The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins

Gene structure of rat BAF60b, a component of mammalian SW1/SNF complexes, and its physical linkage to the growth hormone gene and transcription factor SUG/proteasome p45 gene

In the +27.6 to +36.7 kb downstream region from the transcriptional start site of the rat growth hormone (GH) gene, a gene encoding BAF60b, a component of mammalian SWI/SNF complexes, was found to have the same transcriptional orientation as the GH gene. The 5' end of the BAF60b gene was heterogeneous and the longest gene was 9060 bp long with 13 exons. The largest of all exons was estimated to be 2774 bases. Deduced rat BAF60b protein was made of 531 amino acids and its amino acid sequence was 97% identical with the human counterpart. No TATA box was found up to the -100 bp region but five GC boxes corresponding to the Sp1 binding site were observed up to 640 bp upstream from the transcriptional start site. Sixty-three bases downstream from the BAF60b gene, the polyadenylation site of the gene encoding transcription factor SUG/proteasome p45, whose expression is constant in many tissues, was identified. The BAF60b gene was expressed as 3.0 kb poly(A)-rich RNA in seven tissues and one cell line from rat but its expression varied considerably according to the tissue.

Conservation of a master hematopoietic switch gene during vertebrate evolution: isolation and characterization of Ikaros from teleost and amphibian species

The generation of T, B and NK lymphocyte lineages from pluripotent hematopoietic stem cells is dependent upon the early expression of the Ikaros locus which by means of alternative splicing produces a variety of zinc finger DNA binding transcription factors. We assessed the general biological importance of Ikaros by studying its conservation and expression in teleost fish and amphibians. Portions of Ikaros cDNA from rainbow trout and Xenopus were amplified by reverse transcription-polymerase chain reaction (RT-PCR). They show roughly 75% conservation of the amino acid sequence with mammalian Ikaros. The trout fragment was then used to isolate full-length Ikaros clones from a trout thymocyte cDNA library. In mice and humans, Ikaros produces six alternatively spliced isoforms, but in trout two additional novel splice variants designated Ik-7 and Ik-8 were also found. Ik-7 is expressed in a similar fashion to Ik-1 and Ik-2, the predominant isoforms expressed in mammalian lymphocytes. In trout and zebrafish, as in mammals, Ikaros is a single-copy gene, but in Xenopus segregation analysis demonstrates that Ikaros has been duplicated, most likely a result of polyploidization. We then examined the expression of Ikaros in trout and Xenopus tumor T cell lines via Northern blot, RT-PCR, immunofluorescence and Western blot analysis. Overall, Ikaros is expressed in a lymphoid-specific fashion similar to that found in mice and humans. In addition Ikaros is expressed early in trout ontogeny, beginning roughly at days 3-4 in the yolk sac and at day 5-6 in the embryo proper. The conservation of Ikaros structure and expression confirms it as a master switch of hematopoiesis.

Characterisation of the human CD30 ligand gene structure

The gene for the human CD30 ligand was molecularly cloned, sequenced and characterised. The gene structure consisted of four exons and three intervening introns spaced over 17.1 kb of genomic DNA. The 5' flanking region of the CD30L gene was sequenced and analysis of the region revealed the presence of several regulatory regions including a poly-dT element directly upstream from the transcription start site and consensus sequences for AP4, IK2, MZF1, E47 and ELK/cETS1. The absence of a canionical TATA motif suggests CD30L gene expression is regulated by a TATA-less promoter.

Bipotential primitive-definitive hematopoietic progenitors in the vertebrate embryo

Two regions of the vertebrate embryo, the blood islands and the dorsal lateral plate (DLP), participate in early hematopoietic development. In Xenopus, primitive erythrocytes are derived solely from the ventral blood islands (VBI), while definitive hematopoietic cells such as lymphocytes are derived from both VBI and DLP. We have utilized a transplantation technique to demonstrate in vivo that all hematopoietic cells (embryonic, fetal, or adult) originate from ventral mesoderm. Reciprocal grafts between VBI and DLP demonstrated that both regions are bipotential with respect to primitive and definitive hematopoiesis. Commitment of the VBI to primitive erythropoiesis and restriction of the DLP to definitive hematopoiesis occurs during neurula stages. Thus, hematopoietic development involves the induction of the blood program on the ventral axis of the embryo followed by environmentally regulated specification to the primitive or definitive lineages.

