bluuebunny/crossref_metadata_2025 huggingface dataset:
Fine mapping of human HOX gene clusters
Authors: Apiou F. , Flagiello D. , Cillo C. , Malfoy B. , Poupon M.-F. , Dutrillaux B.
Published: May 2008

The chromosome localization of human HOX gene clusters has been reinvestigated by fluorescence in situ hybridization (FISH). Three loci were precisely localized in 7p15.3 (HOXA@), 17q21.3 (HOXB@) and 12ql3.3 (HOXC@). The localization of HOXD@ was confirmed to 2q31.
Chromosomal evolution in duiker antelope (Cephalophinae: Bovidae): karyotype comparisons, fluorescence in situ hybridization, and rampant X chromosome variation
Authors: Robinson T.J. , Wilson V. , Gallagher, Jr. D.S. , Taylor J.F. , Davis S.K. , Harrison W.R. , Elder F.F.B.
Published: May 2008

Fluorescence in situ hybridization (FISH) and conventional banding techniques were used to identify patterns of similarity among the genomes of six species of antelope, subfamily Cephalophinae. The G-banded euchromatic portions of the autosomes were invariable in all species; however, significant modifications of the X chromosomes were detected. Two of the taxa, Cephalophus maxwellii and C. monticola, were characterized by acrocentric X’s, while X chromosome morphology varied from submetacentric to metacentric in the remaining species (C. dorsalis, C. natalensis, Sylvicapra grimmia, and C. silvicultor). The short arm of the X was heterochromatic in each species. Total genomic DNAs from these antelope were used as hybridization probes against Cephaîophus metaphase chromosomes and resulted in robust fluorescence in the pericentromeric region of each autosome and in the heterochromatic short arm of the X chromosome, indicating complimentarity of DNA sequences in these regions. Conversely, chromosome painting involving genomic DNAs derived from the subfamilies Alcelaphinae (Pygargus dorcas) and Neotraginae (Oreotragus oreotragus) showed a marked absence of hybridization at these sites. Additionally, X chromosome comparisons between the Cephalophinae and Bovinae (represented by Bos taurus) revealed two euchromatic pericentric inversions which had occurred since their common ancestry. There is good G-band homoeology between the inverted cattle chromosome region Xq12→q34 and most of the proximal portion of Xq in duikers, as well as between the distal third of the duiker Xq and the cattle Xp. The latter rearrangement was further confirmed by in situ hybridization using a probe containing an insert spanning bands p12 to p14 of the cattle X chromosome.
A stable marker chromosome with a cryptic centromere: evidence for centromeric sequences associated with an inverted duplication
Authors: Sacchi N. , Magnani I. , Fuhrman-Conti A.M. , Monard S.P. , Darfler M.
Published: May 2008

Centromere activation, an important mechanism in karyotype evolution, is occasionally observed in some human chromosome rearrangements. We report a possible occurrence of centromere activation in a marker chromosome containing an atypical centromere associated with an inverted duplication of the region 14q32→qter. The marker chromosome’s reduced centromere lacks both the α and β satellite sequences usually found at normal centromeres. In an attempt to identify the centromeric sequences, the marker chromosome was flow-sorted and amplified by a degenerate oligonucleotide primer polymerase chain reaction. Reverse chromosome painting experiments showed that the marker chromosome contains sequences that are unique to the distal region of chromosome 14, as well as a low copy number of (centromeric) sequences that are also highly represented in the centromeres of chromosomes 18 and 19. These data suggest the activation of a novel centromere in the 14q32→qter region, very likely consequent to the duplication of the region itself.
Isolation and mapping of a human gene (RABL) encoding a small GTP-binding protein homologous to the Ras-related RAB gene
Authors: Han H.-J. , Sudo K. , Inazawa J. , Nakamura Y.
Published: May 2008

