Characterization and mapping of human genes encoding zinc finger proteins

From repression domains to designer zinc finger proteins: a novel strategy of intracellular immunization against HIV

Tissue-specific gene regulation of eukaryotic organisms is to a large extent mediated by transcription factors that interact with genomic DNA sequences in a sequence-specific manner. The purpose of this synopsis is to put forward the potential of designer zinc finger proteins in treating infections of human immunodeficiency virus (HIV). Artificial transcription factors containing designer zinc finger structures fused to activator or repressor domains have been designated Transcription Response Modifiers (TRMs). The principle of engineering TRMs has been derived from the analysis of human Krüppel-type zinc finger genes and their products. Our research efforts encompass two fascinating features that are displayed by the human Krüppel-type zinc finger protein KOX1: 1) the Krüppel-type zinc finger domains display rules of sequence-specific DNA recognition, and 2) the evolutionarily conserved Krüppel-associated box (KRAB) presents one of the strongest transcriptional repressors identified so far in mammalian organisms. The KRAB repressor activity is postulated to be mediated through co-repressor molecules, such as Silencing Mediating Protein-1 (SMP-1). Thus, the structural organization and functional analysis of zinc finger proteins revealed principles of zinc finger transcription factors that are applicable for reducing the viral load in individuals infected with HIV. In this article, a novel concept of generating therapeutic proteins is outlined that might be conceptually promising in modulating gene expressions of any kind.

The Human KROX-26/ZNF22 Gene is Expressed at Sites of Tooth Formation and Maps to the Locus for Permanent Tooth Agenesis (He-Zhao Deficiency)

Tooth development is mediated by sequential and reciprocal interactions between dental epithelium and mesenchyme under the molecular control of secreted growth factors and responsive transcription factors. We have previously identified the transcription factor Krox-26 as a potential regulator of tooth formation in mice. The purpose of this study was to investigate a potentially similar role for the human KROX-26 orthologue. We cloned the KROX-26 gene and found its single mRNA transcript (2.4 kb) to be expressed in multiple adult tissues. During fetal development, KROX-26 is expressed in the epithelial component of the developing tooth organ during early bud and cap stages as well as in osteoblasts of craniofacial bone and the developing tongue. The KROX-26 gene was mapped to chromosome 10q11.21, a locus that has been associated with permanent tooth agenesis (He-Zhao deficiency). These results indicate a potential function for KROX-26 in the molecular regulation of tooth formation in humans.

Establishment of a monoclonal antibody against a peptide of the novel zinc finger protein ZNF32 proved to be specific and sensitive for immunological measurements

Background

ZNF32 has been predicted to be a zinc finger protein and is involved in cell differentiation and tumor development, but its precise function is unknown. Specific monoclonal antibodies (mAbs) have been widely used in research and clinical diagnosis and treatments. Therefore, we established an anti-ZNF32 mAb to characterize this protein’s function.

Material/Methods

Peptide^49–63, a specific small peptide of ZNF32, was chosen and the synthetic keyhole limpet hemocyanin (KLH)-peptide^49–63 was used as an antigen to immunize mice. A mAb against peptide^49–63 was generated by hybridoma technology, and hybridoma cells were screened by limiting dilution. The isoform of mAb-pZNF32-8D9 was identified by double agar diffusion. The sensitivity and specificity of the mAb and expressed levels of ZNF32 in various cells and tissues were identified by enzyme-linked immunosorbent assay (ELISA), immunocytochemistry, immunohistochemistry, and Western blotting.

Results

A stable anti-pZNF32-8D9 hybridoma secreting the anti-peptide^49–63 mAb was established and the clone positive to the peptide^49–63 in supernatant was 92% in ELISA. The mAb-pZNF32-8D9 is an immunoglobulin-1 that can be used for detecting the ZNF32 protein by immunocytochemistry, immunohistochemistry, and Western blotting and is highly sensitive and specific. We also found ZNF32 expressed at high levels in Jurkat and pulmonary squamous carcinoma cells, but it was not expressed in squamous epidermis cells.

Conclusions

mAb-pZNF32-8D9 can be used for the identification and expression of ZNF32. It might also provide a new tool for diagnostics or therapy for ZNF32-related diseases.

Thyroid transcription factor-1 (TTF-1) gene: identification of ZBP-89, Sp1, and TTF-1 sites in the promoter and regulation by TNF-α in lung epithelial cells

