bluuebunny/crossref_metadata_2025 huggingface dataset:
Allelic fusion of DNA topoisomerase IIα and retinoic acid receptor α genes in Adriamycin-resistant p388 murine leukemia revealed by fluorescence in situ hybridization
Authors: Squire J.a. , McPherson J.P. , Beatty B.G. , Goldenberg G.J.
Published: May 2008

Fluorescence in situ hybridization (FISH) analysis of metaphase and decondensed free chromatin fibers from Adriamycin (ADR)-sensitive and ADR-resistant murine cells demonstrated a close juxtaposition of topoisomerase IIα (Top2a) and retinoic acid receptor α (Rara) genes in adjacent chromatin in the drug-resistant cells, and a close but separate genetic proximity in normal murine chromatin. This provides physical evidence that the chromosome 11 allelic rearrangement resulting in a chimeric truncated Top2a/Rara transcript in the ADR-resistant cells is due to a novel fusion of the Topo2a and Rara genes. This is the first description of a Rara gene disruption in cells selected for antineoplastic drug resistance.
Conservation of human chromosome 18 in baboons (Papio hamadryas):a linkage map of eight human microsatellites
Authors: Perelygin A.A. , Kammerer C.M. , Stowell N.C. , Rogers J.
Published: May 2008

A panel of 25 microsatellite loci known to map to human chromosome 18 was screened for length polymorphisms in a multigenerational pedigree of baboons (Papio hαmadryas). Eight of these loci were polymorphic in the baboon pedigrees, with observed heterozygosity values ranging from 0.16 to 0.88. All eight loci show strong evidence of linkage. The most likely map order among the microsatellite loci for Pαpio is completely compatible with the locus order found in the human genome, and sex differences in recombination rates are also similar in the two species. We conclude that the organization of the chromosomal region defined by these loci is largely conserved between baboons and humans.
Complete coding sequence, exon/intron arrangement and chromosome location of ZNF45, a KRAB-domain-containing gene
Authors: Constantinou Deltas C. , Bashiardes E. , Patsalis P.C. , Hadjimarcou M. , Kroisel P.M. , loannou P.A. , Roses A.D. , Lee J.E.
Published: May 2008

Zinc finger genes represent a large multigene family present in mammalian and other genomes. A subgroup of these genes contain a conserved motif, the KRAB domain, at the NH2-terminal region, which was recently shown to posses a potent transcriptional repression activity. For one such gene, ZNF45, we determined the complete coding sequence, along with the exon/intron arrangement and the splice junctions. Exon 2 codes exclusively for the KRAB-A element of 42 amino acids, and exon 4 contains the 19 zinc finger repeats. In addition, we generated an EST (expressed sequence tag) from the 3’-end of ZNF45 that we used for polymerase chain reaction screening of a Pl-derived genomic library. We isolated a 65-kb clone that was used for localizing this gene on chromosome 19ql 3.2 by fluorescence in situ hybridization.
Six antimicrobial peptide genes of the cathelicidin family map to bovine chromosome 22q24 by fluorescence in situ hybridization
Authors: Castiglioni B. , Scocchi M. , Zanetti M. , Ferretti L.
Published: May 2008

Six phage clones containing gene members of the family of antimicrobial peptides named cathelicidins, were mapped to bovine chromosome 22q24, by means of fluorescence in situ hybridization. The mapping data suggest the clustering of cathelicidins into a CATHL@ locus, in a similar manner as for β-defensins, another family of antimicrobial peptides, defining the locus DEFB@ mapped to 27q13→q14.
FISH detection of chromosome polymorphism and deletions in the spinal muscular atrophy (SMA) region of 5q13
Authors: Rajcan-Separovic E. , Mahadevan M.S. , Lefebvre C. , Besner-Johnston A. , Ikeda J.-E. , Korneluk R.G. , MacKenzie A.
Published: May 2008

The search for the SMA defect has culminated in the identification of two candidate 5q13.1 SMA genes, NAIP and SMN both of which are deleted in individuals with SMA. It was postulated that the intact and degenerate versions of NAIP are present in variable and frequently high copy numbers in this region while SMN was proposed to be present in only two copies. In order to assess the copy number of NAIP and SMN we have conducted interphase FISH analysis using NAIP and SMN gene-containing cosmid and plasmid probes. Our results confirm the variability in the number of NAIP signals in non-SMA chromosomes (2–6) and show that SMN is present on average twice per chromosome although in one chromosome 4–5 signals for the SMN-containing cosmid probe were detected. Our analysis reveals that one of four and three of six type I SMA chromosomes had a lower than normal number of NAIP and SMN signals, respectively. In two of six SMA type I chromosomes, complete loss of hybridization signal was observed on one chromosome 5 with our SMN cosmid probe possibly reflecting a large scale deletion. Large scale deletions were not detectable when metaphase chromosomes of an SMA type II and III patient were analyzed.
A new method for detecting pericentric inversions using COD-FISH
Authors: Bailey S.M. , Meyne J. , Cornforth M.N. , McConnell T.S. , Goodwin E.H.
Published: May 2008

