DNA sequence localization in metaphase and interphase cells by fluorescence in situ hybridization

Comparative fitness assessment of Anopheles stephensi transgenic lines receptive to site-specific integration

Genetically modified mosquitoes that are unable to transmit pathogens offer opportunities for controlling vector-borne diseases such as malaria and dengue. Site-specific gene recombination technologies are advantageous in the development of these insects because antipathogen effector genes can be inserted at integration sites in the genome that cause the least alteration in mosquito fitness. Here we describe Anopheles stephensi transgenic lines containing phi C31 attP'docking' sites linked to a fluorescent marker gene. Chromosomal insertion sites were determined and life-table parameters were assessed for transgenic mosquitoes of each line. No significant differences in fitness between the transgenic and nontransgenic mosquitoes were detected in this study. These transgenic lines are suitable for future site-specific integrations of antiparasite transgenes into the attP sites.

Mutations in a gene encoding a midbody kelch protein in familial and sporadic classical Hodgkin lymphoma lead to binucleated cells

Classical Hodgkin lymphoma (cHL) is a malignancy of B-cell origin in which the neoplastic cells, known as "Reed-Sternberg" (RS) cells, are characteristically binucleated. Here we describe a family where multiple individuals developing cHL have inherited a reciprocal translocation between chromosomes 2 and 3. The translocation disrupts KLHDC8B, an uncharacterized gene from a region (3p21.31) previously implicated in lymphoma and related malignancies, resulting in its loss of expression. We tested KLHDC8B as a candidate gene for cHL and found that a 5'-UTR polymorphism responsible for decreasing its translational expression is associated with cHL in probands from other families with cHL and segregates with disease in those pedigrees. In one of three informative sporadic cases of cHL, we detected loss of heterozygosity (LOH) for KLHDC8B in RS cells, but not reactive T lymphocytes, purified from a malignant lymph node. KLHDC8B encodes a protein predicted to contain seven kelch repeat domains. KLHDC8B is expressed during mitosis, where it localizes to the midbody structure connecting cells about to separate during cytokinesis, and it is degraded after cell division. Depletion of KLHDC8B through RNA interference leads to an increase in binucleated cells, implicating its reduced expression in the formation of cHL's signature RS cell.

A palindrome-driven complex rearrangement of 22q11.2 and 8q24.1 elucidated using novel technologies

Constitutional translocations at the same 22q11.21 low copy repeat B (LCR-B) breakpoint involved in the recurrent t(11;22) are relatively abundant. A novel 46,XY,t(8;22)(q24.13;q11.21) rearrangement was investigated to determine whether the recurrent LCR-B breakpoint is involved. Investigations demonstrated an inversion of the 3Mb region typically deleted in patients with the 22q11.2 deletion syndrome. The 22q11.21 inversion appears to be mediated by low copy repeats, and is presumed to have taken place prior to translocation with 8q24.13. Despite predictions based on inversions observed in other chromosomes harboring low copy repeats, this 22q11.2 inversion has not been observed previously. The current studies utilize novel laser microdissection and MLPA (multiplex ligation-dependent probe amplification) approaches, as adjuncts to FISH, to map the breakpoints of the complex rearrangements of 22q11.21 and 8q24.21. The t(8;22) occurs between the recurrent site on 22q11.21 and an AT-rich site at 8q24.13, making it the fifth different chromosomal locus characterized at the nucleotide level engaged in a translocation with the unstable recurrent breakpoint at 22q11.21. Like the others, this breakpoint occurs at the center of a palindromic sequence. This sequence appears capable of forming a perfect 145 bp stem-loop. Remarkably, this site appears to have been involved in a previously reported t(3;8) occurring between 8q24.13 and FRA3B on 3p14.2. Further, the fragile site-like nature of all of the breakpoint sites involved in translocations with the recurrent site on 22q11.21, suggests a mechanism based on delay of DNA replication in the initiation of these chromosomal rearrangements.

Depletion of the Ras association domain family 1, isoform A-associated novel microtubule-associated protein, C19ORF5/MAP1S, causes mitotic abnormalities

Ras association domain family 1, isoform A (RASSF1A) is a novel tumor suppressor gene that is found to be inactivated in more than 40 types of sporadic cancers. In addition, mouse Rassf1a knockout models have an increased frequency of spontaneous and induced tumors. The mechanisms by which RASSF1A exerts its tumor suppression activities or the pathways it can regulate are not yet fully understood. Using yeast two-hybrid system, we have previously identified C19ORF5/MAP1S as the major RASSF1A-interacting protein. C19ORF5 has two conserved microtubule-associated regions and may function to anchor RASSF1A to the centrosomes. In this study, we have analyzed the cellular functions of C19ORF5. By using small interfering RNA-mediated depletion and time-lapse video microscopy, we show that C19ORF5 knockdown causes mitotic abnormalities that consist of failure to form a stable metaphase plate, premature sister chromatid separation, lagging chromosomes, and multipolar spindles. We also show that a fraction of C19ORF5 localizes to the spindle microtubules. Additionally, we show here that C19ORF5 localizes to the microtubule-organizing centers during microtubule regrowth after nocodazole washout. Knockdown of C19ORF5 disrupts the microtubule-organizing center and results in microtubule nucleation from several sites. Whereas the localization of pericentrin is not affected, alpha- and gamma-tubulin localization and sites of nucleation are greatly altered by C19ORF5 depletion. This may indicate that C19ORF5 plays a role in anchoring the microtubule-organizing center to the centrosomes. In addition, we show that the NH2 terminus of C19ORF5 is essential for this process. This novel role for C19ORF5 could explain the resulting mitotic abnormalities that occur on its depletion and can potentially provide an underlying mechanism for the frequent centrosome and microtubule abnormalities detected in several cancers.