Many subgroups of the RAB gene, a member of the RAS superfamily have been identified. Here we report the isolation and analysis of a cDNA encoding a putative small GTP-binding protein, designated RABL, from a human fetal lung cDNA library. RABL encodes 216 amino acids that are 86 % identical to members of the RAB5 subfamily and it shows 94% homology in nucleotide sequence with RAB5C of dog. This gene was expressed ubiquitously in all human tissues examined. By fluorescence in situ hybridization we mapped RABL to chromosome band 17q21.2.
An extended nomenclature of the canine karyotype
Authors: Reimann N. , Bartnitzke S. , Bullerdiek J. , Schmitz U. , Rogalla P. , Nolte I. , Rønne M.
Published: May 2008

In contrast to many other animals, knowledge about the canine karyotype is quite sparse. This is due in part to the rather difficult canine karyotypic pattern. Except for the X and the Y chromosome, there are only acrocentric chromosomes, which appear to be quite small and difficult to identify unambiguously. In previous reports, schematic representations of the canine karyotype have been described. However, a nomenclature comparable to that of the human karyotype or the karyotypes of sheep, cattle, or goats does not yet exist for the dog. Based on high-resolution banding of metaphase chromosomes from canine fibroblasts, we propose an ideogram of the canine karyotype with 460 numbered bands and characteristic landmarks. In addition, the centromere positions of the canine chromosomes are determined by a combined GTG-banding/ FISH approach, and the R- and G-banding patterns are compared.
Chromosomal localization of the major and 5S rRNA genes in the European eel (Anguilla anguilla)
Authors: Martínez J.L. , Morán P. , García-Vázquez E. , Pendás A.M.
Published: May 2008

The major (18S, 5.8S, and 28S) and 5S rRNA genes have been mapped by double fluorescent in situ hybridization to European eel metaphase chromosomes. The major rRNA genes were localized to a submetacentric pair of chromosomes that showed a consistent size polymorphism among the individuals studied. The 5S rRNA genes were clustered in a single locus that mapped to the centromeric region of an acrocentric pair. In contrast to the major rRNA genes, no detectable polymorphism, in either size or intensity of the fluorescent signal, was observed. The chromosomal organization of both families of rRNA genes are discussed in terms of genomic organization and chromosomal evolution.
The three genes of the human FCGR1 gene family encoding FcγRI flank the centromere of chromosome 1 at 1p12 and 1q21
Authors: Maresco D.L. , Chang E. , Theil K.S. , Francke U. , Anderson C.L.
Published: May 2008

The high-affinity receptor for immunoglobulin G, FcγRI (FCGR1), is encoded by a family of three genes within humans that share over 98% of DNA sequence homology. Efforts to define the location of the FCGR1 genes within chromosome 1 have been made to determine if they are tightly linked to the five other FCGR genes present at 1q23. Our results, obtained through both fluorescence in situ hybridization analysis of human cells and Southern analysis of cell lines containing 1p and 1q, show instead that the three genes flank the centromere of chromosome 1 at bands 1p12 and 1q21. FCGR1B was found at 1p12, whereas both FCGR1A and FCGR1C were localized to 1q21. This places the FCGRl gene family within a large pericentric linkage group which is conserved between humans and mice. We hypothesize that the three FCGRl genes were separated by a pericentric inversion, known to have occurred on human chromosome 1 which relocated FCGR1A and FCGR1C to the long arm and left FCGR1B positioned on the short arm. We have also performed FCGRl gene copy number experiments which indicate the existence of three FCGR1 genes within the human genome.
A novel Krüppel-associated box containing the SSX gene (SSX3) on the human X chromosome is not implicated in t(X;18)-positive synovial sarcomas
Authors: de Leeuw B. , Balemans M. , Geurts van Kessel A.G.
Published: May 2008