A new approach for detecting chromosomal inversions, based on the recently developed technique of chromosome orientation and direction fluorescence in situ hybridization (COD-FISH), is presented. COD-FISH is a strand-specific modification of standard FISH technology which allows the hybridization of single-stranded probes to one, and only one, chromatid of a metaphase chromosome. It can be used to determine the absolute 5’-to-3’ direction of DNA target sequences with respect to the short-to-long arm direction of a given chromosome. Since an inversion reverses the orientation of DNA sequences within the inverted region, an inversion becomes detectable as a “switch” in probe signal from one chromatid to the other, when compared to a reference probe outside of the inverted region. Pericentric inversions in chromosomes 1, 8, 10, and X, which had previously been identified by chromosome banding, were analyzed by the COD-FISH technique. The results presented here demonstrate that COD-FISH can be used for the detection of pericentric inversions and that, in some instances, it provides additional information not obtainable by more conventional methods of cytogenetic analysis. Practical limitations of the COD-FISH technique are also discussed.
Horseradish peroxidase-labeled oligonucleotides and fluorescent tyramides for rapid detection of chromosome-specific repeat sequences
Authors: van Gijlswijk R.P.M. , Wiegant J. , Vervenne R. , Lasan R. , Tanke H.J. , Raap A.K.
Published: May 2008

We present a sensitive and rapid fluorescence in situ hybridization (FISH) strategy for detecting chromosome-specific repeat sequences. It uses horseradish peroxidase (HRP)-labeled oligonucleotide sequences in combination with fluorescent tyramide-based detection. After in situ hybridization, the HRP conjugated to the oligonucleotide probe is used to deposit fluorescently labeled tyramide molecules at the site of hybridization. The method features full chemical synthesis of probes, strong FISH signals, and short processing periods, as well as multicolor capabilities.
Simultaneous enumeration of chromosomes 13, 18, 21, X, and Y in interphase cells for preimplantation genetic diagnosis of aneuploidy
Authors: Munné S. , Weier H.-U.G.
Published: May 2008

A fluorescence in situ hybridization (FISH) protocol to simultaneously enumerate chromosomes 13, 18, 21, X, and Y in interphase cell nuclei for application in preimplantation genetic diagnosis (PGD) of aneuploidy was tested. Strict scoring criteria were developed to minimize recording errors. The protocol used optimized probes for chromosome-specific DNA repeat and single-copy loci and showed a significantly higher efficiency (95%) than previously published protocols. The other purpose of this study was to differentiate between two signals originating from a single split target or from two targets in close proximity. These criteria were based on the FISH results obtained from the analysis of all or most of the cells from 50 chromosomally normal or mosaic human embryos, 20 aneuploid embryos, and five polyploid embryos donated for research. Subsequently, 183 human embryos underwent PGD of aneuploidy in one of their cells. In 64 embryos that were not transferred back to the uterus, the rest of cells were also analyzed, and the previous results were confirmed in 91 % of these embryos, with 0 % (0/21) of the embryos classified as normal embryos being abnormal and 14% (6/43) of the embryos classified as abnormal being normal. Compared to previous protocols, these criteria minimize the risk of transferring abnormal embryos after PGD analysis.
Hypomethylation of human sperm pronuclear chromosomes
Authors: Martorell M.R. , Navarro J. , Márquez C. , Egozcue J. , Benet J.
Published: May 2008

Using the methylase Sssl enzyme, we have analyzed the degree of in situ methylation of human sperm pronuclear chromosomes obtained by fertilizing hamster oocytes with human sperm. Untreated (control) sperm chromosome complements showed a higher degree of in situ methylation, compared to sperm complements previously treated with 5-azadeoxycytidine or lymphocyte chromosomes. This indicates that human sperm pronuclear chromosomes have a lower degree of genomic methylation compared to that of other somatic cells. The similarity in the degree of in situ methylation of the euchromatic and heterochromatic regions of chromosomes 1,9, 15, and 16 and the Y chromosome in human sperm does not support the existence of a possible correlation between hypomethylation and heterochromatin decondensation.
Increased aneuploid frequency in spermatozoa from a Hodgkin’s disease patient after chemotherapy and radiotherapy
Authors: Monteil M. , Rousseaux S. , Chevret E. , Pelletier R. , Cozzi J. , Sèle B.
Published: May 2008

The frequency of sperm aneuploidy was investigated by fluorescence in situ hybridization (FISH) in a Hodgkin’s disease patient shortly after he had received chemotherapy and radiotherapy. Sperm karyotyping of the same patient had previously shown multiple structural abnormalities in most spermatozoa immediately after radiotherapy (day 0), whereas most spermatozoa collected 5 wk later (day 38) exhibited normal metaphase divisions (Rousseaux et al., 1993). Variations in the frequency of aneuploidy could not be detected by sperm karyotyping. Multicolor FISH on interphase spermatozoa revealed an increase in the rate of disomy for chromosomes 1, 6, 11, X, and Y at day 0 as well as at day 38. The high frequency of 24, XY (nondisjunction at meiosis I) and 24, XX (nondisjunction at meiosis II) spermatozoa (8.46% and 1.64% at day 0, respectively) from the Hodgkin’s disease patient suggests that both meiosis I and II are affected and that the X chromosome is frequently involved in such malsegregation events. The rate of 46, XY diploidy was also increased in the patient’s sperm, up to 0.62% at day 0. While radiotherapy probably affected the postmeiotic cells (spermatids), the patient’s cancer and/or chemotherapy are the two major factors that could have affected the dividing spermatogonia and/or spermatocytes, resulting in high aneuploidy rates.
Chromosome assignment of 115 expressed sequence tags (ESTs) from human skeletal muscle
Authors: Muraro T. , Stephan D. , Tiso N. , Zimbello R. , Danieli G.A. , Hoffman E.H. , Valle G. , Lanfranch G.
Published: May 2008