Thyroid transcription factor-1 (TTF-1/Nkx2.1/TITF1) is a homeodomain-containing transcription factor essential for the morphogenesis and differentiation of the lung. In the lung, TTF-1 controls the expression of surfactant proteins that are essential for lung stability and lung host defense. In this study, we identified functionally important transcription factor binding sites in the TTF-1 proximal promoter and studied tumor necrosis factor-α (TNF-α) regulation of TTF-1 expression. TNF-α, a proinflammatory cytokine, has been implicated in the pathogenesis of acute respiratory distress syndrome (ARDS) and inhibits surfactant protein levels. Deletion analysis of TTF-1 5'-flanking DNA indicated that the TTF-1 proximal promoter retained high-level activity. Electrophoretic mobility shift assay, chromatin immunoprecipitation, and mutational analysis experiments identified functional ZBP-89, Sp1, Sp3, and TTF-1 sites in the TTF-1 proximal promoter. TNF-α inhibited TTF-1 protein levels in H441 and primary alveolar type II cells. TNF-α inhibited TTF-1 gene transcription and promoter activity, indicating that transcriptional mechanisms play important roles in the inhibition of TTF-1 levels. TNF-α inhibited TTF-1 but not Sp1 or hepatocyte nuclear factor-3 DNA binding to TTF-1 promoter. Transactivation experiments in A549 cells indicated that TNF-α inhibited TTF-1 promoter activation by exogenous Sp1 and TTF-1 without altering their levels, suggesting inhibition of transcriptional activities of these proteins. TNF-α inhibition of TTF-1 expression was associated with increased threonine, but not serine, phosphorylation of Sp1. Because TTF-1 serves as a positive regulator for surfactant protein gene expression, TNF-α inhibition of TTF-1 expression could have important implications for the reduction of surfactant protein levels in diseases such as ARDS.

The type 1 diabetes - HLA susceptibility interactome--identification of HLA genotype-specific disease genes for type 1 diabetes

Background

The individual contribution of genes in the HLA region to the risk of developing type 1 diabetes (T1D) is confounded by the high linkage disequilibrium (LD) in this region. Using a novel approach we have combined genetic association data with information on functional protein-protein interactions to elucidate risk independent of LD and to place the genetic association into a functional context.

Methodology/Principal Findings

Genetic association data from 2300 single nucleotide polymorphisms (SNPs) in the HLA region was analysed in 2200 T1D family trios divided into six risk groups based on HLA-DRB1 genotypes. The best SNP signal in each gene was mapped to proteins in a human protein interaction network and their significance of clustering in functional network modules was evaluated. The significant network modules identified through this approach differed between the six HLA risk groups, which could be divided into two groups based on carrying the DRB1*0301 or the DRB1*0401 allele. Proteins identified in networks specific for DRB1*0301 carriers were involved in stress response and inflammation whereas in DRB1*0401 carriers the proteins were involved in antigen processing and presentation.

Conclusions/Significance

In this study we were able to hypothesise functional differences between individuals with T1D carrying specific DRB1 alleles. The results point at candidate proteins involved in distinct cellular processes that could not only help the understanding of the pathogenesis of T1D, but also the distinction between individuals at different genetic risk for developing T1D.

Molecular characterization and gene disruption of a novel zinc-finger protein, HIT-4, expressed in rodent brain

To identify a novel regulatory factor involved in brain development or synaptic plasticity, we applied the differential display PCR method to mRNA samples from NMDA-stimulated and un-stimulated neocortical cultures. Among 64 cDNA clones isolated, eight clones were novel genes and one of them encodes a novel zinc-finger protein, HIT-4, which is 317 amino acid residues (36-38 kDa) in length and contains seven C2H2 zinc-finger motifs. Rat HIT-4 cDNA exhibits strong homology to human ZNF597 (57% amino acid identity and 72% homology) and identity to rat ZNF597 at the carboxyl region. Furthermore, genomic alignment of HIT-4 cDNA indicates that the alternative use of distinct promoters and exons produces HIT-4 and ZNF597 mRNAs. Northern blotting revealed that HIT-4 mRNA (approximately 6 kb) is expressed in various tissues such as the lung, heart, and liver, but enriched in the brain, while ZNF597 mRNA (approximately 1.5 kb) is found only in the testis. To evaluate biological roles of HIT-4/ZNF597, targeted mutagenesis of this gene was performed in mice. Homozygous (-/-) mutation was embryonic lethal, ceasing embryonic organization before cardiogenesis at embryonic day 7.5. Heterozygous (+/-) mice were able to survive but showing cell degeneration and vacuolization of the striatum, cingulate cortex, and their surrounding white matter. These results reveal novel biological and pathological roles of HIT-4 in brain development and/or maintenance.

Molecular and developmental biology of the hemangioblast

The hemangioblast hypothesis was proposed a century ago. The existence of hemangioblasts is now demonstrated in mouse and human embryonic stem cell (ESC)-derived embryoid bodies (EBs), in the mouse and zebrafish gastrula, and in adults. The hemangioblast is believed to derive from mesodermal cells, and is enriched in the Bry+Flk1+ and Flk1+Scl+ cell populations in EBs and in the posterior primitive streak of the mouse gastrula and in the ventral mesoderm of the zebrafish gastrula. However, recent studies suggest that the hemangioblast does not give rise to all endothelial and hematopoietic lineages in mouse and zebrafish embryos. Although several signaling pathways are known to involve the generation of hemangioblasts, it remains largely unknown how the hemangioblast is formed and what are the master genes controlling hemangioblast development. This review will summarize our current knowledge, challenges, and future directions on molecular and developmental aspects of the hemangioblast.