Cytogenetic mapping of immunity-related genes in the domestic horse

Chromosomal locations of 19 horse immunity-related loci (CASP1, CD14, EIF5A, FCER1A, IFNG, IL12A, IL12B, IL12RB2, IL1A, IL23A, IL4, IL6, MMP7, MS4A2, MYD88, NOS2A, PTGS2, TFRC and TLR2) were determined by fluorescence in situ hybridization. For IFNG and PTGS2, this study is a confirmation of their previously reported position. In addition, microsatellite (HMBr1) was localized in the same region as IFNG. All genes were assigned to regions of conserved synteny and the data obtained in this study enhance the comparative human-horse map. Cytogenetic localization of IL6 to ECA4q14-q21.1 suggested a new breakage point that changes the order of loci compared with HSA7. The map assignments of these loci serve as anchors for other loci and will aid in the search for candidate genes associated with traits in the horse.

New approaches to fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a nonisotopic labeling and detection method that provides a direct way to determine the relative location or copy number of specific DNA sequences in nuclei or chromosomes. With recent advancements, this technique has found increased application in a number of research areas, including cytogenetics, prenatal diagnosis, cancer research and diagnosis, nuclear organization, gene loss and/or amplification, and gene mapping. The availability of different types of probe and the increasing number of FISH techniques has made it a widespread and diversely applied technology. Multicolor karyotyping by multicolor FISH and spectral karyotyping interphase FISH and comparative genomic hybridization allow genetic analysis of previously intractable targets. We present a brief overview of FISH technology and describe in detail methods of probe labeling and detection for different types of tissue sample, including microdissected nuclei from formalin-fixed paraffin-embedded tissue sections.

Comparative and genetic analysis of the porcine glucocerebrosidase (GBA) gene

The genomic sequence of the porcine (Sus scrofa) glucocerebrosidase (GBA) gene (approximately 5.7 kb), encoding glucocerebrosidase (glucosylceramidase; acid beta-glucosidase; EC 3.2.1.45), was determined and compared with human (Homo sapiens) GBA and GBAP (pseudogene). The porcine gene harbours 11 exons and 10 introns, and the genomic organization is identical with human GBA. The exon sequences, coding for signal peptide and mature protein, show 81% and 90% sequence identity, respectively, with the corresponding human GBA sequences. Short interspersed elements, SINEs (PREs), are present in introns 2, 4 and 7. There is no evidence of a pseudogene in pig. The deduced protein sequence of GBA consists of 39 amino acids of signal peptide (long form) and 497 amino acids of the mature protein; the latter shows 90% sequence identity with the human protein. Four polymorphisms were observed within the porcine gene: insertion/deletion of one of the two SINEs (PREs) in intron 2 (locus PREA); deletion of a 37- to 39-bp stretch in intron 4 (one direct repeat and 5' end of PRE); deletion of a 47-bp stretch in the middle part of PRE in intron 4 (locus PREB); and single-base transition (C-T) in intron 6 (locus HaeIII-RFLP). GBA was assigned to chromosome 4q21 by FISH and was localized to the same region by linkage analysis and RH mapping, i.e., to the chromosome 4 segment where quantitative trait loci for growth and some carcass traits are located.

A complex rearrangement of chromosome 7 in human astrocytoma

Chromosome 7 is a frequent site of cytogenetic aberrations in human astrocytomas. One region that is often targeted in human astrocytomas is on 7p. The U251 human glioblastoma cell line has a region of gain of genetic material on 7p similar to that seen in human astrocytomas. We used several cytogenetic techniques to study chromosome 7 in U251 cells and identified a complex rearrangement that accounts for gain of chromosome 7 genetic material in the cell line. The characteristic rearrangement suggests a mechanism leading to 7p gain in primary grade IV astrocytomas.

Molecular analysis of region t(5;6)(q21;q21) in Wilms tumor

We have previously described the physical localization of a constitutional t(5;6)(q21;q21) in a patient (tumor cell sample designated as MA214) with bilateral Wilms tumor (WT). We have now physically refined the breakpoints and identified putative gene targets within this region. The translocation breakpoints are contained within a 2.5-Mbp region on 5q21 containing four candidate genes and a 1.3-Mbp region on 6q21 that contains three candidate genes. To explore the role of this region in WT genesis, we have performed loss of heterozygosity (LOH) analysis with markers flanking the translocation breakpoints in tumor from MA214 and a panel of sporadic WT. Alleles were retained for all informative markers used in the MA214 tumor. In sporadic tumors LOH was found in 6 of 63 (9.5%) and 5 of 62 (8%) informative cases for flanking markers D6S301 and D6S1592 on 6q21. LOH was found in 3 of 58 (5.2%) and 2 of 54 (3.6%) for flanking markers D5S495 and D5S409 on 5q21. These preliminary data suggest LOH at the t(5;6)(q21;q21) region is unlikely to be a mechanism for tumor development in MA214, but may be important for a subgroup of sporadic WT.

Characterization of the NRAMP1 (SLC11A1) gene in the horse (Equus caballus L.)