The chromosome assignment of 115 expressed sequence tags (ESTs) from human skeletal muscle, 101 of which identify unknown human genes, is reported. The ESTs were selected among over 4,000 obtained from systematic sequencing of a skeletal muscle cDNA library containing 3’ portions of the mRNAs. Chromosome assignments were ob tained by PCR amplification of two panels of human × rodent somatic cell hybrids. Analysis of these preliminary data suggests a nonrandom distribution of muscle ESTs in the human chromosome complement. The unexpected occurrence of multiple chromosome localizations for some ESTs is discussed.
Robertsonian chromosomal rearrangements in the short-tailed shrew, Blarina carolinensis, in western Tennessee
Authors: Qumsiyeh M.B. , Coate J.L. , Peppers J.A. , Kennedy P.K. , Kennedy M.L.
Published: May 2008

We report significant heterozygosity for numerous Robertsonian translocations in the southern short-tailed shrew (Blarina carolinensis) in western Tennessee. Eight Robertsonian rearrangements were documented using G-banding techniques that explain the variability in diploid numbers from 46 throughout most of the range of the species to 34–40 in western Tennessee. These fusions resulted in the loss of telomere sequences and were not associated with nucleolar organizer regions. When heterozygocity is considered, the lowest diploid number possibly present would be 30. Four localities with distances of over 180 km apart were sampled, and 80–90% of the collected animals were heterozygous for at least one rearrangement. No putative parental type was found in western Tennessee. Heterozygosity for the same rearrangements was found in these different localities, and no monobrachial fusions were noted. Thus, this is a very wide hybrid zone with rare or absent parental types in the areas sampled or is an evolutionary stage preceding establishment of Robertsonian races. Selective forces, if any, were minimal, as evidenced by the wide area of polymorphism, significant heterozygosity, and the fact that the Robertsonian translocations were in Hardy-Weinberg equilibrium. The origin of such extensive polymorphism in western Tennessee is discussed, especially in light of putative effects of the New Madrid seismic activity. Similarities and differences are noted between the Blαrinα model and the well-documented variation in the European common shrew (Sorex αrαneus) and Mus musculus groups.
The murine Ext1 gene shows a high level of sequence similarity with its human homologue and is part of a conserved linkage group on chromosome 15
Authors: Lohmann D.R. , Buiting K. , Lüdecke H.-J. , Horsthemke B.
Published: May 2008

We have cloned and sequenced the murine homologue of the human EXT1 gene. At the protein level, these genes show almost complete identity as divergence is limited to only 5 amino acid positions that are scattered about the whole sequence. In addition, similarity searches identified a protein from chromosome III of C. elegans that shows significant similarity to the human and murine EXT/Ext genes. Using high resolution backcross mapping, the murine Ext1 was mapped at 26.55 cM between D15Mit143 and D15Mit153 on mouse chromosome 15. Therefore, Ext1 is part of an evolutionarily conserved linkage group including SDC2/Hspgl, TKHR/Trhr, EXT1/Extl, MYC/Myc, and TG/Tgn.
A somatic cell hybrid panel for distal 17q: GDIA1 maps to 17q25.3
Authors: Wagner T. , Tommerup N. , Wirth J. , Leffers H. , Zimmer J. , Back E. , Weissenbach J. , Scherer G.
Published: May 2008

A somatic cell hybrid panel was constructed consisting of seven hybrids with translocation breakpoints spanning the region 17q23→q25. Hybrid clones carrying the long-arm derivative of chromosome 17 in the absence of the normal chromosome 17 and of the derivative 17 were initially identified by PCR typing for a proximal and distal 17q marker. The translocation breakpoints of the hybrids were then mapped in more detail by PCR analysis for a number of microsatellite markers from chromosome 17q as well as for five gene loci (CACNLG, GH1, SOX9, TIMP2, TK1) previously mapped to the region 17q23→q25. In addition, the locus for GDIA1 was mapped by FISH to 17q25.3 and fine mapped with the help of the hybrid panel. These seven new hybrids complement the existing somatic cell hybrid panel for the long arm of chromosome 17q.
Incidence of chromosome 1 disomy in human sperm estimated by the primed in situ (PRINS) labeling technique
Authors: Pellestor F. , Girardet A. , Andréo B. , Lefort G. , Charlieu J.P.
Published: May 2008

The primed in situ (PRINS) labeling technique was used to determine the rate of disomy of chromosomes 1 and 16 in sperm of two normal subjects. Two different but specific primers (α-satellite and satellite II) for chromosome 1 were used in parallel experiments to test the efficiency of PRINS labeling in sperm nuclei. A minimum of 10,000 sperm nuclei per chromosome primer was analyzed, leading to a total number of 41,651 scored spermatozoa. Similar rates of chromosome 1 disomy (mean values, 0.18% and 0.20 %) were found in both donors when the α-satellite and satellite II primers were used, demonstrating the reliability of PRINS labeling on sperm nuclei. For chromosome 16, the disomy rate among the two donors ranged from 0.20% to 0.24%. This study confirms that PRINS provides a rapid and efficient method for in situ chromosomal screening of sperm nuclei.
Generation of small insert genomic FISH probes with high signal intensity suitable for deletion mapping
Authors: Dreyling M.H. , Olopade O.I. , Bohlander S.K.
Published: May 2008

We have developed a method to generate FISH probes from small (2–4 kb) nonrepetitive genomic restriction fragments. The probes showed a high hybridization efficiency of up to 90% in metaphase cells from normal peripheral blood. With the use of these probes, homozygous as well as hemizygous 9p deletions were reliably identified in nine leukemia-derived cell lines.
Integration of 101 DNA markers across human Xp11 using a panel of somatic cell hybrids
Authors: Boycott K.M. , Moore B.J. , Gratton K.J. , Stoddart K.L. , Roland B. , Bech-Hansen N.T.
Published: May 2008

