Positional cloning of a novel potassium channel gene: KVLQT1 mutations cause cardiac arrhythmias

Genetic factors contribute to the risk of sudden death from cardiac arrhythmias. Here, positional cloning methods establish KVLQT1 as the chromosome 11-linked LQT1 gene responsible for the most common inherited cardiac arrhythmia. KVLQT1 is strongly expressed in the heart and encodes a protein with structural features of a voltage-gated potassium channel. KVLQT1 mutations are present in affected members of 16 arrhythmia families, including one intragenic deletion and ten different missense mutations. These data define KVLQT1 as a novel cardiac potassium channel gene and show that mutations in this gene cause susceptibility to ventricular tachyarrhythmias and sudden death.

Increased exon-trapping efficiency through modifications to the pSPL3 splicing vector

Exon trapping allows for the rapid identification and cloning of coding regions from cloned eukaryotic DNA. In preliminary experiments, we observed two phenomena which limited the exon-trapping efficiency of pSPL3-based systems. The first factor that affected performance was revealed when we found that up to 50% of the putative trapped exons contained sequences derived from the intron of the pSPL3 trapping vector. Removal of the DNA sequences responsible for the cryptic splice event from the original splicing vector resulted in a new vector, pSPL3B. We demonstrate that pSPL3B virtually eliminates pSPL3-only spliced products while maximizing the proportion of exon traps containing genomic DNA (> 98%). The other step which impacted performance was our observation that a majority of the ampicillin-resistant (APR) clones produced after shotgun subcloning from ApR cosmids into pSPL3 were untrappable, pSPL3-deficient, recircularized cosmid vector fragments. Replacement of the pSPL3 ApR gene with the CmR cassette encoding chloramphenicol (Cm) acetyltransferase enabled selection for only pSPL3-containing CmR clones. We show a 30-40-fold increase in the initial subcloning efficiency of cosmid-derived fragments with pSPL3-CAM, when compared to pSPL3. The collective vector alterations described improve the overall exon-trapping efficiency of the pSPL3-based trapping system.

Analysis of the genomic sequence for the autosomal dominant polycystic kidney disease (PKD1) gene predicts the presence of a leucine-rich repeat. The American PKD1 Consortium (APKD1 Consortium)

The complete genomic sequence of the gene responsible for the predominant form of polycystic kidney disease, PKD1, was determined to provide a framework for understanding the biology and evolution of the gene, and to aid in the development of molecular diagnostics. The DNA sequence of a 54 kb interval immediately upstream of the poly(A) addition signal sequence of the PKD1 transcript was determined, and then analyzed using computer methods. A leucine-rich repeat (LRR) motif was identified within the resulting predicted protein sequence of the PKD1 gene. By analogy with other LRR-containing proteins, this may explain some of the disease-related renal alterations such as mislocalization of membrane protein constituents and changes in the extracellular matrix organization. Finally, comparison of the genomic sequence and the published partial cDNA sequence showed several differences between the two sequences. The most significant difference detected predicts a novel carboxy-terminus for the PKD1 gene product.

Monocyte chemoattractant protein-1 gene is expressed in activated neutrophils and retinoic acid-induced human myeloid cell lines

We have used differential display polymerase chain reaction to identify genes that are upregulated after retinoic acid (RA) treatment of human myeloblastic HL-60 cells. Three of the cDNAs cloned hybridized to RA-inducible transcripts on Northern blots, one of which was shown to encode sequences for monocyte chemoattractant protein-1 (MCP-1), a recently described cytokine that is chemotactic for monocytes but not for neutrophils. Nuclear run-on analysis indicated that the upregulation of the MCP-1 gene occurs at the transcriptional level in HL-60 cells. MCP-1 transcript levels also increased after RA treatment of the NB4 acute promyelocytic cell line. MCP-1 transcripts were undetectable in freshly isolated neutrophils by Northern analysis or reverse transcription-polymerase chain reaction but were readily detectable in neutrophils after incubation in media at 37 degrees C for 20 hours, suggesting that an activation event can lead to MCP-1 expression in neutrophils. Immunocytochemistry confirmed the presence of MCP-1 protein in activated neutrophils. This is the first report that the MCP-1 gene is RA-responsive in myeloid cell lines and is expressed in neutrophils. MCP-1 expression by activated neutrophils may play an important role in attracting monocytes to the site of tissue damage or infection.