A novel zinc finger protein, Finb, is a transcriptional activator and localized in nuclear bodies

cDNAs encoding a novel DNA binding protein, termed Finb (finger protein in nuclear bodies) were molecularly cloned. The Finb protein consists of 1656 amino acids, containing 15 C2H2-type zinc fingers and three proline-rich regions. Finb efficiently activates transcription from the promoters of the metallothionein and thymidine kinase genes. The finb mRNA is ubiquitously expressed in various cell lines and tissues. The protein product is localized in nuclear bodies, whereas the N-terminally truncated protein spreads throughout the nucleus and cytoplasm. Further characterization of Finb would unravel an important role of nuclear body-involved transcriptional regulation.

Avian Ikaros gene is expressed early in embryogenesis

Ikaros transcription factors dictate the key steps in lymphoid lineage determination. To reveal the evolutionary aspects of regulatory molecules involved in early lymphocyte development, we studied the cDNA of the avian Ikaros homolog. We demonstrate here that the Ikaros gene is highly conserved across avian and mammalian species. Importantly, the Ikaros mRNA is already expressed in early chicken embryos, from embryonic day 2 onwards, thus markedly before the traffic of the first precursor cells to the lymphoid primordia, thymus and the bursa of Fabricius. We suggest that the embryonic expression of the Ikaros transcripts represents an early onset of lymphoid differentiation.

The hardwiring of development: organization and function of genomic regulatory systems

The gene regulatory apparatus that directs development is encoded in the DNA, in the form of organized arrays of transcription factor target sites. Genes are regulated by interactions with multiple transcription factors and the target sites for the transcription factors required for the control of each gene constitute its cis-regulatory system. These systems are remarkably complex. Their hardwired internal organization enables them to behave as genomic information processing systems. Developmental gene regulatory networks consist of the cis-regulatory systems of all the relevant genes and the regulatory linkages amongst them. Though there is yet little explicit information, some general properties of genomic regulatory networks have become apparent. The key to understanding how genomic regulatory networks are organized, and how they work, lies in experimental analysis of cis-regulatory systems at all levels of the regulatory network.

The Pax-5 gene is alternatively spliced during B-cell development

The transcription factor Pax-5 is expressed during the early stages of B-cell differentiation and influences the expression of several B-cell-specific genes. In addition to the existing isoform (Pax-5, which we have named Pax-5a), we have isolated three new isoforms, Pax-5b, Pax-5d, and Pax-5e, from murine spleen and B-lymphoid cell lines using library screenings and polymerase chain reaction amplification. Isoforms Pax-5b and Pax-5e have spliced out their second exon, resulting in proteins with only a partial DNA-binding domain. Isoforms Pax-5d and Pax-5e have deleted the 3'-region, which encodes the transactivating domain, and replaced it with a novel sequence. The existence of alternative Pax-5 transcripts was confirmed using RNase protection assays. Furthermore, Pax-5a and Pax-5b proteins were detected using Western blot analysis. Pax-5a was detectable in pro-, pre-, and mature B-cell lines, but not in two plasmacytomas; Pax-5b was shown to be present at low levels in mature B-cell lines and, unexpectedly, in one plasma cell line, but not in pro-B-cell or T-cell lines. Mobility shift assays showed that in vitro translated Pax-5a and Pax-5d, but not Pax-5b or Pax-5e, could interact with a B-cell-specific activator protein-binding site on the blk promoter. Using this assay, we also showed that Pax-5d was present in nuclear extracts of some (but not all) B-lymphoid lines and interacts with the B-cell-specific activator protein-binding site. The pattern of differential expression of alternatively spliced Pax-5 isoforms suggests that they may be important regulators of transcription during B-cell maturation.

Human dipeptidyl-peptidase I. Gene characterization, localization, and expression

Dipeptidyl-peptidase I, a lysosomal cysteine proteinase, is important in intracellular degradation of proteins and appears to be a central coordinator for activation of many serine proteinases in immune/inflammatory cells. Little is known about the molecular genetics of the enzyme. In the present investigation the gene for dipeptidyl-peptidase I was cloned and characterized. The gene spans approximately 3.5 kilobases and consists of two exons and one intron. The genomic organization is distinct from the complex structures of the other members of the papain-type cysteine proteinase family. By fluorescence in situ hybridization, the gene was mapped to chromosomal region 11q14.1-q14.3. Analysis of the sequenced 5'-flanking region revealed no classical TATA or CCAAT box in the GC-rich region upstream of cap site. A number of possible regulatory elements that could account for tissue-specific expression were identified. Northern analyses demonstrated that the dipeptidyl-peptidase I message is expressed at high levels in lung, kidney, and placenta, at moderate to low levels in many organs, and at barely detectable levels in the brain, suggesting tissue-specific regulation. Among immune/inflammatory cells, the message is expressed at high levels in polymorphonuclear leukocytes and alveolar macrophages and their precursor cells. Treatment of lymphocytes with interleukin-2 resulted in a significant increase in dipeptidyl-peptidase I mRNA levels, suggesting that this gene is subjected to transcriptional regulation. The results provide initial insights into the molecular basis for the regulation of human dipeptidyl-peptidase I.