The complete coding cDNA sequence of the horse NRAMP1 (SLC11A1) gene was determined (GenBank accession number AF354445). The nucleotide sequence of the horse NRAMP1 gene is similar to sequences of this gene in other species. The gene contains 15 exons whose total length of 1,635 bp corresponds to 544 amino acids constituting the resulting putative protein. Hydrophobicity profile analysis of the deduced horse NRAMP1 gene product showed a nearly identical structure with the mouse NRAMP1 protein. The gene was found to be located on the short arm of ECA 6p12-13 by fluorescence in situ hybridization (FISH) analysis. Five allelic variants of the 5' untranslated region (UTR) were identified at the nucleotide sequence level. PCR-RFLP polymorphisms for NlaIII, TaqI, MspI and AciI were detected. Four out of five alleles could be detected using TaqI and MspI restriction enzymes. Their haplotype frequencies were different in four genetically distinct horse breeds.

Assignment of porcine cyclin-dependent kinase 4 (CDK4) and oncogene c-mos (MOS) by nonradioactive nonfluorescence in situ hybridization

Two pig genes, cyclin-dependent kinase 4 (CDK4) and the oncogene c-mos (MOS) were mapped by means of nonradioactive nonfluorescence in situ hybridization. Our approach was based on the detection of hybridized biotinylated probe by peroxidase conjugated extravidin and the reaction of peroxidase with its substrate diaminobenzidine (DAB) resulting in a dark precipitate. To increase the sensitivity of the method in single-copy gene mapping, two amplifications of the peroxidase signal were used: immunological amplification by biotinylated antiavidin, and peroxidase-catalysed deposition of biotinylated tyramide. Using this method, two 2-kb-long probes for the porcine genes CDK4 and MOS were mapped to pig chromosomes 5p12 and 4q14-15, respectively. Non-radioactive nonfluorescence in situ hybridization described here is a method of choice for gene mapping of short probes.

Hypothesis: a novel route for immortalization of epithelial cells by Epstein-Barr virus

Transfection of primate tissue explants with a specific sub-fragment (p31) of EBV DNA results in epithelial (but no other) cells proliferating indefinitely (becoming 'immortalized') without evidence of a 'growth crisis'. Molecular evidence supports integration of viral information into the host chromosome, and an early genotypic alteration involving specific amplification of a sub-component (IR1) of p31 DNA, followed by apparent loss of viral DNA from chromosomes, consistent with a 'hit and run' mechanism. However, analysis at the individual cell level during long-term culture, by FISH techniques, reveals chromosomal alterations, and viral sequences surviving within double minute (DM) bodies. Changing growth patterns occurring at different stages during propagation (>a year in culture) may be explained by sporadic reintegration of surviving viral DNA into the host chromosome. Notably, throughout culture, telomere lengths in chromosomal DNAs do not alter but rather retain the length observed in the primary cell populations. Introduction of a growth stimulating function of EBV, BARF1, into the immortalized, non-clonable epithelial cells under conditions which permit overexpression, allows clonal populations to be derived. Based on the data, mechanisms of immortalization, in the absence of a proven viral oncogene in p31 DNA, and possible genes involved, are considered.

Sex determination in cattle based on simultaneous amplification of a new male-specific DNA sequence and an autosomal locus using the same primers

A PCR-based method for sex determination of bovine DNA samples and embryo biopsies is presented. Using only one primer pair both the male-specific sequence FBNY (127 bp) and a sex-independent control PCR-fragment, the microsatellite marker FBN17 (136-140 bp) are generated in the same PCR reaction. Synteny mapping assigned the male-specific sequence to bovine chromosome Y (BTA Y), whereas FBN17 was mapped to bovine chromosome 2. Localisation of FBNY on BTA Y was confirmed by fluorescence in hybridisation of two BAC clones containing the male-specific sequence. There was no amplification of the male-specific target sequence FBNY in sheep, pig, goat, mice, man, and several wild species of the tribe Bovini. The bovine male-specific fragment was detected in dilutions containing as little as 10 pg genomic DNA and in blastomeres from embryo biopsies. The PCR assay presented here does require neither restriction endonuclease digestion of the PCR product nor additional nested PCR steps. Owing to the advantage of parallel amplification of the autosomal locus FBN17 no additional control fragment is necessary to detect PCR failure. The results of sex determination in embryo biopsies using FBNY were in agreement with the outcome from a reference assay used in commercial breeding programs.

Chromosomal alterations in squamous cell carcinomas of the head and neck: window to the biology of disease

BACKGROUND

Cytogenetic alterations underlie the development of squamous cell carcinomas of the head and neck (SCCHN). Because many of the molecular genetic changes in SCCHN result from chromosomal alterations, a complete perspective on the genetic changes in tumors requires a basic introduction to cytogenetics. This review presents a brief description of the latest cytogenetic techniques and a description of chromosomal alterations in SCCHN, their molecular correlates, and clinical implications.

RESULTS

The most frequent cytogenetic alterations in SCCHN are gains of 3q, 8q, 9q, 20q, 7p, 11q13, and 5p and losses of 3p, 9p, 21q, 5q, 13q, 18q, and 8p. The karyotypes often provide an explanation for the mechanism by which the molecular genetic alterations arose. For example, the coordinate gains and losses involving whole arms of chromosomes 3, 5, 7, 8, and 9 often result from isochromosome formation. In addition, apparent allelic imbalances may not represent loss of heterozygosity but gene amplification. These results suggest that cytogenetic analysis is valuable for placing the molecular genetic findings in perspective at the cellular level.