The human synovial sarcoma-specific transloca-tion t(X;18) results in the fusion of the SYT gene on chromosome 18 with either one of the Krüppel-associated box (KRAB) containing SSX1 or SSX2 genes on the X chromosome, depending on the exact location of the breakpoint within band Xp11.2. Screening of a testis cDNA library yielded several SSX-positive clones. Subsequent sequence analysis revealed that one third of these clones represent an SSX gene that differs from both SSX 1 and SSX2. This novel member of the family of KRAB containing SSX genes, which we designated SSX3, is 90 % homologous to SSX 1 and 95 % homologous to SSX2 at the cDNA level. Somatic ce11 hybrid analysis indicated that SSX3 maps within Xp11.2→p11.1, the region that also harbors the SSX1 and SSX2 genes. However, we conclude from our RT-PCR data and from results reported in the literature that SSX3 does not act as a fusion partner to SYT in any of the 44 independent synovial sarcomas thus far tested.
Seven genes from human chromosome 18 map to chromosome 24 in the bovine
Authors: Larsen N.J. , Womack J.E. , Kirkpatrick B.W.
Published: May 2008

Bovine sequence tagged sites (STSs) were developed for seven genes and used for synteny mapping with a hybrid bovine × rodent cell line panel. The genes were thymidylate synthase (TYMS), pituitary adenylate cyclase activating peptide (ADCYAP1), and melanocortin-2 receptor (MC2R) from the short arm of human chromosome (HSA) 18 and N-cadherin (CDH2), transthyretin (TTR), gastrin-releasing peptide (GRP), and plasminogen activator inhibitor 2 (PAI2) from the long arm of HSA 18. Primers for these genes were designed with human, ovine, or bovine sequences aligned with a sequence from a second species. The bovine PCR product was cloned, and the fragment was sequenced to verify that the homologous gene was indeed amplified. A second set of bovine-specific PCR primers were developed for each gene from these sequences. These STSs were used for synteny mapping, and all seven genes were syntenic with markers of bovine chromosome (BTA) 24. The concordance with BTA 24 was at least 96.5 % for all genes.
Localization of rat K51 keratin-like locus (Kr10I) to human and animal chromosomes by in situ hybridization
Authors: Biltueva L.S. , Sablina O.V. , Beklemisheva V.R. , Shvets Yu. , Tkachenko A. , Dukhanina O. , Lushnikova T.P. , Vorobieva N.V. , Graphodatsky A.S. , Kisselev L.L.
Published: May 2008

The rat K51 locus (gene symbol Krt10I) was mapped using isotopic in situ hybridization to rat chromosome 3, human chromosome 9, pig chromosome 6, cattle chromosome 18, and mink chromosome 1.
Cloning, expression pattern and mapping to 12p13.2→p13.1 of CLAPS3, a gene encoding a novel clathrin-adaptor small chain
Authors: Watanabe T.K. , Shimizu F. , Nagata M. , Takaichi A. , Fujiwara T. , Nakamura Y. , Takahashi E. , Hirai Y.
Published: May 2008

From a human fetal-brain cDNA library we isolated a novel gene encoding a peptide homologous to clathrin-adaptor small chains in rat, mouse, and yeast. The cDNA, designated CLAPS3 (clathrin-associated/assembly/adaptor protein, small 3, 22 kDa), contained an open reading frame of 579 nucleotides encoding 193 amino acids. Northern-blot analysis revealed expression of a 1.35-kb transcript in all human tissues examined. This gene was mapped to chromosome bands 12p13.2→p13.1 by FISH.
Isolation and mapping of a human gene (DIFF6) homologous to yeast CDC3, CDC10, CDC11, and CDC12, and mouse Diff6
Authors: Mori T. , Miura K. , Fujiwara T. , Shin S. , Inazawa J. , Nakamura Y.
Published: May 2008