The transcription factor ZBP-89 controls generation of the hematopoietic lineage in zebrafish and mouse embryonic stem cells

Hematopoietic development is closely linked to that of blood vessels and the two processes are regulated in large part by transcription factors that control cell fate decisions and cellular differentiation. Both blood and blood vessels derive from a common progenitor, termed the hemangioblast, but the factor(s) specifying the development and differentiation of this stem cell population into the hematopoietic and vascular lineages remain ill defined. Here, we report that knockdown of the Krüppel-like transcription factor ZBP-89 in zebrafish embryos results in a bloodless phenotype, caused by disruption of both primitive and definitive hematopoiesis, while leaving primary blood vessel formation intact. Injection of ZBP-89 mRNA into cloche zebrafish embryos, which lack both the hematopoietic and endothelial lineages, rescues hematopoiesis but not vasculogenesis. Injection of mRNA for Stem Cell Leukemia (SCL), a transcription factor that directs hemangioblast development into blood cell precursors, rescues the bloodless phenotype in ZBP-89 zebrafish morphants. Forced expression of ZBP-89 induces the expansion of hematopoietic progenitors in wild-type zebrafish and in mouse embryonic stem cell cultures but inhibits angiogenesis in vivo and in vitro. These findings establish a unique regulatory role for ZBP-89, positioned at the interface between early blood and blood vessel development.

Key role of Krüppel-like factor proteins in pancreatic cancer and other gastrointestinal neoplasias

PURPOSE OF REVIEW

To describe recent studies on Krüppel-like factor transcription factors and their relationship with gastrointestinal neoplasias, in particular pancreatic cancer.

RECENT FINDINGS

Krüppel-like factor proteins are a subfamily of transcription factors characterized by the presence of a conserved DNA-binding domain comprising three Krüppel-like zinc fingers. Each distinct family member differs in its ability to regulate transcription, and, as a consequence, to influence cellular processes including cell growth and differentiation. Recently, a number of publications have provided evidence of the implication of Krüppel-like factor proteins in gastrointestinal carcinogenesis.

SUMMARY

This article will focus on the results of studies in the field published in the last year.

Discrimination of vanadium from zinc using gene profiling in human bronchial epithelial cells

We hypothesized that gene expression profiling may discriminate vanadium from zinc in human bronchial epithelial cells (HBECs). RNA from HBECs exposed to vehicle, V (50 microM), or Zn (50 microM) for 4 hr (n = 4 paired experiments) was hybridized to Affymetrix Hu133A chips. Using one-class t-test with p < 0.01, we identified 140 and 76 genes with treatment:control ratios > or = 2.0 or < or = 0.5 for V and Zn, respectively. We then categorized these genes into functional pathways and compared the number of genes in each pathway between V and Zn using Fisher's exact test. Three pathways regulating gene transcription, inflammatory response, and cell proliferation distinguished V from Zn. When genes in these three pathways were matched with the 163 genes flagged by the same statistical filtration for V:Zn ratios, 12 genes were identified. The hierarchical clustering analysis showed that these 12 genes discriminated V from Zn and consisted of two clusters. Cluster 1 genes (ZBTB1, PML, ZNF44, SIX1, BCL6, ZNF450) were down-regulated by V and involved in gene transcription, whereas cluster 2 genes (IL8, IL1A, PTGS2, DTR, TNFAIP3, CXCL3) were up-regulated and linked to inflammatory response and cell proliferation. Also, metallothionein 1 genes (MT1F, MT1G, MT1K) were up-regulated by Zn only. Thus, using microarray analysis, we identified a small set of genes that may be used as biomarkers for discriminating V from Zn. The novel genes and pathways identified by the microarray may help us understand the pathogenesis of health effects caused by environmental V and Zn exposure.

Molecular cloning, structure, expression, and chromosomal localization of the human Osterix (SP7) gene

We report the isolation of the human orthologue of the mouse Osterix (Osx/Sp7) gene, a C2H2 zinc finger transcription factor of the SP gene family and putative "master" regulator of bone cell differentiation. The human SP7 cDNA encodes a putative 431 amino acid protein that contains three consecutive C2H2 zinc finger repeats. The SP7 protein is highly conserved between mice and humans with an overall sequence identity of 95%. The expression of a SP7 mRNA transcript of approximately 3.2 kb is restricted to bone-derived cell lines in vitro but undetectable in any adult tissues including mandibular bone by Northern blot hybridization. The specific expression of SP7 mRNA in osteoblasts in vivo was further confirmed by in situ hybridization on human embryonic tissues. The highly restricted expression pattern and the divergence of the sequence outside of the zinc finger region distinguish SP7 as a unique member of the SP family. The SP7 gene consists of two exons, with exon 2 containing most of the protein coding sequence. The gene locus was mapped to chromosome 12q13.13 by fluorescent in situ hybridization (FISH). The identification and initial characterization of the SP7 gene will facilitate the study of the molecular regulation of osteoblast differentiation in humans.