Expression of the RT6 mono(ADP-ribosyl)transferases is regulated by two promoter regions

The structure of the RT6 mono(ADP-ribosyl)transferase gene was studied. Analysis of cDNA clones revealed eight exons and suggested two independent transcriptional start sites. The existence of the downstream initiation site was confirmed by S1-nuclease protection and localized to position +29 of exon 2. The corresponding 5' flanking regions were found to contain typical promoter structures such as TATA- and CCAAT-boxes. Comparison with sequences deposited in the TRANSFAC database of transcription factor binding sites revealed few putative regulatory elements in the region associated with exon 1 (promoter 1). In contrast, several elements contained in the regulatory regions of other T cell-specific genes, such as ets, lyf-1 and ikaros were found in in promoter 2. Analysis of RT6-transcripts showed this region to be the most active promoter in spleen cells of adult rats. Finally, transient transfection assays with reporter gene constructs showed promoter 2 to mediate T-cell specific transcription.

Early B cell factor binds to a site critical for lambda5 core enhancer activity

The pre-B cell-specific expression of the lambda5 gene is regulated at the level of transcription. The 5' region of the lambda5 gene has been shown to contain an enhancer that activates heterologous promoters. Here, we show that this enhancer, B(lambda5), also acts as a lineage- and tissue-restricted enhancer on its own promoter. We define the enhancer core, b(lambda5), that carries around 50% of the total enhancer activity. We also demonstrate that the transcription factor early B cell factor (EBF) binds to a DNA motif in the lambda5 core enhancer which is crucial for enhancer activity, suggesting that lambda5 is a second target gene of EBF.

Zinc finger-mediated protein interactions modulate Ikaros activity, a molecular control of lymphocyte development

The Ikaros gene, an essential regulator of lymphocyte differentiation, encodes, by means of differential splicing, protein isoforms with a distinct number of Kruppel-type zinc fingers organized in two domains. Deletion of the N-terminal zinc finger domain responsible for the sequence-specific DNA binding of the Ikaros proteins results in an early and complete arrest in lymphocyte development in homozygous mutant mice. In sharp contrast, heterozygotes reliably develop T cell leukemias and lymphomas. Here we show that the C-terminal zinc finger domain present in all of the Ikaros wild-type and mutant isoforms is responsible for their stable interactions off DNA and plays a pivotal role in determining their overall activity. Mutations in the C-terminal zinc fingers which ablate Ikaros protein interactions have a dramatic effect on the ability of these proteins to bind DNA and activate transcription. Therefore, interactions between Ikaros isoforms with an intact DNA binding domain are essential for their function. In contrast, interactions between isoforms with and without a DNA binding domain result in Ikaros complexes that do not bind DNA and, as a consequence, cannot activate transcription. Dominant-negative Ikaros isoforms are generated in smaller amounts by the wild-type Ikaros gene but are also produced exclusively by the N-terminally deleted Ikaros locus. Given these data, we propose that interactions between Ikaros isoforms are essential for normal progression through the lymphoid pathways. Mutations in the Ikaros gene that prevent Ikaros protein interactions or which change the relative ratio of DNA to non-DNA binding isoforms have profound effects in both lymphoid specification and homeostasis.

Analysis of the megakaryocyte glycoprotein IX promoter identifies positive and negative regulatory domains and functional GATA and Ets sites

The glycoprotein (GP) Ib-V-IX multisubunit complex binds to von Willebrand factor and mediates the adhesion of platelets to the subendothelium of damaged blood vessels. Expression of the GPIX subunit is required for stability of the complex, and its absence in platelets is associated with the rare bleeding disorder Bernard-Soulier syndrome. Comparative analyses indicate that the four GPIb-V-IX subunits are members of the leucine-rich repeat family and suggest that GPIX resembles a possible primitive progenitor of this group. To characterize GPIX transcriptional regulation, a series of 5' deletion constructs was made linking the GPIX upstream flanking sequence to the luciferase marker gene, and promoter activity was measured in transiently transfected human erythroleukemia cells. This analysis identified two negative regulatory domains between -686 to -423 and -311 to -203 and two positive regulatory domains at -323 to -311 and -151 to -100 relative to the GPIX transcription start site. In addition, site-directed mutagenesis experiments and in vitro gel retardation assays identified Ets and GATA elements at -42 and -65, which positively regulate GPIX promoter activity and specifically bind nuclear factors derived from human erythroleukemia cells. DNase I protection experiments identified a protein-dependent "footprint" and hypersensitive site within the GPIX Ets sequence. These results provide a framework for comparison of the GPIX promoter with others of the GPIb-V-IX system, other megakaryocyte-specific genes, and other members of the leucine-rich repeat family.

