in skeletal muscle. In COS-7 cells, ZNF383 protein is localized to nucleus and cytoplasm. ZNF383 is a transcription repressor when fused to Gal-4 DNA-binding domain and cotransfected with VP-16. Deletion analysis indicates that the KRAB box of ZNF383 is responsible for the transcriptional repressor activity. Overexpression of ZNF383 in cells inhibits the transcriptional activities of AP-1 and SRE, suggesting that ZNF383 may act as a negative regulator in MAPK-mediated signaling pathways.

ZNF411, a novel KRAB-containing zinc-finger protein, suppresses MAP kinase signaling pathway

Cardiac differentiation involves a cascade of coordinated gene expression that regulates cell proliferation and matrix protein formation in a defined temporo-spatial manner. The zinc-finger-containing transcription factor has been implicated as a critical regulator of multiple cardiac-expressed genes as well as a regulator of inducible gene expression in response to hypertrophic stimulation. Mitogen-activated protein kinase (MAPK) signal transduction pathways are among the most widespread mechanisms of eukaryotic cell regulation. The MAPKs function inside the nucleus and target transcription factors that are prebound to DNA. Many transcription factors are probably important MAPK targets. Here, we have cloned a new zinc-finger gene named ZNF411 using degenerate primers from an early embryo heart cDNA library, which mapped to 19p13.11. The ZNF411 gene consists of 2360 nucleotides and encodes a protein of 499 amino acids with an amino-terminal KRAB domain and eleven carboxy-terminal C2H2 zinc-finger units. Northern blot analysis indicates that a 2.4 kb transcript specific for ZNF411 is expressed in heart, skeletal muscle, and placenta at adult stage and is expressed in most of the examined embryonic tissues, especially at a higher level in skeletal muscle, heart, and pancreas. ZNF411 protein distributes evenly in nuclei when overexpressed in the cells. Reporter gene assays show that ZNF411 is a transcriptional repressor and overexpression of ZNF411 in the COS-7 cells inhibits the transcriptional activities of AP-1 and SRE. These results indicate that ZNF411 is a member of the zinc-finger transcription factor family and may be involved in the heart development, and it probably works as a negative regulator in MAPK signaling pathway.

Identification of a KRAB-containing zinc finger protein, ZNF304, by AU-motif-directed display method and initial characterization in lymphocyte activation

A novel human Krüppel-associated box (KRAB) type zinc finger protein encoding gene, ZNF304, was obtained by AU-motif-directed display and RACE. This gene, which contains a tandem AU motif in the 3 ′ untranslated region, has an ORF 1977-bp long that codes for a putative 659 residue protein with an amino-terminal KRAB domain and 13 carboxyl-terminal C2H2 zinc finger units. The gene maps to chromosome 19q13.4, a region that contains the largest zinc finger cluster so far identified in the human genome. Structurally, ZNF304 is related to a family of repressor transcription factors. ZNF304 expression was higher in lymphoid tissues but it was also detected in the following tissues, ordered by abundance: thyroid, adrenal gland, prostate, pancreas, and skeletal muscle. Jurkat, U937, and THP1 cell lines showed a relatively low expression of ZNF304. By contrast, PBLs stimulated with PHA or PMA + ionomycin showed a biphasic expression with a sharp increase at 6 h. This induction was closely parallel to IFN-γ expression and partially to IL-4 and IL-10. The tissue distribution and kinetics of induction suggest that ZNF304 may be involved in the regulation of lymphocyte activation.

Identification of transcripts expressed under functional differentiation in primary culture of cerebral cortical neurons.

In this study, we utilized primary cultures of cerebral cortical neurons and RNA arbitrarily primed polymerase chain reaction (RAP-PCR) to identify differentially expressed transcripts in neurons of different culture ages. Eleven cDNA fragments with high sequence similarity to known genes and Expressed Sequence Tags (ESTs) were cloned. From the National Center for Biotechnology Information (NCBI) sequence database, two clones were shown to be identical to known sequences, Mus musculus HP1-BP74 protein mRNA and Mus musculus KRAB-containing zinc finger protein, both were up-regulated. These genes have never before been shown to be involved in neuronal functional maturation. Among the remaining clones, clone 8-14 (239 bp) was very similar to Rattus norvegicus rS-Rex-b mRNA, which was further confirmed by sequencing its shortest isoform (1.5 kb) obtained by computer cloning. This study has identified eleven potential genes and transcripts, which might be involved in the development and differentiation of GABAergic neurons in culture.