One hundred and one DNA markers previously assigned to the short arm of the human X chromosome were localized on a hybrid mapping panel consisting of ten radiation-reduced, and four classical somatic cell hybrids. Of the 101 DNA markers, 16 are genes, two are pseudogenes, 13 are expressed sequence tags, 32 are simple tandem repeats (STRs), four are restriction fragment length polymorphisms, one is a variable number of tandem repeats, and 33 are sequence tagged sites (STSs). Three of these markers, two STSs and one STR, were generated from the products of an inter-Alu PCR library of a radiation-reduced hybrid containing Xp11.4→p11.22 as its only human DNA content. A second STR was isolated from a region-specific cosmid containing the gene ZNF21. The 101 DNA markers fell into 22 bins based on their retention on the hybrids of this panel, which, in combination with YAC contig data, could be further resolved into 24 bins. This hybrid map of Xpl 1 has an average resolution of approximately 0.8 Mb.
Multiple human endogenous retrovirus (HERV-K) loci with gag open reading frames in the human genome
Authors: Mayer J. , Meese E. , Mueller-Lantzsch N.
Published: May 2008

Human endogenous retrovirus HERV-K is present in 25–30 copies per haploid human genome. At least one of these loci is capable of producing full-length Gag protein, high amounts of which have been detected in germ cell tumors and derived cell lines. The latter display HERV-K Gag-encoded retroviral particles. Here, we employed the protein truncation test (PTT) in combination with a monochromosomal hybrid mapping panel to identify the human chromosomes harboring HERV-K gag genes with an open reading frame for Gag protein. Eight human chromosomes were found to contain intact HERV-K gag genes. PTT results were corroborated by partial sequencing of subregions from different HERV-K gag genes. The high number of HERV-K Gag open reading frames supports the idea of retroviral sequences retaining a biological benefit in the human genome.
Complex FISH probes for the subtelomeric regions of all human chromosomes: comparative hybridization of CEPH YACs to chromosomes of the Old World monkey Presbytis cristata and great apes
Authors: Kingsley K. , Wirth J. , van der Maarel S. , Freier S. , Ropers H.-H. , Haaf T.
Published: May 2008

We have generated a human subtelomere probe panel, utilizing well characterized CEPH YACs, for the investigation of human chromosome pathology and evolution through fluorescent in situ hybridization (FISH). Region-specific FISH probes will be extremely valuable for detecting cytogenetically cryptic telomere abnormalities. Here, we present the first comparative mapping study (with 29 subtelomere probes and 6 chromosome paints) to the Old World monkey Presbytis cristαtα, followed by hybridizations to the great apes, gorilla and orangutan, when rearrangements were detected. We observed that the position of telomere-associated genomic sequences has been only moderately conserved during primate evolution. YAC 364f9, specific for the subtelomeric long arm of human chromosome 3, contains an evolutionary inversion breakpoint that was involved in independent chromosome rearrangements in P. cristαtα and gorilla.
M33, a mammalian homologue of Drosophila Polycomb localises to euchromatin within interphase nuclei but is enriched within the centromeric heterochromatin of metaphase chromosomes
Authors: Wang G. , Horsley D. , Ma A. , Otte A.P. , Hutchings A. , Butcher G.W. , Singh P.B.
Published: May 2008

We have raised a monoclonal antibody (MoAb), MAC 402, to the mouse M33 protein, a mammalian homologue of the Drosophila Polycomb protein. MAC 402 recognises a band of 59.7 kDa by Western blot analysis and gives rise to two types of staining pattern within interphase nuclei. Surprisingly, at metaphase, M33 protein is enriched within centromeric heterochromatin. This pattern is also seen for the product of the bmi-1 gene, which is a homologue of the Drosophila Polycomb-group (Pc-G) gene Posterior sex combs. We speculate as to the reasons for this relocalisation of mammalian Pc-G gene products to the centromere at metaphase and its implication for the cell-to-cell inheritance of the states of gene repression that are conferred by this highly conserved group of genes.
Mapping the distribution of the telomeric sequence (T2AG3)n in rock-wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization. I. The penicillata complex
Authors: Metcalfe C.J. , Eldridge M.D.B. , McQuade L.R. , Johnston P.G.
Published: May 2008

The eight Petrogale (rock-wallaby) species of the penicillata complex have a variable rate of karyotypic evolution, with species differing from the ancestral karyotype by two to six rearrangements. The distribution of the predominant vertebrate telomeric sequence (T2AG3)n was examined by fluorescence in situ hybridization (FISH) to determine if this sequence is retained during centric fusion events or is involved in other rearrangements. In all submetacentric chromosomes derived by centric fusions, the telomeric sequence was identified at or near the centromere, indicating that the (T2AG3)n  sequence is consistently retained. In two acrocentric chromosomes, derived by centromeric transpositions from submetacentric fusion chromosomes, an interstitial signal was observed at the presumed site of the fusion. This represents the identification of a novel mechanism by which the (T2AG3)n sequence may become interstitial. Other interstitial telomeric signals were identified just below the centromere of chromosome 1 and interstitially on chromosome 4 in all eight species of the penicillata complex. These may be related to, respectively, the formation of euchromatic short arms on chromosome 1 and a more ancient rearrangement of chromosome 4 within marsupials.
cDNA cloning, characterization, and chromosome mapping of UBE2E2 encoding a human ubiquitin-conjugating E2 enzyme
Authors: Kimura M. , Hattori T. , Matsuda Y. , Yoshioka T. , Sumi N. , Umeda Y. , Nakashima S. , Okano Y.
Published: May 2008