Inhibition of hematopoiesis by competitive binding of transcription factor PU.1

Transcription factors have been shown to play a role as "master switch" factors in the programming of hematopoietic cell commitment and differentiation. PU.1 is a hematopoietic-specific member of the Ets family of transcription factors. In human bone marrow CD34-enriched progenitor cells, PU.1 expression was upregulated during the early phases of granulocytic/monocytic differentiation, preceding expression of its target genes encoding CD11b and the macrophage-colony-stimulating factor receptor, whereas PU.1 was expressed at stable levels throughout erythroid differentiation. To study PU.1 function, we synthesized double-stranded phosphorothioate oligonucleotides containing a characterized PU.1 site and demonstrated their ability to specifically compete for PU.1 DNA binding. When added to CD34+ cells in vitro, wild-type PU.1-binding oligonucleotides significantly blocked hematopoietic colony formation, whereas mutated PU.1 oligonucleotides which no longer bind PU.1 had no specific inhibitory effect. These results demonstrate that PU.1 is developmentally upregulated during normal human myelopoiesis and that the function of PU.1 is critical for the development of in vitro hematopoiesis.

The human CD34 hematopoietic stem cell antigen promoter and a 3' enhancer direct hematopoietic expression in tissue culture

The human CD34 hematopoietic stem cell antigen is a highly glycosylated type 1 membrane protein of unknown function. CD34 is expressed on 1% to 4% of bone marrow cells, including pluripotent stem cells and committed progenitors of each hematopoietic lineage. CD34 has also been shown to be expressed on the small vessel endothelium of a variety of tissues and on a subset of bone marrow stromal cells. We have chosen to use the human CD34 gene as model to examine the transcription factors and cis-elements required for stem cell/progenitor cell-specific gene regulation. We show here that the CD34 gene is transcriptionally regulated in tissue culture cells. Using a luciferase reporter gene, we have isolated and characterized an active CD34 promoter. A CD34-luciferase construct, containing 4.5 kb of 5' flanking DNA from a CD34 genomic clone, was 30-fold more active in CD34+ tissue culture cells than in HeLa cells. Sequences from the 3' end of the CD34 gene were shown to have enhancing activity in CD34+ T-lymphoblastic RPMI-8402 cells and not in CD34- U937 cells or in nonhematopoietic HeLa cells. We also show that a cytidine-guanosine island in the 5' end of the CD34 gene is heavily methylated in two CD34- hematopoietic cell lines and demethylated in two CD34+ cell lines. Analysis of the CD34 promoter should result in the identification of stem cell/progenitor cell-specific transcription factors and should provide a means to direct the expression of heterologous genes in hematopoietic stem cells and progenitors.

Structure of the gene encoding CD34, a human hematopoietic stem cell antigen

CD34 is a cell surface antigen of unknown function expressed in humans in hematopoietic stem cells, vascular endothelium, and blasts from 30% of patients with acute myeloid and lymphocytic leukemia. To begin to investigate the cis-acting elements required for this tissue-specific expression, the human CD34 locus was isolated and its genomic structure and transcriptional start site were characterized. The human CD34 gene spans 26 kb and has 8 exons, a structure quite similar to that of the murine gene. The start site of CD34 transcription was determined to be 258 bp upstream of the translational start site using RNase protection. These experiments also indicated that the 5' untranslated region has extensive secondary structure. In addition, fluorescence in situ hybridization was used to map the CD34 locus to band 1q32.

Optimization of transient transfection into human myeloid cell lines using a luciferase reporter gene

Leukemic cell lines such as HL-60, U937, and KG-1 provide an excellent model for studying human myeloid differentiation. These cells can be induced to differentiate from their immature state to form cells resembling more morphologically and functionally mature monocytes, macrophages, and granulocytes. During differentiation, expression of gene products such as myeloperoxidase and the integrin cell surface antigen CD11b is decreased or increased, respectively. Thus, these cell lines constitute an excellent model system in which to study the regulation of such differentially expressed genes. However, these myeloid cell lines are refractory to transfection by calcium phosphate or diethylaminoethyl (DEAE) dextran. Here we have optimized the transient transfection of myeloid cell lines using electroporation and the firefly luciferase reporter gene driven by viral promoters. The luciferase assay is extremely sensitive; transcription that is not detectable by Northern blot or run-on assays can be measured with this system. The system can be used in combination with the inducing agent 12-o-tetradecanoylphorbol-13-acetate (TPA), thus allowing analysis of developmentally regulated genes in these cells. Preliminary results suggest that this system can be applied to study the promoter for the myeloid specific gene, CD11b.