We have isolated a novel human cDNA that encodes a protein homologous to murine H5 and Diff6, and to yeast CDCIO, and mapped it to chromosome region 2q37 by fluorescent in situ hybridization. Its transcript has an open reading frame of 1,218 nucleotides encoding 406 amino acids. The deduced peptide sequence contained conserved domains rich in basic residues, GXXGXGKS- -DXXG- -TKXD, a motif of the GTPase superfamily. Different polyA sites accounted for generation of two transcripts. The major type, 3.5 kb long, was expressed ubiquitously in all human tissues examined, but a 2.0-kb alternative transcript lacking any long AU-rich element in the 3’ non-coding region was expressed abundantly only in testis, heart and skeletal muscle.
Structures and chromosome locations of the human MEF2A gene and a pseudogene MEF2AP
Authors: Suzuki E. , Lowry J. , Sonoda G. , Testa J.R. , Walsh K.
Published: May 2008

The MEF2 family of transcription factors control the expression of muscle-specific and mitogen-induced genes. Here we describe the isolation and structure of the human MEF2A gene. The protein coding region of MEF2A is divided by 10 introns. The 3’ untranslated region (UTR) is 3.7 kb in length, and it contains a region that is highly homologous with a portion of the 3’ UTR of Xenopus MEF2A. A partially processed pseudogene (MEF2AP) corresponding to MEF2A was also isolated and characterized. Human MEF2A was mapped by fluorescence in situ hybridization to chromosome 15q26, and MEF2AP was mapped to chromosome 1q24→q25.
Structure and chromosomal assignment of the murine sterol carrier protein 2 gene (Scp2) and two related pseudogenes by in situ hybridization
Authors: Raabe M. , Seedorf U. , Hameister H. , Ellinghaus P. , Assmann G.
Published: May 2008

The murine sterol carrier protein 2 gene (Scp2) has been mapped to chromosome 4C5→D1 by in situ hybridization. This location is syntenic with the locus of SCP2 on human chromosome 1p32. We found the overall structure of murine Scp2 to be identical to that of the human SCP2 gene. In addition, two Scp2 pseudogenes have been isolated and mapped to chromosomes 3H2→4 and 9F.
Localization of ribosomal genes in human spermatogonia by fluorescent in situ hybridization and confocal microscopy
Authors: Lévy N. , Navarro A. , Depetris D. , Moretti C. , Stahl A.
Published: May 2008

The distribution of ribosomal RNA genes in nucleoli is still a matter of controversy. We have investigated the nucleolus of human type A spermatogonia, which displays a single, large fibrillar center. Silver-staining was used to localize the fibrillar center by light microscopy. Fluorescent in situ hybridization was performed on the same cell, using a 5.8-kb probe specific for a transcribed region of the ribosomal genes. The fluorescent area exactly corresponded to the silver-stained area. The three-dimensional distribution of rDNA was studied in horizontal and orthogonal sections using a confocal laser scanning microscope. The presence of the fluorescent signal throughout the whole silver-stained structure demonstrated that the fibrillar center, and at least a part of the dense fibrillar component, contained most of the rDNA.
M32, a murine homologue of Drosophila heterochromatin protein 1 (HP1), localises to euchromatin within interphase nuclei and is largely excluded from constitutive heterochromatin
Authors: Horsley D. , Hutchings A. , Butcher G.W. , Singh P.B.
Published: May 2008

Mice possess two structural homologues of Drosophila HPl, termed M31 and M32 (Singh et al., 1991). We have previously shown that an M31-specific monoclonal antibody (MoAb), MAC 353, localises to constitutive heterochromatin (Wreggett et al., 1994). Here we report that a MoAb raised against the M32 protein (MAC 385) recognises a 22-kDa protein in murine nuclear extracts and that M32 is distributed in a finegrain “speckled” pattern within interphase nuclei. M32 is also largely excluded from the large masses of constitutive heterochromatin that are labelled by MAC 353.
Genomic cloning and localization to chromosome 11p15.5 of the human achaete-scute homolog 2 (ASCL2)
Authors: Miyamoto T. , Jinno Y. , Sasaki T. , Ikeda Y. , Masuzaki H. , Niikawa N. , Ishikawa M.
Published: May 2008