CONCLUSIONS

Cytogenetic endpoints may be useful tools for dissecting clinical differences in tumor behavior and response to therapy. Numerous studies are underway to examine the biology of and genetic alterations in SCCHN that will lead to additional markers for use as rapid, noninvasive screening methods for individuals at high risk for primary or recurrent SCCHN. Our goal is to minimize morbidity and mortality from SCCHN by identifying useful predictors of disease and recurrence risk and response to therapy to implement earlier detection and more effective prevention and/or treatment strategies.

Comparative structure, proximal promoter elements, and chromosome location of the human eosinophil major basic protein genes

Human eosinophil major basic protein (MBP) is strongly implicated as a mediator of disease, especially bronchial asthma. We recently isolated a highly divergent human homologue of MBP (MBPH). Given human MBP's importance in disease and the restricted expression of it and human MBPH, we isolated the 4.6-kb human MBPH gene (HGMW-approved symbol PRG3). Comparisons among the human MBP (PRG2), human MBPH, and murine MBP-1 (mMBP-1; Prg2) genes suggest that the human MBP and mMBP-1 genes are more closely related than either is to the human MBPH gene. Proximal promoters of these three genes show conservation of potential binding sites for IK2 and STAT and of a known GATA site. However, a known C/EBP site is altered in the human MBPH gene's proximal promoter. The human MBP and MBPH genes localized to chromosome 11 in the centromere to 11q12 region. Thus, the human MBP and MBPH genes have diverged considerably, probably following a gene duplication event. Furthermore, the identified conserved and distinct proximal promoter elements likely contribute to the eosinophil-restricted and relatively reduced transcription of the human MBPH gene.

Europium cryptate-tethered ribonucleotide for the labeling of RNA and its detection by time-resolved amplification of cryptate emission

TRACE (time-resolved amplification of cryptate emission), also called HTRF for pharmaceutical applications, is a homogeneous time-resolved fluorescence technique well adapted for the study of molecular interactions. It is based on fluorescence resonance energy transfer (FRET) between europium trisbipyridine cryptate (TBPEu(3+)) as energy donor and cross-linked allophycocyanin, symbolized by XL665, as acceptor, leading to a long-lived FRET signal. TBPEu(3+)-labeled uridine triphosphate (UTP), referred to as K-11-UTP in the text, was obtained by coupling TBPEu(3+) moiety to a C-5 functionalized UTP analog. K-11-UTP can be directly incorporated in RNA strands during enzymatic synthesis. This was demonstrated in an in vitro transcription reaction promoted by T(7) RNA polymerase. The reaction was performed in the presence of K-11-UTP and biotin-labeled cytidine triphosphate (biotin-16-CTP) in admixture with natural ribonucleotides. After the addition of streptavidin-XL665 conjugate (SA-XL665), which binds on biotinylated cytidine residues, a long-lived FRET signal was obtained. This proved that both europium cryptate and biotin were incorporated into the same RNA strand and are close enough to generate a FRET signal. The study of this FRET detection assay format showed that such doubly labeled RNA can be easily detected even when a very low percentage of K-11-UTP is used (less than 1% of total UTP concentration). Europium-cryptate-labeled RNA can also be monitored using a homogeneous hybridization assay format involving a biotinylated probe. After the addition of SA-XL665, the FRET signal generated demonstrates the formation of RNA:DNA hybrids. Europium-cryptate-labeled nucleotide thus gives access to a new type of RNA nonisotopic labeling and homogeneous detection assays.

Synteny and regional marker order assignment of 26 type I and microsatellite markers to the horse X- and Y-chromosomes

The hypothesis that the conservation of sex-chromosome-linked genes among placental mammals could be extended to the horse genome was tested using the UCDavis horse-mouse somatic cell hybrid (SCH) panel. By exploiting the fluorescence in-situ hybridization (FISH) technique to localize an anchor locus, X-inactivation-specific transcript (XIST) on the horse X chromosome, together with the fragmentation and translocation of the X- and Y-chromosome fragments in a somatic cell hybrid panel, we regionally assigned 13 type I and 13 type II (microsatellite) markers to the horse X- and Y-chromosomes. The synteny groups that correspond to horse X- and Y-chromosomes were identified by synteny mapping of sex-specific loci zinc finger protein X-linked (ZFX), zinc finger protein Y-linked (ZFY) and sex-determining region Y (SRY) on the SCH panel. A non-pseudoautosomal gene in the human steroid sulfatase (STS) was identified in both X- and Y-chromosome-containing clones. The regional order of the X-linked type I markers examined in this study, from Xp- to Xq-distal, was [STS-X, the voltage-gated chloride channel 4 (CLCN4)], [ZFX, delta-aminolevulinate synthase 2 (ALAS2)], XIST, coagulation factor IX (F9) and [biglycan (BGN), equine F18, glucose-6-phosphate dehydrogenase (G6PD)] (precise marker order could not be determined for genes within the same brackets). The order of the Y-linked type I markers was STS-Y, SRY and ZFY These orders are the same arrangements as reported for the human X- and Y-chromosomes, supporting the conservation of genomic organization between the human and the horse sex chromosomes. Regional ordering of X-linked type I and microsatellite markers provides the first integration of type I and type II markers in the horse X chromosome.