A cDNA encoding a human ubiquitin-conjugating enzyme (E2) with N-terminal extension (UBE2E2/UbcH8) was isolated. Amino acid sequence within the UBC domain of UBE2E2 shares over 90% identity with human UbcH6, mouse UbcM2, and Drosophila UbcD2, whereas the N-terminal region shows little amino acid sequence similarity with known proteins. The UBE2E2 gene is transcribed in various tissues as a 1.9-kb transcript. The UBE2E2 protein formed a thioester bond with ubiquitin in an E1-dependent manner, indicating that the gene product is a functional E2 enzyme. The UBE2E2 gene was assigned to human chromosome 3p24.2 by fluorescence in situ hybridization.
Fluorescence in situ hybridization with a synthetic (T2AG3)n polynucleotide detects several intrachromosomal telomere-like repeats on human chromosomes
Authors: Azzalin C.M. , Mucciolo E. , Bertoni L. , Giulotto E.
Published: May 2008

(T2AG3) repeats comprise the telomeres of human chromosomes and also are present at interstitial locations. Using a long synthetic (T2AG3)n probe, we have localized telomere-like repeats at several internal sites on human chromosomes.
Analysis of human sperm karyotypes in testicular cancer patients before and after chemotherapy
Authors: Martin R.H. , Ernst S. , Rademaker A. , Barclay L. , Ko E. , Summers N.
Published: May 2008

Sperm karyotype analysis was performed on testicular cancer patients before and after treatment with BEP (bleomycin, etoposide, and cisplatin). A total of 788 sperm chromosome complements was studied, 236 before chemotherapy (CT) and 552 post-CT. There was no significant difference in the total frequency of sperm chromosomal abnormalities pre-CT (10.2%) compared to post-CT (10.7 %). Similarly, there were no significant differences in the frequencies of numerical abnormalities (2.5% pre-CT vs. 2.4% post-CT) or structural abnormalities (6.4% pre-CT vs. 7.4% post-CT). The percentage of X-bearing sperm was also not significantly different before (46.3%) and after CT (50.1%). The results in cancer patients were not significantly different from those in control donors. This study corroborates results from our previous analysis of these same men using multicolor fluorescence in situ hybridization for assessment of aneuploidy for chromosomes 1, 12, X, Y, and XY. Together, these two studies suggest that the sperm of men receiving BEP chemotherapy are not at increased risk of chromosomal abnormalities two or more years after treatment.
Generation of chicken Z-chromosome painting probes by microdissection for screening large-insert genomic libraries
Authors: Zimmer R. , King W.A. , Verrinder Gibbins A.M.
Published: May 2008

A strategy for rapid generation of chicken sex chromosome-Z painting probes has been developed using microdissection. Whole chromosome painting probes (WCPs) were prepared from 10–15 copies of mitotic metaphase chicken Z chromosomes. The microisolated chromosomes were subjected to PEG/proteinase K treatment in a collection drop to release DNA, which was then amplified using a degenerate oligonucleotide-primed shuttle PCR (DOP-Shuttle-PCR) strategy. Size distributions of the PCR products were analyzed by agarose gel electrophoresis and smears of DNA were revealed that ranged in size from 200–800 bp, without any evidence of preferential amplification. Both specificity and complexity of the probes have been analyzed by Southern blot and fluorescence in situ hybridization (FISH). Non-specific hybridization was efficiently blocked by using chicken competitor DNA. Analysis of the WCPs produced shows that collectively they provide uniform hybridization signals along the entire length of the chicken Z chromosome. To demonstrate one possible application of these complex probes, we screened a large-insert bacterial artificial chromosome (BAC) chicken genomic library to select Z chromosome-specific clones. To address specificity of the selected clones and to physically map them to the Z chromosome, FISH analysis was used. Of the 3 clones initially tested, one clone (C3) carrying a 250-kb insert mapped to the distal portion of the short arm of the chicken Z chromosome. Therefore, this technique has provided appropriate probes for screening large-insert genomic libraries. Further application of these probes includes the analysis of chromosome rearrangements, studies of cases of heteroploidy involving the Z chromosome, positional cloning of Z-linked genes and studies on mechanisms of sex-chromosome evolution in birds.
Mapping of the Olf 89 and Rfp genes to the rat genome: comparison with the mouse and human and new insights into the evolution of the rodent genome
Authors: Szpirer C. , Szpirer J. , Rivière M. , Tazi R. , Pontarotti P.
Published: May 2008

The Rfp (ret finger protein) and Olf89 (olfactory receptor 89) genes were assigned to rat chromosomes 17 and 20, respectively. These two genes are syntenic in human (RFP and OLF89) as they both map to chromosome 6, less than 300 kb apart. The mouse homologs are located on two different chromosomes, namely 13 and 17, respectively. It was shown that these two genes delineate the UA/UB break point, and that this chromosome break occurred in the rodent lineage, before the mouse radiation. Our data indicate that this break occurred before the rat/ mouse split, therefore before the Murinae radiation.
Chromosome painting: a method for testing chromosomal changes in lemur evolution
Authors: Vezuli A. , Hauwy M. , Warter S. , Rumpler Y.
Published: May 2008

Chromosome painting using commercially available human chromosome-specific DNA libraries was performed to elucidate chromosomal rearrangements in lemur evolution. Human-specific probes for chromosomes 3, 14, 15, and 21 were used to paint chromosomes of six species: Eulemur fulvus mayottensis, Varecia variegata, Lemur catta, Hapalemur simus, H. griseus griseus, and H. aureus. All human chromosome libraries hybridized specifically to chromosome segments of varying length or to whole arms of Lemur chromosomes. The labeling was clearly visualized and permitted precise delineation of the hybridized Lemur chromosomal segments. The use of commercial probes of human chromosomes for chromosome painting appears efficient enough to investigate homology in different species of Lemur. In general, the results obtained by chromosome painting in this study confirm results previously obtained by the R-banding technique but modify the location of some chromosomal rearrangements on different branches of the evolutionary tree of the Lemuridae and reveal some new rearrangements that were not detectable with banding techniques. These results show that chromosome painting with human chromosome-specific DNA libraries can provide useful information in comparative studies on karyotypes of distantly related mammalian species, providing a powerful tool for evolutionary studies, especially in phylogeny.
Cytogenetic analysis of meiotic segregation in sperm from two males heterozygous for reciprocal translocations using PRINS and humster techniques
Authors: Pellestor F. , Girardet A. , Coignet L. , Andréo B. , Lefort G. , Charlieu J.P.
Published: May 2008