The zinc finger transcription factor ZBP-89 is a repressor of the human beta 2-integrin CD11b gene

Integrin CD11b is a differentiation marker of the myelomonocytic lineage and an important mediator of inflammation. Expression of the CD11b gene is transcriptionally induced as myeloid precursors differentiate into mature cells, then drops as monocytes further differentiate into macrophages. Previous studies have identified elements and factors involved in the transcriptional activation of the CD11b gene during myeloid differentiation, but no data exist regarding potential down-regulatory factors, especially in the later stages of differentiation. Using 2 copies of a GC-rich element (-141 to -110) in the CD11b promoter, we probed a cDNA expression library for interacting proteins. Three clones were identified among 9.1 million screened, all encoding the DNA-binding domain of the zinc finger factor ZBP-89. Overexpression of ZBP-89 in the monocyte precursor cell line U937 reduced CD11b promoter-driven luciferase activity when U937 cells were induced to differentiate into monocytelike cells using phorbol esters. To identify the differentiation stage at which ZBP-89 repression of the CD11b gene is exerted, the protein level of ZBP-89 was correlated with that of CD11b mRNA in differentiating U937 as well as in normal human monocytes undergoing in vitro differentiation into macrophages. A clear inverse relationship was observed in the latter but not the former state, suggesting that ZBP-89 represses CD11b gene expression during the further differentiation of monocytes into macrophages.

The murine BTB/POZ zinc finger gene Znf131: predominant expression in the developing central nervous system, in adult brain, testis, and thymus

The Znf131/ZNF131 protein belongs to the superfamily of POK proteins containing a BTB/POZ domain in its N-terminal part and 5 typical C2H2 zinc fingers and an additional C2HC zinc finger structure in its C-terminal region. In mouse and human two alternatively spliced transcripts are expressed from the Znf131/ZNF131 gene, resulting from intraexonic splicing. While the longer transcript encodes for three double zinc finger structures the shorter transcript lacks the region coding for the first zinc finger. Although the murine Znf131 gene is ubiquitously expressed, expression analysis applying whole mount in situ hybridization showed a predominant expression in the developing central nervous system with strongest signals in the forebrain, midbrain, and hindbrain areas and in the neural tube. Further dominant expression was seen in embryonic limb buds. In human adult tissues a predominant expression of ZNF131 was seen in different brain areas, i.e., the occipital and temporal lobe, the nucleus caudatus, hippocampus, and the cerebellum as well as in testis and thymus. Therefore, it is possible that Znf131/ZNF131 plays a role during development and organogenesis as well as in the function of the adult central nervous system.

A novel zinc finger protein mRNA in human umbilical vein endothelial cells is profoundly induced by tumor necrosis factor alpha

Zinc finger proteins are known to mediate various transcriptional control mechanisms and other cellular functions in human cells. Tumor necrosis factor alpha (TNFalpha) induces a variety of genes in human endothelial cells including A20, an antiapoptotic zinc finger protein. In order to identify other zinc finger protein genes induced by TNFalpha, we studied the gene expression profile of human umbilical vein endothelial cells (HUVECs) stimulated by TNFalpha by means of oligonucleotide microarrays. Among the 155 genes encoding zinc finger motif, the level of EST M88357 mRNA encoding a novel designated EZFIT (endothelial zinc finger protein induced by TNFalpha) was induced most profoundly (>19 fold). The EZFIT gene is located on the chromosome 19q13.4. Isolation of the full length cDNA coding sequence by PCR using primers architected from the genomic sequence revealed that EZFIT has 490 amino acids which contain 13 C2H2 zinc finger motifs. Among 24 human organs and cell types studied, EZFIT mRNA was found to be most highly expressed in the placenta followed by the brain, testis, pancreas, heart, small intestine, muscle, uterus, prostate and peripheral blood leukocytes. EZFIT mRNA was not detected in the liver, lung, colon, stomach, the salivary gland or the thyroid gland.

Identification and characterization of DPZF, a novel human BTB/POZ zinc finger protein sharing homology to BCL-6

The C2H2 zinc finger protein family is one of the largest families of transcription factors. We identified a novel BTB/POZ zinc finger gene from human dendritic cells (DC), which encodes a 733-residue protein with a BTB/POZ domain at the N-terminal and 4 C2H2 zinc fingers at C-terminal. It was designated dendritic cell-derived BTB/POZ zinc finger (DPZF). DPZF protein shares closest homology to BCL-6, with the highest homology present in the BTB/POZ and zinc finger domains. Like BCL-6, DPZF gene is localized on chromosome 3. It is widely expressed in hematopoietic tissues, including DC, monocytes, B cells, and T cells. DPZF protein expression is detectable in lymphoid neoplasm with a molecular mass of 100 kD, especially in B lymphoma. These indicate that DPZF may be a transcription factor closely related to BCL-6, and may be involved in hematopoiesis, oncogenesis, and immune responses.