YAC transgene-mediated olfactory receptor gene choice

In the mouse, individual olfactory neurons express one of a thousand distinct olfactory receptor genes. Furthermore, only one allele of the expressed gene is transcribed. This phenomenon, random allelic inactivation, along with the observation that the olfactory receptor genes reside in large chromosomal arrays, suggests a role for long-range gene regulation in olfactory receptor gene choice. We have constructed a 300-kb yeast artificial chromosome (YAC) transgene in which a single receptor gene is marked while maintaining its coding region. This 300-kb piece of DNA functions as an independent olfactory receptor gene locus in directing olfactory receptor gene choice in both the olfactory system and the accessory olfactory system (vomeronasal organ, VNO). Furthermore, the transgene, like endogenous olfactory receptor loci, is subject to allelic inactivation.

Imaging of single DNA molecule: applications to high-resolution genomic studies

Single molecule analysis of DNA has revealed new insights into its structural and physical properties. The application of new methods for manipulating and visualizing DNA has resulted in important advances in high-resolution physical mapping of the genome and quantitative cytogenetic studies of genomic abnormalities (Lichter 1997). Studies of single molecules of DNA have employed a variety of approaches including electron microscopy, atomic force microscopy, scanning-tunneling microscopy and fluorescence microscopy. A number of new technologies have recently been developed to exploit fluorescence microscopy's full potential for genomic analysis and the fine mapping of subtle genetic alterations. In the case of the latter application, particular emphasis has been placed on developing new methods for stretching DNA for high-resolution fluorescence in-situ hybridization studies. We have recently described a process called molecular combing according to which single DNA molecules bound by their extremities to a solid surface are uniformly stretched and aligned by a receding air/water interface (Bensimon et al. 1994). In the following, we will review recent developments concerning molecular combing and discuss its current and potential applications for the high-resolution mapping of the human genome, the detection and quantification of subtle genomic imbalances and the positional cloning of disease-related genes.

Genomic structure and functional characterization of NBPhox (PMX2B), a homeodomain protein specific to catecholaminergic cells that is involved in second messenger-mediated transcriptional activation

Homeodomain proteins play essential roles in basic processes during embryogenesis and development. NBPhox, a vertebrate paired-like homeodomain protein specific to catecholaminergic cells, may have a fundamental role in determining and maintaining the catecholaminergic phenotype. Here we describe the human and mouse genomic structures and the functional characterization of NBPhox. The genomic structure of NBPhox is highly conserved at the nucleotide level between human and mouse and is also quite similar to that of other paired-like homeodomain proteins, Arix/Phox2a, CRX, OTX1, and OTX2. The human NBPhox gene (HGMW-approved symbol PMX2B) maps to chromosomal region 5p12-p13. When the NBPhox expression plasmid was introduced into PC12h cells, the transcription from the promoter of the dopamine beta-hydroxylase (DBH) gene was slightly stimulated. However, NBPhox substantially enhances second messenger-mediated activation of the DBH promoter by forskolin and/or phorbol ester. Furthermore, we found that NBPhox can also enhance second messenger-mediated activation of the c-fos promoter and several enhancers, including cyclic AMP-response element, the binding site for activator protein 1, and serum-response element. Our findings provide strong evidence that a homeodomain protein is involved in the activation of several genetic regulatory elements responsive to second messenger-mediated signals. These data suggest that this family of proteins may be involved in determining and maintaining a cell-specific phenotype through regulation of certain genes responsive to second messenger-mediated signals.

Structure and chromosomal localization of the human and murine genes for the macrophage MARCO receptor

The structures of the human and mouse genes for the macrophage receptor with collagenous structure were determined. Both genes have 17 exons, of which exons 4-15 encode the collagenous domain. The transcription initiation sites in the mouse gene were identified using primer extension, SI nuclease mapping, and 5' capturing rapid amplification of cDNA ends assays. All three methods revealed two major initiation sites, one starting 27 bp downstream of a TATA box and another at positions -63 and -66 downstream of an AT-rich region. Several potential binding sites for transcription factors were identified in the promoter region, neither gene has a CAAT box or GC boxes. The human and mouse genes were localized to syntenic regions on chromosomes 2 and 1, respectively, using fluorescence in situ hybridization.

Metabolic instability of plasmid DNA in the cytosol: a potential barrier to gene transfer

Inefficient nuclear delivery of plasmid DNA is thought to be one of the daunting hurdles to gene transfer, utilizing a nonviral delivery system such as polycation-DNA complex. Following its internalization by endocytosis, plasmid DNA has to be released into the cytosol before its nuclear entry can occur. However, the stability of plasmid DNA in the cytoplasm, that may play a determinant role in the transfection efficiency, is not known. The turnover of plasmid DNA, delivered by microinjection into the cytosol, was determined by fluorescence in situ hybridization (FISH) and quantitative single-cell fluorescence video-image analysis. Both single- and double-stranded circular plasmid DNA disappeared with an apparent half-life of 50-90 min from the cytoplasm of HeLa and COS cells, while the amount of co-injected dextran (MW 70,000) remained unaltered. We propose that cytosolic nuclease(s) are responsible for the rapid-degradation of plasmid DNA, since (1) elimination of plasmid DNA cannot be attributed to cell division or to the activity of apoptotic and lysosomal nucleases; (2) disposal of microinjected plasmid DNA was inhibited in cytosol-depleted cells or following the encapsulation of DNA in phospholipid vesicles; (3) generation and subsequent elimination of free 3'-OH ends could be detected by the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling assay (TUNEL), reflecting the fragmentation of the injected DNA; and finally (4) isolated cytosol, obtained by selective permeabilization of the plasma membrane, exhibits divalent cation-dependent, thermolabile nuclease activity, determined by Southern blotting and 32P-release from end-labeled DNA. Collectively, these findings suggest that the metabolic instability of plasmid DNA, caused by cytosolic nuclease, may constitute a previously unrecognized impediment for DNA translocation into the nucleus and a possible target to enhance the efficiency of gene delivery.