The meiotic segregation patterns of 2 reciprocal translocations t(7;9)(q33;p21) and t(7;18)(q35;q11) were analyzed in sperm of 2 heterozygote carriers. Both sperm karyotyping and in situ PRINS labeling of sperm nuclei were performed on a sperm sample from each subject. Using the humster technique, 54 and 72 sperm chromosome complements were successfully analyzed for the t(7;9) and the t(7;18) respectively. The frequencies of alternate, adjacent 1, adjacent 2 and 3:1 segregations were 44.44%, 37.04%, 12.96% and 5.56% for the t(7;9) and 33.33%, 43.05%, 19.45% and 4.17% for the t(7;18). The PRINS procedure allowed the rapid screening of large samples of spermatozoa. However, alternate and adjacent 1 segregants were not discriminated because of the generation of centromeric signals. The segregation pattern was determined on 10,658 spermatozoa for the t(7;9) and 10,462 for the t(7;18). The distributions of segregants were similar to those obtained by sperm karyotyping. These data were pooled with results from 37 reciprocal translocations previously studied by sperm karyotyping and 6 recently investigated by FISH. The analysis of these compiled data demonstrates the particularity of the production of imbalances in male gametes; independent of the predisposition for a type of imbalance at term, there is a preferential production of adjacent 1 imbalance in sperm.
Instability of the D4Mit12 microsatellite marker in C57BL/6J × BALB/cJ F1 hybrid mice is independent of the tumor phenotype
Authors: Herranz M. , Santos J. , Pérez de Castro I. , Meléndez B. , Fernández-Piqueras J..
Published: May 2008

We examined the stability of different types of DNA microsatellite markers in γ-radiation-induced thymic lymphomas as well as normal, nontumorous tissues of F1 hybrid mice derived from the parental strains C57BL/6J, RF/J, and BALB/cJ. Surprisingly, the D4Mit12 microsatellite showed genomic instability in a significant fraction of DNAs of the (C57BL/6J × BALB/cJ) F1 hybrids with independence of the tumor phenotype. This instability was not found in the reciprocal F1 DNAs, in DNAs of the parental strains, or in DNAs of (C57BL/6J × RF/J) F1 hybrid mice. These results suggest that the instability of the D4Mitl2 microsatellite is dependent on its repeat length, the genetic background of F1 hybrids, and the maternal origin of the C57BL/6J allele.
ZOO-FISH of a microdissection DNA library and G-banding patterns reveal the homeology between the Brazilian rodents Akodon cursor and A. montensis
Authors: Fagundes V. , Scalzi-Martin J.M. , Sims K. , Hozier J. , Yonenaga-Yassuda Y.
Published: May 2008

The neotropical rodents Akodon cursor (2n = 14, 15, and 16) and A. montensis (2n = 24 and 25), two closely related and morphologically indistinguishable species, have been compared by G-banding and chromosome painting. In situ hybridization of a biotinylated DOP-PCR product obtained from a microdissected chromosome of A. cursor onto A. montensis chromosomes was performed in combination with localization of telomeric sequences using a (TTAGGG)n oligomer as a FISH probe. The results provide evidence of the complex chromosomal rearrangements suggested by GTG-banding analysis, indicating the origin of one A. cursor autosome from three different A. montensis autosomes. Furthermore, the complete cytogenetic homeology between the A. cursor and A. montensis karyotypes was determined, along with the occurrence of tandem fusions and pericentric inversions and the loss of telomeres, centromeres, and chromosome arms. Evidence for the ancestral origin of the A. cursor karyotype is also provided.
Meiosis and fertility in common shrews, Sorex araneus from a chromosomal hybrid zone in central Sweden
Authors: Narain Y. , Fredga K.
Published: May 2008

Adult male common shrews from the Uppsala and Hällefors Robertsonian chromosomal races and hybrids were collected from the area of Surahammar in Sweden. Meiosis and fertility of hybrid (complex heterozygotes) and nonhybrid (homozygotes) individuals were compared based on an analysis of chromosomal interactions and synapsis at pachytene, chiasma characteristics at diakinesis, and germ-cell death. No individuals suffered severe germ-cell loss, and the differences found among the Uppsala and Hällefors homozygotes and the hybrids were not significant. In complex heterozygotes, ring configurations of four elements were observed at meiosis I, with one chiasma per chromosome arm. Abnormal rings were frequent at pachytene, but interactions between the ring and other chromosomes were seldom found. There is no indication from this study of a differential fertility between homozygotes and ring IV-forming complex heterozygotes in males.
Cloning, expression and mapping of a novel human zinc-finger gene TCF17 homologous to rodent Kid1
Authors: Omori Y. , Kyushiki H. , Takeda S. , Suzuki M. , Kawai A. , Fujiwara T. , Takahashi E. , Nakamura Y.
Published: May 2008