The mouse achaete-scute homolog-2 gene (Mash2), a member of the achaete-scute gene family, encodes a transcription factor that plays an important role in the development of the trophoblast. It has recently been reported that Mash2 is genomically imprinted and mapped to the distal region of mouse chromosome 7, where other imprinted genes, Ins2, Igf2 and H19 are located. We isolated a clone carrying the partial human homolog, ASCL2, from a human genomic phage library using a PCR product for the rat Ascl2-cDNA as a probe. By fluorescence in situ hybridization using a phage clone as a probe whose insert contained the partial human ASCL2, we assigned ASCL2 to human chromosome 11p15.5. Sequence comparisons of the human ASCL2 clone and the rat Ascl2-cDNA showed 86.9% identity spanning 206 nucleotides and 85.3% deduced polypeptide-sequence identity over 68 residues.
MDM2 amplification in a primary alveolar rhabdomyosarcoma displaying a t(2;13)(q35;q14)
Authors: Meddeb M. , Valent A. , Danglot G. , Nguyen V.C. , Duverger A. , Fouquet F. , Terrier-Lacombe M.J. , Oberlin O. , Bernheim A.
Published: May 2008

This report describes a case of rhabdomyosarcoma associated with a 2;13 translocation and multiple double minute chromosomes. The origin of the amplified DNA was identified using comparative genomic hybridization, which pinpointed a unique spot at 12q→13q14. Band 12q13 has been shown to contain several genes that are occasionally amplified in other sarcomas. Fluorescence in situ hybridization to tumor metaphases with probes specific for this region indicated that the double minutes contained the MDM2 gene but not the CDK4 gene. MDM2 amplification was further quantified by Southern hybridization, which showed a mean value of 25 copies per haploid genome. This is the first example of MDM2 amplification in a rhabdomyosarcoma.
Sex-ratio distortion associated with the presence of a B chromosome in Astyanax scabripinnis (Teleostei, Characidae)
Authors: Vicente V.E. , Moreira-Filho O. , Camacho J.P.M.
Published: May 2008

Cytogenetic studies were conducted on 154 specimens of AstyΑnΑx scabripinnis collected at three localities in the Campos do JordÃo region (State of SÃo Paulo, Brazil). The C-banding pattern suggested that the metacentric B chromosome found in most of the specimens is an isochromosome derived from chromosome 24, the only chromosome in the standard complement that carries interstitial C-bands similar to those present in each arm of the B chromosome. The sex ratio was biased toward females in the CÓrrego das Pedras and RibeirÃo do Casquilho streams and toward males in the RibeirÃo das Perdizes stream. In all three populations analyzed, the B chromosome was more frequent in females than in males. In the most exhaustively sampled population (those from CÓrrego das Pedras), there was a highly significant association between B-chromosome frequency and sex-ratio distortion, with a disproportionately high number of males without B chromosomes and females with one B chromosome.
Sheep CENPB and CENPC genes show a high level of sequence similarity and conserved synteny with their human homologs
Authors: Burkin D.J. , Jones C. , Burkin H.R. , McGrew J.A. , Broad T.E.
Published: May 2008

Sheep CENPB and CENPC clones were isolated from a lung cDNA library. The DNA and predicted amino acid sequences of these clones were compared with their human and mouse homologs and shown to contain a high degree of sequence similarity. Sheep chromosomal assignments were made using a sheep × hamster somatic cell hybrid mini-panel. CENPB was assigned to sheep chromosome 13 and CENPC to chromosome 6. The previously reported assignments of CENPB and CENPC to human chromosomes 20 and 4, respectively, suggest conserved synteny between sheep chromosome 13 and human chromosome 20 and support conserved synteny between sheep chromosome 6 and human chromosome 4.
Simultaneous obtention of an intense G-banding and chromosome painting
Authors: Richard F. , Dutrillaux B.
Published: May 2008