Stem Cell Factor as a Single Agent Induces Selective Proliferation of the Philadelphia Chromosome Positive Fraction of Chronic Myeloid Leukemia CD34+ Cells

The interaction between p145c-KIT and p210bcr-abl in transduced cell lines, and the selective outgrowth of normal progenitors during long-term culture of chronic myeloid leukemia (CML) cells on stroma deficient in stem-cell factor (SCF) suggests that the response of CML cells to SCF may be abnormal. We examined the proliferative effect of SCF(100 ng/mL), provided as the sole stimulus, on individual CD34+ cells from five normal donors and five chronic-phase CML patients. Forty-eight percent of isolated single CML CD34+ cells proliferated after 6 days of culture to a mean of 18 cells, whereas only 8% of normal CD34+ cells proliferated (mean number of cells generated was 4). SCF, as a single agent, supported the survival and expansion of colony-forming unit–granulocyte-macrophage (CFU-GM) from CML CD34+CD38+ cells and the more primitive CML CD34+CD38− cells. These CFU-GM colonies were all bcr-abl positive, showing the specificity of SCF stimulation for the leukemic cell population. Coculture of CML and normal CD34+ cells showed exclusive growth of Ph+cells, suggesting that growth in SCF alone is not dependent on secretion of cytokines by CML cells. SCF augmentation of β1-integrin–mediated adhesion of CML CD34+cells to fibronectin was not increased when compared with the effect on normal CD34+ cells, suggesting that the proliferative and adhesive responses resulting from SCF stimulation are uncoupled. The increased proliferation may contribute to the accumulation of leukemic progenitors, which is a feature of CML.

Stem Cell Factor as a Single Agent Induces Selective Proliferation of the Philadelphia Chromosome Positive Fraction of Chronic Myeloid Leukemia CD34+ Cells

The interaction between p145c-KIT and p210bcr-abl in transduced cell lines, and the selective outgrowth of normal progenitors during long-term culture of chronic myeloid leukemia (CML) cells on stroma deficient in stem-cell factor (SCF) suggests that the response of CML cells to SCF may be abnormal. We examined the proliferative effect of SCF(100 ng/mL), provided as the sole stimulus, on individual CD34+ cells from five normal donors and five chronic-phase CML patients. Forty-eight percent of isolated single CML CD34+ cells proliferated after 6 days of culture to a mean of 18 cells, whereas only 8% of normal CD34+ cells proliferated (mean number of cells generated was 4). SCF, as a single agent, supported the survival and expansion of colony-forming unit–granulocyte-macrophage (CFU-GM) from CML CD34+CD38+ cells and the more primitive CML CD34+CD38− cells. These CFU-GM colonies were all bcr-abl positive, showing the specificity of SCF stimulation for the leukemic cell population. Coculture of CML and normal CD34+ cells showed exclusive growth of Ph+cells, suggesting that growth in SCF alone is not dependent on secretion of cytokines by CML cells. SCF augmentation of β1-integrin–mediated adhesion of CML CD34+cells to fibronectin was not increased when compared with the effect on normal CD34+ cells, suggesting that the proliferative and adhesive responses resulting from SCF stimulation are uncoupled. The increased proliferation may contribute to the accumulation of leukemic progenitors, which is a feature of CML.

Promoter sequence, expression, and fine chromosomal mapping of the human gene (MLP) encoding the MARCKS-like protein: identification of neighboring and linked polymorphic loci for MLP and MACS and use in the evaluation of human neural tube defects

The MARCKS-like protein (MLP), also known as F52, MacMARCKS, or MARCKS-related protein, is a widely distributed substrate for protein kinase C (PKC). Recent studies using gene disruption in vivo have demonstrated the importance of both MARCKS and MLP to the development of the central nervous system; specifically, mice lacking either protein exhibit a high frequency of neural tube defects. We isolated a genomic clone for human MLP and discovered a directly linked polymorphism (MLP1) useful for genetic linkage analysis. The MLP promoter was 71% identical over 433 bp to that of the corresponding mouse gene, Mlp, with conservation of many putative transcription factor-binding sites; it was only 36% identical over 433 bp to the promoter of the human gene, MACS, which encodes the MLP homologue MARCKS. This 433-bp fragment drove expression of an MLP-beta-galactosidase transgene in a tissue-specific and developmental expression pattern that was similar to that observed for the endogenous gene, as shown by in situ hybridization histochemistry. In contrast to MACS, the MLP and Mlp promoters contain a TATA box approximately 40 bp 5' of the presumed transcription initiation site. MLP was localized to chromosome 1p34-->1pter by analysis of human-mouse somatic cell hybrid DNA and to 1p34 by fluorescence in situ hybridization. Radiation hybrid mapping of MLP placed it between genetic markers D1S511 (LOD > 3.0) and WI9232. MACS was localized to 6q21 between D6S266 (LOD > 3.0) and AFM268uh5 by the same technique. We tested the novel MLP1 polymorphism and the MACS flanking markers in a series of 43 Caucasian simplex families in which the affected child had a lumbosacral myelomeningocele. We found no evidence of linkage disequilibrium, suggesting that these loci were not major genes for spina bifida in these families. Nonetheless, the identification of linked and neighboring polymorphisms for MACS and MLP should permit similar genetic studies in other groups of patients with neural tube defects and other neurodevelopmental abnormalities.