We isolated a novel human zinc-finger gene TCF17 homologous to rat Kid1, a zinc-finger gene of the Krüppel type expressed predominantly in kidney. In the rat this gene seems to be a transcription factor expressed in response to renal injury and ischemia. The 2435-bp human cDNA contained an open reading frame encoding 605 amino acids. The deduced amino acid sequence showed 86.0% and 87.2% identity (91.6% and 92.8% similarity) with the rat Kid1 and mouse Tcf17 respectively. In contrast with rat Kid1, human TCF17 was expressed in all human tissues examined, including kidney. This gene was mapped by FISH to chromosome 5q35.3, where cytogenetic and molecular abnormalities have been reported often in renal cell carcinomas.
Molecular cloning of a novel gene similar to myeloid antigen CD33 and its specific expression in placenta
Authors: Takei Y. , Sasaki S. , Fujiwara T. , Takahashi E. , Muto T. , Nakamura Y.
Published: May 2008

We have isolated a novel gene that encodes a protein sharing significant similarity with myeloid antigen CD33. The complete cDNA contains an open reading frame of 1,326 nucleotides encoding 442 amino acids. The deduced amino acid sequence indicates that this molecule belongs to the immunoglobulin (1g) superfamily and is likely to be a new member of the sialoadhesin sub-family. It is composed of three 1g-like domains; its high degree of similarity to CD33 (70% identity) in the first and second of these domains implies that the placenta-specific gene product is likely to be associated with cell-cell interaction. Northern-blot analysis revealed transcripts of four distinct sizes, 7.5 kb, 5.0 kb, 4.1 kb, and 2.0 kb, specifically in the placenta. Consequently, we termed this gene CD33L (CD33 antigen-like). An alternatively-spliced transcript encoding a 342-amino-acid peptide which lacked the transmembrane region and the cytoplasmic tail was also isolated. We mapped CD33L by fluorescence in situ hybridization (FISH) to human chromosome 19q13.3, where the CD33 gene is also located.
Chromosomal localization of four MAPK signaling cascade genes: MEK1, MEK3, MEK4 and MEKK5
Authors: Rampoldi L. , Zimbello R. , Bortoluzzi S. , Tiso N. , Valle G. , Lanfranchi G. , Danieli G.A.
Published: May 2008

The mitogen-activated protein kinase (MAPK) signaling cascade is one of the most important mechanisms for the cytoplasmic transduction of extracellular signals. We report the chromosomal localization of the human MEKl, MEK3, MEK4 and MEKK5 genes, involved in the MAPK cascade. Using radiation hybrid mapping, MEKl was assigned to chromosome 15q22.1→q22.33, MEK3 to chromosome 17q11.2, MEK4 to chromosome 17p12 and MEKK5 to chromosome 6q22.33.
A panel of transferable fragments of human chromosome 11q
Authors: Robertson G.P. , Hufford A. , Lugo T.G.
Published: May 2008

Cytogenetic and molecular studies have implicated one or more tumor suppressor genes on the long arm of human chromosome 11 in the malignant progression of several human solid tumors, including malignant melanoma and carcinomas of the breast, cervix, ovary, and lung. Microcell-mediated chromosome transfer of an intact copy of chromosome 11 into tumor cell lines has provided additional evidence of tumor suppressor gene function in melanoma, breast cancer, and cervical cancer. However, sublocalization of the region(s) conferring the tumor suppressive effect has been difficult. To facilitate mapping of tumor suppressor gene(s) on chromosome 11, we have generated a panel of 25 mouse donor cell lines containing neo-taggedfragments of human chromosome 11q which can be transferred into cell lines to test for tumor suppressor activity. The chromosome fragments in these cell lines have been characterized by fluorescence in situ hybridization with probes to human DNA and to the centromere of chromosome 11, and also by analysis of microsatellite markers spanning chromosome 11. Finally, to demonstrate the usefulness of these cell lines as donors for microcell-mediated chromosome transfer, two fragments were transferred into the human melanoma cell line UACC 903. This panel of selectable subchromosomal fragments, derived from the long arm of human chromosome 11, will be useful for the regional localization of tumor suppressors and other genes by means of functional assays.
Construction of two near-kilobase resolution restriction maps of the 5’ regulatory region of the human apolipoprotein B gene by quantitative DNA fiber mapping (QDFM)
Authors: Duell T. , Nielsen L.B. , Jones A. , Young S.G. , Weier H.-U.G.
Published: May 2008

Quantitative DNA fiber mapping (QDFM) is a high-resolution technique for physical mapping of DNA. The method is based on hybridization of fluorescently labeled DNA probes to individual DNA molecules stretched on a chemically modified glass surface. We now demonstrate and validate a rapid QDFM-based approach for the mapping of multiple restriction sites and precise localization of restriction fragments in large genomic clones. Restriction fragments of a 70-kb P1 clone (P1-70) containing the 5’ region of the human apolipoprotein B gene (APOB) were subcloned and mapped along straightened P1-70 DNA molecules. Multicolor fluorescence in situ hybridization (FISH) and digital image analysis allowed us to rapidly position 29 restriction fragments, ranging in size from 0.5 kb to 8 kb, and to map 43 restriction sites. The restriction map obtained by QDFM was in excellent agreement with information obtained by RecA-assisted restriction endonuclease (RARE) cleavage, long-range PCR, and DNA sequence analyses of the P1-70 clone. These data demonstrate that QDFM is a rapid, reliable method for detailed restriction site-mapping of large DNA clones.
A proposed nomenclature of the domestic cat karyotype
Authors: Cho K.-W. , Youn H.-Y. , Watari T. , Tsujimoto H. , Hasegawa A. , Satoh H.
Published: May 2008