In vivo regulation of murine granzyme B gene transcription in activated primary T cells

A murine granzyme B promoter fragment that extends 243 base pairs upstream of the transcription start site confers high levels of luciferase reporter gene activity in transient transfection assays into T cells and mouse L cell fibroblasts. This promoter fragment contains canonical binding sites for the transcription factors AP-1, core binding factor (CBF), Ikaros, and the cyclic AMP responsive element binding protein (CREB). Oligonucleotides containing the granzyme B AP-1 or CBF elements form specific complexes with proteins present in nuclear extracts from activated CD8(+) splenocytes, MTL cells, EL4 T cells, and L cells. A strong DNase1 hypersensitive site that coincides with the closely associated AP-1, CBF, Ikaros, and CRE elements is present in activated CD8(+) T cells but not in resting T cells or L cells. Both in vitro and in vivo footprints are observed at these sequence elements in activated cytotoxic T cells (CTL) but not in resting T cells. The endogenous granzyme B gene is CTL-specific as no mRNA is detectable in EL4 or L cells. We propose that a condensed chromatin structure at the granzyme B promoter is responsible for transcription factor inaccessibility and repression of transcription in non-T cells.

Early T lymphocyte progenitors

The earliest steps along the pathway leading to T cells in mice and humans are reviewed. These are the steps between the multipotent hemopoietic stem cell (HSC) and the fully committed precursors undergoing T cell receptor (TCR) gene rearrangement. At this level significant differences between adult and fetal lymphopoiesis have been demonstrated. The extent of lymphoid commitment of precursors within bone marrow is still unresolved, although HSCs clearly undergo developmental changes before migration to the thymus. Both multipotent and T-restricted precursors have now been isolated from fetal blood, suggesting both may seed the thymus. Within the thymus, several minute but discrete populations of T precursors precede the stage of TCR gene rearrangement. They include precursors that are not exclusively T-lineage committed, although they are distinct from HSCs. These precursors have a potential to form NK cells, B cells, dendritic cells, and sometimes other myeloid cells. Some factors that control early lymphoid development are discussed, including IL-7 and the Ikaros transcription factors. These will eventually help to clarify the process of T-lineage commitment.

A dominant mutation in the Ikaros gene leads to rapid development of leukemia and lymphoma

The Ikaros gene is essential for lymphoid lineage specification. As previously reported, mice homozygous for a mutation in the Ikaros DNA-binding domain fail to generate mature lymphocytes as well as their earliest described progenitors. In addition, our studies with mice heterozygous for this mutation establish the Ikaros gene as an essential regulator of T cell proliferation. Thymocytes display augmented TCR-mediated proliferative responses, and peripheral T cells are autoproliferative. A general lymphoproliferation precedes the T cell leukemia and lymphoma that rapidly develop in all heterozygotes. The first step toward leukemic transformation occurs within the maturing thymocyte population and is demarcated by clonal expansions and loss of the single Ikaros wild-type allele. From these studies, we propose that within developing and mature T lymphocytes, distinct thresholds of Ikaros activity are required to regulate proliferation. A decrease in Ikaros activity below the first threshold causes the rapid accumulation of T lymphoblasts, whereas a further decrease leads to neoplastic transformation.

Cloning and expression analysis of a human cDNA homologous to Xenopus TFIIIA

We report here the nucleotide sequence of a clone, C2H2-34.10, isolated from a human brain cDNA library using degenerate oligodeoxyribonucleotide hybridization. C2H2-34.10 has extensive homology to the Xenopus laevis 5S DNA/RNA-binding protein, TFIIIA. The deduced amino acid (aa) sequence of the human clone gives a protein of 363 aa with identity to TFIIIA from both X. laevis (57%) and Rana pipiens (59%). This human clone contains nine C2H2-type zinc fingers like frog TFIIIA. Northern blot analysis indicates that the C2H2-34.10 RNA is expressed in human ovary, as well as human neuronal cell lines.