Complete coding sequence, exon/intron arrangement and chromosome location of ZNF45, a KRAB-domain-containing gene

Identification of novel Drosophila neural precursor genes using a differential embryonic head cDNA screen

During Drosophila neuroblast lineage development, temporally ordered transitions in neuroblast gene expression have been shown to accompany the changing repertoire of functionally diverse cells generated by neuroblasts. To broaden our understanding of the biological significance of these ordered transitions in neuroblast gene expression and the events that regulate them, additional genes have been sought that participate in the timing and execution of these temporally controlled events. To identify dynamically expressed neural precursor genes, we have performed a differential cDNA hybridization screen on a stage specific embryonic head cDNA library, followed by whole-mount embryo in situ hybridizations. Described here are the embryonic expression profiles of 57 developmentally regulated neural precursor genes. Information about 2389 additional genes identified in this screen, including 1614 uncharacterized genes, is available on-line at 'BrainGenes: a search for Drosophila neural precursor genes' (http://sdb.bio.purdue.edu/fly/brain/ahome.htm).

Genomic structure and regulation of a novel human gene, Klp1

Klp1 (K562 cells-derived leucine zipper-like protein 1) is a transcription factor which binds to the coproporphyrinogen oxidase promoter regulatory element (GGACTACAG). In order to clarify the function of Klp1, we determined the complete human Klp1 genomic structure and regulatory element in the promoter region. The gene spans about 2.4 kb and has three exons. Its promoter region has multiple GC boxes, E2F binding site, one cAMP response element (CRE), and no TATA box with multiple transcription initiation sites, which is characteristic of housekeeping and growth regulating genes. Promoter analysis showed that the promoter was more active in K562 cells entered into the cell cycle by serum stimulation than quiescent cells. Further promoter analysis revealed that CRE at -42 is essential for full promoter activity, and c-Jun and activation transcription factor 1/cAMP response element binding protein 1 proteins bind to this element. These structural characteristics and the promoter function suggest that Klp1 may play a role in cell cycle regulation.

Tandem zinc-finger gene families in mammals: insights and unanswered questions

Evidence for the remarkable conservation of mammalian genomes, in both content and organization of resident genes, is rapidly emerging from comparative mapping studies. The frequent occurrence of familial gene clustering, presumably reflecting a history of tandem in situ duplications starting from a single ancestral gene, is also apparent from these analyses. Genes encoding Kruppel-type zinc-finger (ZNF) proteins, including those containing Kruppel-associated box (KRAB) motifs, are particularly prone to such clustered organization. Existing data suggest that genes in KRAB-ZNF gene clusters have diverged in sequence and expression patterns, possibly yielding families of proteins with distinct, yet related, functions. Comparative mapping studies indicate that at least some of the genes within these clusters in mammals were elaborated prior to the divergence of mammalian orders and, subsequently, have been conserved. These data suggest a possible role for these tandem KRAB-ZNF gene families in mammalian evolution.

Comparative analysis of KRAB zinc finger proteins in rodents and man: evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes

Although the KRAB zinc finger proteins probably constitute the single largest class of transcription factors within the human genome, almost nothing is known about their biological function. To increase our knowledge about this interesting and relatively unexplored family of potent transcriptional repressors, we here present the cloning, structural analysis, and expression study of three novel mouse KRAB zinc finger proteins. In addition, we present an extensive comparative analysis of various members of this gene family based on the structure of the common KRAB A motif. At least three larger subfamilies of KRAB zinc finger proteins are identified: one carrying the classical KRAB A motif only, another holding both a classical KRAB A and a classical KRAB B motif, and a third holding a classical KRAB A and a highly divergent KRAB B domain, named b. A large variation both in size and in primary amino acid sequence was observed in the linker region between the KRAB domain and the C-terminally located zinc finger repeats. This variability indicates that this region is of minor importance for the biological function of KRAB-containing zinc finger proteins. The fact that in many zinc finger genes, the entire or almost the entire linker region is composed of degenerate finger motifs substantiates this conclusion. The absence of identifiable KRAB A and B motifs in the genome of yeast, Saccharomyces cerevisiae, indicates a relatively late appearance of the KRAB domain in evolution and may suggest that the biological functions are restricted to multicellular organisms. In addition, we show that the expression of individual members of one subfamily of KRAB zinc finger genes is restricted to specific hematopoietic cell lineages. This finding suggests that KRAB zinc finger proteins may play a role in lineage commitment, possibly silencing leakage transcription from nonlineage-expressed genes.

Zebrafish YAC, BAC, and PAC genomic libraries

Numerous positional cloning projects directed at isolating genes responsible for the myriads of observed developmental defects in the zebrafish are anticipated in the very near future. In this chapter, we have reviewed the YAC, BAC, and PAC large-insert genomic resources available to the zebrafish community. We have discussed how these resources are screened and used in a positional cloning scheme and have pointed out frequently formidable logistical considerations in the approach. Despite being extremely tedious, positional cloning projects in the zebrafish will be comparatively easier to accomplish than in human and mouse, because of unique biological advantages of the zebrafish system. Moreover, the ease and speed at which genes are identified and cloned should rapidly increase as more mapping reagents and information become available, thereby paving the way for meaningful biological studies.

Complex beta-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12

We investigated the organization, architecture, and evolution of the largest cluster ( approximately 4 Mb) of Krüppel-associated box zinc finger (KRAB-ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map ( approximately 700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150-180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal to ZNF208. Large blocks of ( approximately 25-kb) inverted beta-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the beta-satellite repeat as a probe indicates that beta-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (approximately 50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the beta satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time. [The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.]

Analysis of homologous XRCC1-linked zinc-finger gene families in human and mouse: evidence for orthologous genes

Genetic and physical mapping studies indicate that hundreds of zinc-finger (ZNF)-containing genes populate the human genome and that many of these genes are arranged in familial clusters. However, the extent to which these tandemly arrayed families are conserved among mammalian species is largely unknown. In a previous study, we identified a conserved cluster of Kruppel-associated box (KRAB)-containing ZNF genes located near the XRCC1 gene in human chromosome 19q13.2 and mouse chromosome 7 and analyzed two members of the murine gene family, Zfp93 and Zfp94, in detail. Here we report the identification and characterization of putative human orthologs of these murine genes. The human genes ZFP93 and ZNF45 are substantially similar to their murine counterparts in overall structure, but two notable differences exist between the sets of genes. First, the human genes encode more ZNF repeats than their murine counterparts. Second, the ZNF repeats that are common to orthologs exhibit varying degrees of conservation. Expression studies indicate that the human genes, like their mouse equivalents, are expressed widely and are coexpressed at similar levels in most adult tissues. These comparative gene sequence and expression studies therefore suggest that at least two members of the mammalian XRCC1-linked KRAB-ZNF gene family were elaborated prior to the divergence of primate and rodent lineages and were well conserved in human and mouse.