Identification and characterization of a transcriptional regulator for the lck proximal promoter

The lck gene encodes a protein-tyrosine kinase that plays a key role in signaling mediated through T cell receptor (TCR) and pre-TCR complexes. Transcription of the lck gene is regulated by two independent promoter elements: the proximal and distal promoters. Previous studies employing transgenic mice demonstrated that the sequence between -584 and -240 from the transcription start site in the mouse lck proximal promoter is required for its tissue-specific expression in the thymus. In this study, we demonstrate that a Krüppel-like zinc finger protein, mtbeta (BFCOL1, BERF-1, ZBP-89, ZNF148), previously cloned as a protein that binds to the CD3delta gene enhancer, binds to the -365 to -328 region of the lck proximal promoter. mtbeta is ubiquitously expressed in various cell lines and mouse tissues. Overexpressed mtbeta is more active in T-lineage cells than B-lineage cells for transactivating an artificial promoter consisting of the mtbeta binding site and a TATA box. Activity of the lck proximal promoter was significantly impaired by mutating the mtbeta binding site or by reducing mtbeta protein expression level by using antisense mRNA. Our results indicate that mtbeta activity is regulated in a tissue-specific manner and that mtbeta is a critical transactivator for the lck proximal promoter.

Noelin-1 is a secreted glycoprotein involved in generation of the neural crest

The vertebrate neural crest arises at the border of the neural plate during early stages of nervous system development; however, little is known about the molecular mechanisms underlying neural crest formation. Here we identify a secreted protein, Noelin-1, which has the ability to prolong neural crest production. Noelin-1 messenger RNA is expressed in a graded pattern in the closing neural tube. It subsequently becomes restricted to the dorsal neural folds and migrating neural crest. Over expression of Noelin-1 using recombinant retroviruses causes an excess of neural crest emigration and extends the time that the neural tube is competent to generate as well as regenerate neural crest cells. These results support an important role for Noelin-1 in regulating the production of neural crest cells by the neural tube.

Cloning and characterization of a novel Kruppel-associated box family transcriptional repressor that interacts with the retinoblastoma gene product, RB

The retinoblastoma gene product, RB, seems to function as a key tumor suppressor by repressing the expression of genes activated by members of the E2F family of transcription factors. In order to accomplish this, RB has been proposed to interact with a transcriptional repressor. However, no genuine transcriptional repressors have been identified by virtue of interaction with RB. By using the yeast two-hybrid system, we have identified a novel member of a known family of transcriptional repressors that contain zinc fingers of the Kruppel type and a portable transcriptional repressor motif known as the Kruppel-associated box (KRAB). The mouse and human forms of the novel RB-associated KRAB protein (RBaK) are widely expressed. The amino acid motif that links the KRAB domain and zinc fingers appears to be required for interaction with RB in vitro. Human RBaK ectopically expressed in fibroblasts is an 80-kDa protein that is localized to the nucleus. The expression of either RB or RBaK in 10T1/2 fibroblasts represses the activation of an E2F-dependent promoter and decreases DNA synthesis to a similar degree. However, a mutant form of RBaK that cannot interact with RB in vitro is unable to prevent DNA synthesis. We present a model in which RB physically interacts with the novel transcriptional repressor RBaK to repress E2F-dependent genes and prevent DNA synthesis.

A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis

Mechanisms regulating plant host differentiation of the nitrogen-fixing root nodules remain mostly unknown. Sinorhizobium meliloti induces this process in Medicago sativa in which the Mszpt2-1 gene is expressed in vascular bundles of roots and nodules. This gene codes for a Krüppel-like zinc finger protein, a class of transcription factors involved in many animal developmental processes. Expression of Mszpt2-1 in yeast cells conferred osmotic tolerance. Antisense plants grew normally but developed nonfunctional nodules, in which differentiation of the nitrogen-fixing zone and bacterial invasion were arrested. Hence, a vascular bundle-associated Krüppel-like gene is required for the formation of the central nitrogen-fixing zone of the root nodule.

A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis

Mechanisms regulating plant host differentiation of the nitrogen-fixing root nodules remain mostly unknown. Sinorhizobium meliloti induces this process in Medicago sativa in which the Mszpt2-1 gene is expressed in vascular bundles of roots and nodules. This gene codes for a Krüppel-like zinc finger protein, a class of transcription factors involved in many animal developmental processes. Expression of Mszpt2-1 in yeast cells conferred osmotic tolerance. Antisense plants grew normally but developed nonfunctional nodules, in which differentiation of the nitrogen-fixing zone and bacterial invasion were arrested. Hence, a vascular bundle-associated Krüppel-like gene is required for the formation of the central nitrogen-fixing zone of the root nodule.

Computer sequence analysis of human highly conserved zinc finger modules

We defined a sub-family of zinc finger proteins by computer analyses and comparisons of five new finger domains against protein databases. This subclass of the cysteine-cysteine/histidine-histidine motif shows additional well conserved amino acid patterns and belongs to the human kox and gli-Kruppel gene family, sharing also the same stretches of regulatory zinc finger-containing proteins of mouse and Xenopus. We particularly describe ZF6 cDNA which contains the most interesting sequence, encoding a putative multi-domain regulatory protein.

Translocation (3;16)(q27;p11) in a patient with diffuse large B-cell lymphoma associated with the BCL-6 gene rearrangement

A patient with B-cell lineage diffuse large-cell lymphoma carrying the t(3;16)(q27;p11) and BCL-6 rearrangement is described. Cytogenetic studies showed 46,XY,t(3;16)(q27;p11.2)[.11]/46,idem,add(18)(q21)[7]/46,XY[2]. The chromosomal translocation involving the 3q27 locus was associated with the BCL-6 gene rearrangement identified by Southern blot analysis. This case involved systemic lymph nodes, as large as 3 cm in diameter, bilaterally in neck, axilla, and inguinal regions. The patient obtained complete remission with chemotherapy.