Molecular Cloning and Characterization of a KRAB-Containing Zinc Finger Protein, ZNF317, and Its Isoforms

To identify zinc finger genes in human primary cultured erythroid progenitor cells, RT-PCR was performed using primers specific for the conserved sequence in zinc finger domains of mouse Friend of GATA-1. We identified a novel Krüppel-associated box (KRAB) zinc finger gene, ZNF317. Evaluation of full-length cDNA obtained by RACE showed that it encoded a protein composed of 13 Krüppel-like zinc fingers and a KRAB domain. RT-PCR analysis revealed four alternatively splicing products (ZNF317-1 through ZNF317-4). The ZNF317 gene has seven exons and is located in human chromosome 19p13. Northern analysis revealed that ZNF317-1 and ZNF317-2 transcripts were ubiquitously expressed, whereas ZNF317-3 and ZNF317-4 transcripts were detected only in lymphocytes, spleen, and lung. Competitive RT-PCR analysis showed that the expression of ZNF317 mRNA significantly decreased during erythroid maturation. In lymphocytes, ZNF317 expression was reduced in response to mitogenic stimulation. We propose that ZNF317 may play an important role in erythroid maturation and lymphoid proliferation.

Targeting of Krüppel-associated Box-containing Zinc Finger Proteins to Centromeric Heterochromatin: IMPLICATION FOR THE GENE SILENCING MECHANISMS

Krüppel-associated box-containing zinc finger proteins (KRAB-ZFPs) repress transcription via functional interaction with the corepressor KRAB-associated protein-1 (KAP-1). KAP-1 directly interacts with heterochromatin protein 1 (HP1), a dose-dependent regulator of heterochromatin-mediated silencing. Here we show that two KRAB-ZFPs that we previously identified, KRAZ1 and KRAZ2, are targeted to foci of centromeric heterochromatin containing HP1alpha through the interaction with KAP-1. Centromeric targeting potential of KRAZ1 and KAP-1 is strictly correlated with their silencing activities; a KRAB mutant of KRAZ1 that is unable to bind KAP-1 and KAP-1 deletions unable to bind HP1 cannot localize to centromeric foci nor repress transcription. We provide evidence that this correlation is likely to be functionally relevant. First, overexpression of the VP16 transactivation domain fused with the KAP-1 deletion that binds to KRAB but not to HP1 leads to dramatic redistribution of KRAZ1 from centromeric foci and simultaneously converts KRAZ1-mediated silencing into strong transcriptional activation. Second, a specific inhibitor of histone deacetylases, trichostatin A, effectively redistributes KRAZ1 and KAP-1 from centromeric foci and partially relieves their silencing activities. These data strongly suggest that KRAB-ZFPs/KAP-1 silence transcription by dynamic recruitment of the target locus to the specific gene silencing compartment, centromeric heterochromatin, in a histone deacetylase-dependent manner.

Emergence of the ZNF91 Krüppel-associated box-containing zinc finger gene family in the last common ancestor of anthropoidea.

The ZNF91 gene family, a subset of the Krüppel-associated box (KRAB)-containing group of zinc finger genes, comprises more than 40 loci; most reside on human chromosome 19p12-p13.1. We have examined the emergence and evolutionary conservation of the ZNF91 family. ZNF91 family members were detected in all species of great apes, gibbons, Old World monkeys, and New World monkeys examined but were not found in prosimians or rodents. In each species containing the ZNF91 family, the genes were clustered at one major site, on the chromosome(s) syntenic to human chromosome 19. To identify a putative "founder" gene, > 20 murine KRAB-containing zinc finger protein (ZFP) cDNAs were randomly cloned, but none showed sequence similarity to the ZNF91 genes. These observations suggest that the ZNF91 gene cluster is a derived character specific to Anthropoidea, resulting from a duplication and amplification event some 55 million years ago in the common ancestor of simians. Although the ZNF91 gene cluster is present in all simian species, the sequences of the human ZNF91 gene that confer DNA-binding specificity were conserved only in great apes, suggesting that there is not a high selective pressure to maintain the DNA targets of these proteins during evolution.