Transcripts of individual Drosophila actin genes are differentially distributed during embryogenesis

The temporal and spatial patterns of accumulation of transcripts from individual actin genes during Drosophila embryogenesis have been determined by in situ hybridization. We describe the subcloning into transcription vectors of unique DNA fragments derived from the 3' transcribed, but nontranslated region of each actin gene. These fragments then served as templates for the synthesis in vitro of single-stranded, radio-active gene-specific RNA probes. Probe characterization and hybridization to developmental RNA blots are presented, demonstrated the independent developmental accumulation of actin transcripts from each gene. Each gene-specific probe has been hybridized in situ to the transcripts present in embryonic frozen sections. The results of these experiments have demonstrated that transcripts from each actin gene accumulate differentially in developing Drosophila tissues. The 5C and 42A actin genes are cytoplasmic actin genes, with transcripts distributed in all cells and tissues of the developing embryo. Therefore these genes presumably encode the cytoplasmic actins used for functions common to all cells. Transcripts from both cytoplasmic actin genes are evenly distributed in preblastoderm embryos, becoming localized to the periphery at blastoderm formation [5C: Burn et al.: Dev Biol 131:345-355, 1989]. Later in development, levels of these cytoplasmic transcripts vary in specific tissues. While the patterns of localization of 5C actin transcripts have been published [Burn et al.: Dev Biol 131:345-355, 1989], differential neurological localization is presented here; 42A transcripts are localized at higher concentrations in the midgut, the brain, nerve cord, and gonad. Both 87E and 57B transcripts accumulated in the developing larval body wall musculature, but at differing levels and in differing patterns. Transcripts of the 79B and the 88F actin genes were undetectable in embryos. The results of these experiments suggest dedicated contributions of individual actin genes to complex developmental processes.

Alternative 5C actin transcripts are localized in different patterns during Drosophila embryogenesis

The Drosophila actin gene located at cytogenetic position 5C forms at least 9 and perhaps as many as 15 different transcripts with the use of alternative transcriptional start points, differential splicing, and different regions of cleavage/polyadenylation. Each transcript contains one of two alternative 5' exons. We have subcloned unique recombinant DNA probes specific for each separate 5' exon and for three polyadenylation regions into vectors containing T3 and T7 promoters. Single stranded, tritium-labeled RNA probes were generated in vitro from these constructs. These probes have been hybridized in situ to RNA transcripts present in tissue sections from Drosophila embryos. The results of these experiments indicate that transcripts homologous to the two separate 5' exon-specific probes accumulate in strikingly different patterns during Drosophila development. Thus the incorporation of a particular 5' exon into a transcript is correlated with tissue-specific localization of that transcript. In contrast, probes for each of the three polyadenylation regions do not detect any tissue-specific localization of transcripts.

A library of trimethylguanosine-capped small RNAs in Physarum polycephalum

We have constructed a cDNA library for the trimethylguanosine-capped small RNAs (sRNAs) in the acellular slime mold Physarum polycephalum. Capped sRNAs were purified from total cellular RNA of vegetative microplasmodia by preparative immunoprecipitation with anti-trimethylguanosine antibody. The purified RNA was analyzed by polyacrylamide gel electrophoresis. Approx. eleven different capped sRNAs were observed with a size range of 70-204 nucleotides (nt). Based on their approximate sizes, the presence of trimethylguanosine cap, and the presence of a lupus type-Sm antigen, molecules U1-U7 (excluding U3) were identified. Further confirmation of the identity of molecule U1a was established by Northern hybridization, U4a by colony hybridization, and U6 and U7a by direct chemical sequence analysis. Purified capped sRNAs were tailed with oligo(A), and inserted into oligo(dT)-tailed plasmid pCDV1. The cDNAs were used to transform Escherichia coli strain HB101. Approx. 1.9 X 10(5) ampicillin-resistant (ApR) transformants were obtained per microgram of tailed sRNA. Dot-blot hybridization, using Physarum RNA precipitated with anti-cap antibody as a probe, indicated that approx. 94% of the ApR colonies contained recombinant DNAs. The library was screened by colony hybridization using heterologous sRNA probes. Clones hybridizing with heterologous sRNAs U1, U2, U4 and U7 were each represented in the library in approximately the same frequency as their relative abundance in the Physarum sRNA population they were derived from. The insert of one Physarum U4 clone was sequenced and was found to have 57.1% homology with nt 1-91 of the published sequence for rat U4 RNA. A 12-nt 'functional' subdomain of the rat U4 molecule was 83.3% conserved in Physarum U4.