Cys2/His2 zinc-finger protein family of petunia: evolution and general mechanism of target-sequence recognition

The EPF family is a group of Cys2/His2zinc-finger proteins in petunia. In these proteins, characteristically long spacer regions have been found to separate the zinc fingers. Our previous DNA-binding studies demonstrated that two-fingered proteins (ZPT2-1 and ZPT2-2), which have spacers of different lengths, bind to two separate AGT core motifs in a spacing specific manner. To investigate the possibility that these proteins might distinguish between the target sequences on the basis of spacing between the core motifs, we screened petunia cDNA library for other proteins belonging to this family. Initial screening by PCR and subsequent cloning of full-length cDNAs allowed us to identify the genes for 10 new proteins that had two, three or four zinc fingers. Among the two-fingered proteins the spacing between zinc fingers varied from 19 to 65 amino acids. The variation in the length of spacers was even more extensive in three- and four-fingered proteins. The presence of such proteins is consistent with our hypothesis that the spacing between the core motifs might be important for target sequence recognition. Furthermore, comparison of diverse protein structures suggests that three- and two-fingered proteins might have resulted due to successive loss of fingers from a four-fingered protein during molecular evolution. We also demonstrate that a highly conserved motif (QALGGH) among the members of EPF family and other Cys2/His2 zinc-finger proteins in plants is critical for the DNA-binding activity.

C2H2-171: a novel human cDNA representing a developmentally regulated POZ domain/zinc finger protein preferentially expressed in brain

We describe a novel human zinc finger cNDA. C2H2-171. This cDNA represents an mRNA which encodes a protein of 484 amino acids and a calculated molecular weight of 54 kD. Four zinc finger-like domains are found in the C-terminal end of the protein. At the N-terminus, C2H2-171 contains a POZ/tramtrack-like domain similar to that found in the tumor associated zinc finger proteins LAZ-3/BCL-6 and PLZ-F, as well as in non-zinc finger proteins. C2H2-171 RNA is preferentially expressed in the brain, and increases during the course of murine development, with maximal expression in the adult. C2H2-171 RNA is differentially expressed in brain regions, with the highest level of expression in the cerebellum. C2H2-171 RNA was expressed at high levels in primary cerebellar granule cell neurons compared to astrocytes. The gene encoding C2H2-171 is highly conserved in vertebrates, and maps to the terminus of human chromosome 1 (1q44-ter). This chromosomal location is associated with a number of cytogenetic aberrations including those involving brain developmental anomalies and tumorigenesis. These data suggest that C2H2-171 may play an important role in vertebrate brain development and function.

Isolation and characterisation of a diverse family of Arabidopsis two and three-fingered C2H2 zinc finger protein genes and cDNAs

In animal systems the C2H2 zinc finger protein (ZFP) gene family is the largest group of regulatory proteins and its members have a wide and important role in growth and development. It is likely that this family of ZFP transcription factors will also be important in plants. We have used a PCR approach employing highly degenerate oligonucleotide primers to isolate several Arabidopsis genomic and cDNA clones encoding potential ZFPs. In addition we have used the sequence information from these clones to identify two ESTs as members of this family. Five two-fingered and one three-fingered ZFPs have been identified. Outside of the zinc finger regions, there is considerable sequence diversity, including the sequence and length of the interfinger region; the expression pattern of each gene is different. This is the first report of the isolation of a three-fingered plant C2H2 ZFP gene and we discuss its possible evolutionary origin from two-fingered ZFP genes.

ZBP-89, a Krüppel-like zinc finger protein, inhibits epidermal growth factor induction of the gastrin promoter

We have shown previously that a GC-rich element (GGGGCGGGGTGGGGGG) conferring epidermal growth factor (EGF) responsiveness to the human gastrin promoter binds Sp1 and additional undefined complexes. A rat GH4 cell line expression library was screened by using a multimer of the gastrin EGF response element, and three overlapping cDNA clones were identified. The full-length rat cDNA encoded an 89-kDa zinc finger protein (ZBP-89) that was 89% identical to a 49-kDa human factor, ht(beta), that binds a GTGGG/CACCC element in T-cell receptor promoters. The conservation of amino acids between the zinc fingers indicates that ZBP-89 is a member of the C2H2 zinc finger family subclass typified by the Drosophila Krüppel protein. ZBP-89 is ubiquitously expressed in normal adult tissues. It binds specifically to the gastrin EGF response element and inhibits EGF induction of the gastrin promoter. Collectively, these results demonstrate that ZBP-89 functions as a repressor of basal and inducible expression of the gastrin gene.

Localization of a novel zinc finger gene to human chromosome 7q22 region by fluorescence in situ hybridization

As part of an endeavour to identify and characterize zinc finger genes of the cardiovascular system, a novel zinc finger gene, HHZ105, was isolated from a human fetal heart cDNA library. This gene was mapped by fluorescence in situ hybridization to human chromosome 7q22, a region associated with a number of genetic disorders and developmental deficiencies.