Segregation of viral plasmids depends on tethering to chromosomes and is regulated by phosphorylation

Eukaryotic viruses can maintain latency in dividing cells as extrachromosomal nuclear plasmids. Segregation and nuclear retention of DNA is, therefore, a key issue in retaining copy number. The E2 enhancer protein of the papillomaviruses is required for viral DNA replication and transcription. Viral mutants that prevent phosphorylation of the bovine papillomavirus type 1 (BPV) E2 protein are transformation-defective, despite normal viral gene expression and replication function. Cell colonies harboring such mutants show sectoring of viral DNA and are unable to maintain the episome. We find that transforming viral DNA attaches to mitotic chromosomes, in contrast to the mutant genome encoding the E2 phosphorylation mutant. Second-site suppressor mutations were uncovered in both E1 and E2 genes that allow for transformation, maintenance, and chromosomal attachment. E2 protein was also found to colocalize to mitotic chromosomes, whereas the mutant did not, suggesting a direct role for E2 in viral attachment to chromosomes. Such viral hitch-hiking onto cellular chromosomes is likely to provide a general mechanism for maintaining nuclear plasmids.

A mutation in the aryl hydrocarbon receptor (AHR) in a cultured mammalian cell line identifies a novel region of AHR that affects DNA binding

Introduction of a retroviral expression vector for the aryl hydrocarbon receptor (AHR) restores CYP1A1 inducibility to a mutant derivative of the Hepa-1 cell line that is defective in induction of CYP1A1 by ligands for the receptor. An AHR protein with normal ligand binding activity is expressed in the mutant but ligand treatment of mutant cell extract fails to induce binding of the AHR. ARNT (aryl hydrocarbon receptor nuclear translocator) dimer to the xenobiotic responsive element (XRE). AHR cDNAs derived from the mutant encode a protein that is unimpaired in ligand-dependent dimerization with ARNT, but the AHR.ARNT dimer so formed is severely impaired in XRE binding activity. The mutant cDNAs contain a C to G mutation at base 648, causing a cysteine to tryptophan alteration at amino acid 216, located between the PER-ARNT-SIM homology region (PAS) A and PAS B repeats. Introduction of the same mutation in the wild-type AHR sequence by site-directed mutagenesis similarity impaired XRE binding activity. Substitution with the conservative amino acid, serine, had no effect on XRE binding. The tryptophan mutation, but not the wild-type allele, was detectable in genomic DNA of the mutant. The implication that an amino acid within the PAS region may be involved in DNA binding indicates that the DNA binding behavior of AHR may be more anomalous than previously suspected.

Molecular cloning, organization and localization of the gene for the mouse neuropeptide Y-Y5 receptor

A cDNA clone homologous with the human neuropeptide Y (NPY)-Y5 receptor has been isolated from a mouse brain cDNA library. Analysis of the predicted amino acid sequence indicates that the polypeptide encoded by this cDNA is 89% and 97% identical to the human and rat NPY-Y5 receptors, respectively, but has a repeat sequence of 21-amino acid residues, unlike the human and rat NPY-Y5 receptors, in its N-terminal region. Northern blot analysis indicated that the mouse NPY-Y5 receptor mRNA was highly expressed in the brain, but not in the heart, kidney, spleen, lung, liver, skeletal muscle, and testis. A genomic DNA clone encoding the mouse NPY-Y5 receptor has also been cloned and used as a probe for fluorescence in situ hybridization analysis. The mouse NPY-Y5 receptor gene consists of at least two exons with a 7.0 kbp-long intronic sequence and is localized in the chromosome 8B3-C2 region. Restriction mapping, partial sequencing, and hybridization analysis of the mouse NPY-Y5 and NPY-Y1 receptor genes were used to determine the relationship between the two genes in the chromosome 8B3-C2 region. The mouse NPY-Y5 receptor gene can map about 10 kbp upstream of the transcriptional initiation sites of the NPY-Y1 receptor gene with an opposite orientation.

Detection of minimal residual disease in an AML patient with trisomy 8 using interphase fish

Patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) often exhibit clonal chromosomal abnormalities. Using a probe for the centromeric region of chromosome 8, fluorescence in situ hybridization (FISH) on interphase cells was used to detect trisomy 8 in an AML patient whose leukemia was characterised by the karyotype 47, XY, +8, del(9) (q21.1q32). We have demonstrated using FISH the presence of the trisomy at all stages of the patient's disease course (including remission, peripheral blood cell harvest and relapse), whereas conventional karyoptypic analysis was only able to detect the trisomy at diagnosis and clinical relapse. We have also shown using immunophenotyping, cell sorting and FISH, that the trisomic cells in this patient were restricted to the CD34+ subset of blood and bone marrow and could not be found in the CD 34-, T or B cell compartment. Overall we have shown FISH to be a rapid, quantitative method for the detection of cells with numerical chromosome abnormalities. FISH analysis of interphase cells provides valuable information on the status of the whole population, rather than just cycling cells, and can be applied successfully to monitor the level of leukemic cells.