High-resolution G- and Q-band patterns of cat (Felis catus) prometaphase chromosomes with more than 450 numbered bands are presented. This number represents approximately twice the number of bands per haploid set exhibited by feline chromosomes at mid-metaphase. A diagrammatic representation of G-banded cat chromosomes has already been described (O’Brien and Nash, 1982); however, precise numbering of bands and landmarks, as in the human karyotype and in the karyotypes of other domestic and laboratory animals, has not yet been available for the domestic cat karyotype, except for the RBG-banded ideograms constructed by Shibasaki et al. (1987) and Rønne and Storm (1995). In this report, we propose a numbering system for the G-banded ideogram reported previously (O’Brien and Nash, 1982) and an extended ideogram at the high-resolution level (473 numbered bands) as a contribution to the future standardization of the feline karyotype.
The inwardly rectifying potassium channel subunit Kir2.2v (KCNJN1) maps to 17p11.2→p11.1
Authors: Namba N. , Mori R. , Tanaka H. , Kondo I. , Narahara K. , Seino Y.
Published: May 2008

Inwardly rectifying K+ (Kir) channels play important roles in various cellular functions in excitable and non-excitable cells. We recently cloned the human genes encoding the Kir channel subunits Kir2.2v (KCNJNl) and Kir2.2 (KCNJ12). However, the physiological role of Kir2.2v has not yet been clarified. Fluorescence in situ hybridization analysis of human metaphase chromosomes assigned both genes to 17p11.2→p11.1. The presence of hybridization signals in the paracentromeric regions of both chromosomes 17 from two Smith-Magenis syndrome (SMS) patients indicated that Kir2.2v and Kir2.2 are not located within the minimum critical region of this syndrome.
Mapping of 22 new ESTs around a tumor suppressor gene and a senescence gene at 6q16→q21
Authors: Morelli C. , Cardona F. , Boyle J.M. , Negrini M. , Barbanti-Brodano G.
Published: May 2008

Twenty two expressed sequence tags (ESTs) have been mapped at the border of 6q16→q21 and at the proximal end of 6q21 a candidate for two tumor suppressor genes and a senescence gene. Use of a translocation and deletion hybrid panel together with a 4-Mb YAC contig allowed us to precisely define the position of the ESTs. Thirteen ESTs were placed within the 4-Mb interval at the proximal portion of 6q21 using a restriction map of the YAC contig, seven ESTs span a 2-Mb region on the 6q16→q21 border, and two are distal to the contig. Refinement of the localization of these ESTs will provide substantial assistance in identifying new genes within the region 6q16→q21.
Molecular cloning and chromosome mapping of rat phospholipase D genes, Pld1a, Pld1b and Pld2
Authors: Nakashima S. , Matsuda Y. , Akao Y. , Yoshimura S. , Sakai H. , Hayakawa K. , Andoh M. , Nozawa Y.
Published: May 2008

We have previously obtained three partial rat phospholipase D (PLD) cDNA fragments by a reverse transcriptase-polymerase chain reaction (RT-PCR) method using degenerate primers based on two conserved amino acid sequences in PLDs of human and yeast. The entire coding regions of these genes were isolated and sequenced. The longest clone, Pld1a encodes a 1075 amino acid (aa) protein that was highly similar (89 % identity) to human PLD1a, especially in four conserved regions present in other PLDs. The nucleotide sequence of the second clone was identical to that of Pld1a except that the clone lacked 114 nucleotides corresponding to 38 aa in the middle. A shorter alternatively spliced form of human PLD1 (PLD1b) lacking the corresponding 38 aa was also identified. Therefore, the second clone (Pld1b) was considered to correspond to the rat counterpart of human PLD1b. The third clone, Pld2 encoding 933 aa was smaller than that of Pld1 and its aa identity to rat Pld1 was 56%. However, it contains four conserved regions and aa sequences of these regions are homologous to those of rat Pldl and human PLDL Its entire aa sequence was very similar (96 % identity) to the recently cloned mouse PLD, Pld2. Chromosome locations of the Pld1a, Pld1b and Pld1 genes were determined in the rat and mouse by fluorescent in situ hybridization. As expected, both Pldla and Pldlb clones were hybridized to the same chromosome regions. The Pld1 and Pld2 genes were localized to rat chromosome 2q23.3→q24 proximal end and the proximal region of mouse Chromosome 3B, and rat chromosome 10q23.3→q24 proximal end and mouse Chromosome 11B3, respectively. They were mapped in regions where conserved linkage homology has been identified between the two species.
Detailed map of a region commonly amplified at 11q13→q14 in human breast carcinoma
Authors: Bekri S. , Adélaïde J. , Merscher S. , Grosgeorge J. , Caroli-Bosc F. , Perucca-Lostanlen D. , Kelley P.M. , Pébusque M.-J. , Theillet C. , Birnbaum D. , Gaudray P.
Published: May 2008

Amplification of loci present on band q13 of human chromosome 11 is a feature of a subset of estrogen receptor positive breast carcinomas prone to metastasis. As many as five distinct amplification units have been described on 11q13. They include particularly a genomic area encompassing the GARP gene at 11q13.5→q14.1. We have reassessed our current knowledge of this region, located telomeric to CCND1 and EMS1, which is amplified in 7–10% of mammary tumors. The loose definition of the driving forces of these amplification events led us to map accurately the boundaries of the amplifiable region, and thus to contribute a physical and transcriptional map of a 3-Mb region of chromosome 11. Four new genes were placed on the regional map, namely CBP2, CLNSIA, UVRAG, and PAKl. We have narrowed the core of the 11q13→q14 amplicon to a 350-kb area encompassing D11S533, mostly on its telomeric side. The map reported here represents an indispensable step toward sequencing the entire region, and thus toward uncovering gene(s) which play(s) a critical role in breast cancer progression.