Localization of a novel zinc finger gene to the human chromosome 7p11.2-p12 by fluorescence in situ hybridization

A novel zinc finger gene (ZNF182) was isolated from a human fetal cardiac cDNA library, using a consensus C2H2 zinc finger oligonucleotide probe. This gene was assigned to human chromosome 7p11.1-p12 by fluorescence in situ hybridization (FISH). Additional FISH signals were identified on both the long and the short arms of chromosome 19, suggesting the presence of homologous genes at these loci.

Identification of a locus of zinc finger genes in human chromosome 19q13.1-q13.3 region by fluorescence in situ hybridization

A group of zinc-binding cDNA clones from a human fetal heart library was isolated using an oligonucleotide probe to the consensus sequence of the linker region of zinc finger proteins. Genes for novel clones were mapped by fluorescence in situ hybridization. In the process, we identified a previously unrecognized locus for two zinc finger-coding genes in human chromosome 19q13.1-q13.3 (ZNF180,ZNF181), where genomic rearrangements were shown to be accompanied by various developmental abnormalities, DNA repair deficiencies, and cellular malignancies.

Localization of three novel zinc finger genes to the centromeric region of human chromosome 10 by fluorescence in situ hybridization

An oligonucleotide probe for the consensus sequence of the linker region of zinc finger proteins was used to isolate cDNA clones from a human fetal heart cDNA library. Following DNA sequencing analysis and comparison, genes for the novel clones were mapped by fluorescence in situ hybridization. We report the chromosomal localization of three zinc finger-coding genes to the region of centromere on human chromosome 10p11.1q-11.2, indicating involvement in gene duplication and chromosome rearrangement during primate evolution.

Isolation by PCR of a cDNA clone from pea petals with similarity to petunia and wheat zinc finger proteins

The C2H2 TFIIIA/Krüppel class of zinc finger proteins are an important group of regulatory nucleic acid binding factors and have been extensively studied in humans, Drosophila and yeast. We have employed 3' RACE PCR, using a highly degenerate oligonucleotide primer, for the facile isolation of a C2H2 zinc finger protein cDNA (Pszf1) from pea petals. The Pszf1 cDNA open reading frame potentially encodes a protein with two widely separated zinc fingers similar to zinc finger proteins from petunia and wheat. This class of two-fingered zinc finger proteins, possessing a wide and variable linker sequence, appears to be unique to plants. Three regions outside the zinc finger domains are also conserved between the members of the plant zinc finger protein family and one of these regions is a candidate nuclear localisation signal. The Pszf1 amino acid sequence is most similar to that of the petunia Epf1 protein, they possess an interfinger linker sequence of approximately the same length and they have a similar expression pattern with maximal transcript accumulation in mature petals, suggesting that Pszf1 may be the pea homologue of the petunia Epf1 zinc finger gene.

Transcription of a new zinc finger gene, rKr1, is localized to subtypes of neurons in the adult rat CNS

Proteins which share zinc finger DNA binding motifs comprise one of the main families of transcription factors. We have previously described rKr1, a new rat Cys2/Hys2 zinc finger gene of the Krüppel gene family. This gene is predominantly expressed in the nervous system, with highest abundance in neurons and with lower abundance in developing oligodendrocytes of the CNS. Here, we have undertaken a detailed anatomical analysis of rKr1 expression in the adult brain of the rat using in situ hybridization. Our results show that rKr1 is expressed in a specific manner in defined subpopulations of neurons in many regions of the adult brain. Moderate levels of rKr1 mRNA were detectable in some structures of the telencephalon (e.g. cerebral cortex and hippocampus) and a few nuclei of the thalamus. The highest degree of labelling was seen in both upper and lower motor neurons of the mesencephalon and rhombencephalon (e.g. red nucleus, gigantocellular reticular nuclei, motor nuclei of the cranial nerves). High levels of rKr1 expression were also present in spinal motoneurons and dorsal root ganglion cells. In order to determine if rKr1 gene expression can be regulated, we have examined the expression pattern of rKr1 in the facial nucleus in response to facial nerve lesion. The expression of rKr1 in the facial nucleus showed a differential downregulation, reaching lowest levels 1 week after transection of the facial nerve. By 3 weeks after lesion, expression of rKr1 on the operated side of the brain reached normal levels and was identical to that of the unoperated side. These data suggest that rKr1 could be involved in the maintenance of the phenotypic differentiation of specific neuronal subtypes including motoneurons.