The human HNP36 gene is localized to chromosome 11q13 and produces alternative transcripts that are not mutated in multiple endocrine neoplasia, type 1 (MEN I) syndrome

Multiple endocrine neoplasia, type 1 (MEN I), is an autosomal dominant syndrome of selected endocrine neoplasms whose causative gene, a suspected tumor suppressor, has been localized to chromosome 11q13, but has not been identified. Recently, the HNP36 cDNA was identified as a novel growth factor responsive gene of undetermined biological function that is expressed in the pituitary and parathyroid glands. In studies seeking the function of the HNP36 gene product, the gene was localized by fluorescence in situ hybridization within the 11q13 segment. Further analysis of radiation-reduced hybrid DNAs and chromosome 11-specific YAC clones established that the HNP36 gene is within 80 kb of D11S913, a marker tightly linked to the MEN1 gene. Consequently, the HNP36 gene was studied as a candidate for the MEN1 gene. The human HNP36 gene was cloned and determined to consist of 12 exons. Expression of the HNP36 gene from pituitary and parathyroid tissue and four patient tumors or lymphoblasts was confirmed by RT-PCR amplification of the coding sequences, and HNP36 transcripts were analyzed for mutations. All tissues expressed three HNP36 gene transcripts that result from alternative splicing and appear to encode related, but distinct, proteins. However, DNA sequence determination of the RT-PCR products from MEN I-associated tumors found no deletions and identified a single nucleotide difference that may be a polymorphism. Thus, mutations in the coding segments of the HNP36 gene are not the cause of the MEN I syndrome. Nevertheless, the assignment of the HNP36 gene to 11q13 and identification of new potential gene products provides a novel growth-regulated genetic candidate for other disorders whose genes map to this locus.

Signal amplification in the detection of single-copy DNA and RNA by enzyme-catalyzed deposition (CARD) of the novel fluorescent reporter substrate Cy3.29-tyramide

We demonstrate that the CAtalyzed Reporter Deposition method (CARD), utilizing the novel fluorescent reporter Cy3.29-tyramide, is successful in the Fluorescent in Situ Hybridization (FISH) detection of RNA and single-copy DNA. Histone 4 expression is detected in RNA extracts of 5-phase, synchronized HeLa cells by dot-blot analysis. Gene expression of histone 4 in HeLa cells is demonstrated by FISH via CARD, utilizing oligonucleotide probes. Fluorescence intensity measurements on CARD-amplified histone 4 RNA detection showed (a) a 25-fold amplification of the signal brightness by biotinylated oligonucleotide probes and (b) a sixfold amplification of the signal brightness by horseradish peroxidase (HRP)-labeled histone 4 probes vs the directly stained control. The sensitivity of the CARD method is demonstrated by the FISH detection of single-copy DNA on human corneal fibroblast and HeLa S5 interphase nuclei. Chromosomal localization of the single copy DNA is demonstrated on HeLa S3 metaphase chromosome spreads.

Optical mapping approaches to molecular genomics

A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged site mapping, restriction enzyme fingerprinting, radiation hybrid mapping and optical mapping. Single-molecule approaches offer numerous advantages, including very high resolution, small sample size requirements, and parallel sample processing. The convergence of recent advances in new single molecule techniques, surface chemistry and machine vision technology has contributed to novel approaches to genome analysis.

Statistical methods for gene map construction by fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) provides an efficient and powerful technique for ordering loci both on metaphase chromosomes and in less condensed interphase chromatin. Two-color metaphase FISH can be used to order pairs of loci relative to the centromere; two- and three-color interphase FISH can be used to accurately order trios of loci spaced within 1 Mb relative to one another. Loci separated by a distance > 1-2 Mb exhibit chromatin loops that often give rise to a statistically significant but incorrect order. We derive Bayesian methods for selecting the best locus order based on microscopic evaluation for each of these types of FISH mapping data. We then describe how the results from several two- and three-locus analyses can be combined to evaluate the approximate posterior probability of a given multilocus order within the limits of the technology utilized. These methods directly address the question of interest: What is the probability that the inferred two-, three-, or multilocus order actually is correct? We illustrate our analysis methods by applying them to previously described FISH mapping data of 14 markers in the BRCA1 region on chromosome 17q12-q21. We also propose design strategies to order a group of closely spaced (< 1 Mb) loci, two and three loci at a time, using a bisection strategy for two-color FISH data and a trisection strategy for three-color FISH data. These strategies have the best worst-case performance for ordering a new locus relative to a group of ordered loci and are nearly optimal for ordering a group of loci of unknown order. These, in conjunction with physical mapping strategies, provide efficient and reliable methods for gene map construction by FISH.

The BAX gene maps to the glioma candidate region at 19q13.3, but is not altered in human gliomas

The bax protein regulates apoptosis in a cellular pathway that involves both bcl-2 and p53, two molecules associated with human glioma tumorigenesis. We therefore evaluated the possibility that BAX functions as a glioma tumor suppressor gene. Somatic cell hybrid panels, fluorescence in situ hybridization and cosmid mapping localized the BAX gene to 19q13.3, approximately 300 kb centromeric to HRC. Thus BAX maps to the region of chromosome 19 most frequently deleted in gliomas. Routine and pulsed-field gel electrophoresis/Southern blotting studies, however, failed to reveal large-scale deletions or rearrangements of the BAX gene in gliomas. In addition, single strand conformation polymorphism analysis of all six BAX exons and flanking intronic sequences did not disclose mutations in 20 gliomas with allelic loss of the other copy of 19q. A C/T polymorphism was detected in intron 3 and was common in the general population. Therefore, although BAX maps to the glioma candidate region on the long arm of chromosome 19, BAX is probably not the 19q glioma tumor suppressor gene.