A method for simultaneously obtaining brilliant G-banding and chromosome painting is described. It is based on a modification of methods enabling the detection of incorporated BrdU by anti-BrdU antibodies conjugated to a fluorochrome. It induces a banding of both painted and non-painted chromosomes. The method was adapted for in situ hybridizations on human and non human (ZOO-FISH) chromosomes.
Sequence analysis and genetic mapping of porcine chromosome 11 centromeric S0048 marker
Authors: Riquet J. , Mulsant P. , Yerle M. , San Cristobal-Gaudy M. , Le Tissier P. , Milan D. , Gellin J.
Published: May 2008

We report the existence of a new family of swine centromeric satellite DNA composed of a 51-bp repeat unit, most specifically found on pig chromosome 11 centromere and with less specificity at the centromeric region of other meta-and submetacentric chromosomes. This satellite DNA family, which has no homologies with the Mel and Ac2 families published previously, was named Mc2. We designed a specific primer set for PCR amplification of this centromeric satellite DNA. Specificity of amplification was checked by using a porcine somatic cell hybrid panel and by FISH. Furthermore, the development of a PCR-RFLP marker of Mc2 repetition allowed its genetic mapping on the PiGMaP reference families panel. The centromere of chromosome 11 was thus integrated to the genetic map previously published.
Shared synteny of human chromosome 17 loci in Canids
Authors: Park J.P.
Published: May 2008

Canids are unusual among mammals in the large degree to which their karyotypes have diverged during speciation. In many instances, chromosome segments from different species share cytogenetic homology, and a presumed phylogenetic tree of Canid evolution can be constructed based on the relative shuffling of chromosomal elements. In this study, four gene probes (myeloperoxidase [MPO], Miller-Dieker [MDCR], ERBB2, and retinoic acid receptor Α [RARA]) from human chromosome 17 were used in fluorescence in situ hybridizations with chromosomes of three different Canids: two subspecies of the Asiatic raccoon dog (Nyctereutes) and the domestic dog (Canis familiaris). The Nyctereutes subspecies have widely diverged karyotypes (2n = 38 versus 2n = 54) and Canis familiaris has a large number (2n = 78) of chromosomes. This study confirms the identity of two shared chromosomes of Nyctereutes. The Japanese raccoon dog chromosome 13 shares linkage with the Chinese raccoon dog chromosome 5. Both of these Nyctereutes chromosomes share synteny with human chromosome 17. Human chromosome 17 shares linkage with Canis famiiiaris chromosome 23. The relative order and spacing of the genes mapped in these species suggests the occurrence of chromosome rearrangements, most notably inversions, during the evolution of these animals.
A periodic tryptophan protein 2 gene homologue (PWP2H) in the candidate region of progressive myoclonus epilepsy on 21q22.3
Authors: Yamakawa K. , Gao D.-Q. , Korenberg J.R.
Published: May 2008

The Unverricht-Lundborg type of progressive myoclonus epilepsy (EPM1) has been mapped to human chromosome 21q22.3, and the candidate region has been narrowed to a region of less than 300 kb. We now report the isolation of a novel gene, PWP2H, from this EPMl candidate region. The putative protein encoded by this gene is a novel member of the beta transducin protein superfamily with high homology to the yeast periodic tryptophan protein 2 (PWP2). PWP2H cDNA was isolated from a 14 week human trisomy 21 fetal brain cDNA library by using a modification of a direct cDNA selection method. PFGE analysis showed that PWP2H is located proximal to D21S25 and distal to TMEM1. Northern analysis of the 3.1-kb PWP2H cDNA revealed that a 3.3-kb major transcript is ubiquitously expressed in human adult tissues. DNA sequence analysis reveals a complete coding region of 2,610 bp as well as 5’- and 3’-UTR. The structure of the putative PWP2H protein contains 6 WD40 repeats, 2 acidic regions and one leucine zipper domain, suggesting that the protein may form specific protein complexes in which the WD40 repeats and the leucine zipper represent protein-protein binding sites. In conclusion, the map location and the homology to a gene family involved in a large variety of biological processes including signal transduction and development make PWP2H an intriguing candidate for EPM1 as well as for APECED (autoimmune polyglandular disease) and HPE1 (holoprosencephaly-1) that also map in this region of chromosome 21.
The gene (PTPN13) encoding the protein tyrosine phosphatase PTP-BL/PTP-BAS is located in mouse chromosome region 5E/F and human chromosome region 4q21
Authors: Van den Maagdenberg A.M.J.M. , Olde Weghuis D. , Rijss J. , Merkx G.F. , Wieringa B. , Geurts van Kessel A. , Hendriks W.J.A.J.
Published: May 2008