Isolation of cDNA clones for 42 different Krüppel-related zinc finger proteins expressed in the human monoblast cell line U-937

To study the complexity and structural characteristics of zinc finger proteins expressed during human hematopoiesis and to isolate novel regulators of blood cell development, a degenerate oligonucleotide probe specific for a consensus zinc finger peptide domain was used to isolate 63 cDNA clones for Krüppel-related zinc finger genes from the human monoblast cell line U-937. By extensive nucleotide sequence and Northern blot analysis, these cDNA clones were found to originate from approximately 42 different genes (HZF 1-42) of which only 8 have previously been described. Northern blot analysis showed that a majority of these genes were expressed at comparable levels in U-937 and HeLa cells. The large number of individual genes represented among the 63 clones and their apparent non-cell-type-specific expression suggest that the majority of the Krüppel-related zinc finger genes are likely to be expressed in most human tissues. In contrast, some of the genes displayed a restricted expression pattern, indicating that they represent potential regulators of monocyte differentiation or proliferation. Detailed structural analysis of the first 12 cDNAs (HZF 1-10) and a partial characterization of HZF 11-42 revealed that a common feature of human Krüppel-related zinc finger proteins is the presence of tandem arrays of zinc fingers ranging in number from 3 to over 20 that are preferentially located in the carboxy-terminal regions of the proteins. In addition, several novel KRAB-containing zinc finger genes and a novel conserved sequence element were identified.

A novel cDNA isolated from the mouse eye lens encoding a protein with zinc fingers and a KRAB domain

A cDNA clone, pMLZ-8, was isolated from a newborn mouse eye lens cDNA library using a consensus zinc finger oligonucleotide hybridization probe. The cDNA contains an open reading frame that conceptually encodes a 606 amino acid protein. The protein possesses a "KRAB" domain at its amino-terminus and has a carboxy-terminal region with fifteen consensus C2H2 zinc fingers. PCR analysis reveals the presence of pMLZ-8 mRNA in lens, liver, kidney, spleen, and brain of newborn mice.

Chromosomal localization of 9 KOX zinc finger genes: physical linkages suggest clustering of KOX genes on chromosomes 12, 16, and 19

Nine KOX zinc finger genes were localized on four human chromosomes by in situ hybridization of cDNA probes to metaphase chromosomes. KOX1 (ZNF10), KOX11 (ZNF18), and KOX12 (ZNF19) were mapped to chromosome bands 12q24.33, 17p13-p12, and 16q22-q23, respectively. Six other KOX genes were localized on chromosome 19: KOX6 (ZNF14) and KOX13 (ZNF20) to 19p13.3-p13.2, KOX5 (ZNF13) and KOX22 (ZNF27) to 19q13.2-qter, and KOX24 (ZNF28) and KOX28 (ZNF30) to 19q13.4. Pulsed field gel electrophoresis experiments showed that the pairs of KOX genes found on the chromosome bands 12q24.33, 16q22-q23, 19p13.3-p13.2, or 19q13.3-qter lie within 200-300 kb DNA fragments. This suggests the existence of KOX gene clusters on these chromosomal bands.

Human zinc finger gene ZNF23 (Kox16) maps to a zinc finger gene cluster on chromosome 16q22, and ZNF32 (Kox30) to chromosome region 10q23-q24

Two members of the KOX gene family, ZNF23 (KOX16) and ZNF32 (KOX30), have been mapped by in situ hybridization to chromosome regions 16q22 and 10q23-q24, respectively. The map location of ZNF23 and ZNF32 placed these zinc finger protein genes near to chromosome loci that, under certain in vitro conditions, are expressed as fragile sites (FRA16B, FRA16C) and (FRA10D, FRA10A, FRA10B and FRA10E). Human zinc finger gene ZNF32 maps to a chromosome region on 10q23-24 in which deletions have been observed associated with malignant lymphoma on 10q22-23 and with carcinoma of the prostate on 10q24. ZNF23 is located on 16q22 in a chromosomal region that has been involved in chromosome alterations characteristic of acute myeloid leukemia. A second Kox zinc finger gene (ZNF19/KOX12) was recently mapped to the same chromosome region on human chromosome 16q22. In the analogous murine position, the murine zinc finger genes Zfp-1 and Zfp-4 are found in the syntenic 16q region of mouse chromosome 8. Thus, ZNF19 and ZNF23 might be members of an evolutionarily conserved zinc finger gene cluster located on human chromosome 16q22.

A 1.5-megabase yeast artificial chromosome contig from human chromosome 10q11.2 connecting three genetic loci (RET, D10S94, and D10S102) closely linked to the MEN2A locus

The genetic loci RET, D10S94, and D10S102 from human chromosome 10q11.2 are very closely linked to a locus responsible for the multiple endocrine neoplasia type 2 (MEN2A and MEN2B) and medullary thyroid carcinoma (MTC1) familial cancer syndromes. We have constructed a 1.5-megabase contig consisting of six genomic yeast artificial chromosome clones which include these loci and define their physical order. A critical crossover event has been identified within the map interval; this event places the MEN2A locus centromeric to D10S102 and defines the orientation of the physical map on the chromosome. The orientation of the contig and order of the markers are centromere-RET-D10S94-D10S102-telomere. In addition, a microsatellite repeat polymorphism with a heterozygosity of 71% at the RET locus and a restriction fragment length polymorphism with a heterozygosity of 42% detected by a lambda clone from the D10S94 locus have been developed for high-resolution genetic linkage mapping and predictive diagnostic testing. These data place three important markers on a contiguous physical map, narrow the MEN2 disease locus interval, and provide a framework for further candidate gene identification efforts. Placement of these genetic loci along a clone-based map and continued expansion of the contig will also facilitate efforts to determine the relationship of physical to genetic distance near the centromeres of human chromosomes.