Both mouse and human genomic clones were isolated for protein tyrosine phosphatase PTP-BL/PTP-BAS (HGM approved gene symbols Ptpn13 and PTPN13, respectively). Using these clones as a probe, PTPN13 was assigned to human chromosome region 4q21 and mouse chromosome region 5E/F by fluorescence in situ hybridization (FISH).
Chromosome microdissection: a brief overview
Authors: Cannizzaro L.A.
Published: May 2008

Chromosome microdissection arose as a means of facilitating long range physical mapping of chromosome regions involved in either a genetic or malignant disorder. However, with the rapid development of improved techniques for mapping and sequencing the human genome, microdissection is considered by many investigators to be a cumbersome and time consuming procedure. Nonetheless, based on the impressive number of informative diagnostic DNA markers that are now available as a result of this technology, microdissection still must be considered one of the most rapid and direct methods available for generating new DNA markers from any chromosome region, irrespective of its sequence composition. In addition, it remains an important means to dissect DNA markers from any organism, eukaryotic and prokaryotic, and has resulted in generating disease associated DNA sequences from both human and animal genomes. Recently, microdissection of single cells has emerged as a viable alternative for isolating pure populations of specific cell types, especially tumor cells, which can then be studied without background contamination from any other cellular constituents. This overview will provide a glimpse into the present applications of the microdissection technology, as well as the importance this technology will have for future exploration into the human genome.
Chromosomal banding patterns in the eyelid-less microteiid radiation: Procellosaurinus and Vanzosaura (Squamata, Gymnophthalmidae)
Authors: Yonenaga-Yassuda Y. , Mori L. , Chu T.H. , Rodrigues M.T.
Published: May 2008

Cytogenetic studies were performed on three species of eyelidless microteiids, Procellosaurinus erythrocerus, P. tetradactylus, and Vanzosaura rubricauda (Squamata, Gymnophthalmidae), all with a diploid number of 2n = 40. The specimens were collected in the palaeoquartenary dune fields of the middle Rio São Francisco in the State of Bahia, Brazil. Chromosomes from fibroblast cultures were studied after routine Giemsa staining, CBG- and RBG-banding, and Ag-NOR staining. Despite similarities in chromosome number and morphology, each species can be differentiated by the position and amount of C-heterochromatin. Our cytogenetic and DNA content data indicate that there are more similarities between the two species of Procellosaurinus than exist between either species and V. rubricauda, reinforcing the importance of banding techniques for the characterization of reptilian species.
High-resolution FISH of the entire integrated Epstein-Barr virus genome on extended human DNA
Authors: Lestou V.S. , Strehl S. , Lion T. , Gadner H. , Ambros P.F.
Published: May 2008

Here we report a high-resolution fluorescence in situ hybridization (FISH) analysis of the integrated Epstein-Barr virus (EBV) genome in chromosomes, decondensed interphase nuclear chromatin, and linearly extended chromatin fibers. We analyzed the EBV DNA integrated into the human genome in the well-characterized Burkitt’s lymphoma cell line Namalwa, which contains two complete EBV genomes. The integration occurs via the terminal repeats of the virus and was always detectable at chromosome band lp35. Using the biotinylated Bam HIW fragment of the viral DNA, we observed distinct pairs of signals or small nuclear RNA “tracks” within interphase nuclei. FISH to stretched DNA fibers has a higher resolving power and, therefore, enables analysis of the structural organization of DNA. Application of this methodology to linearly extended chromatin of Namalwa cells using different EBV fragments allowed us to visualize the ordered arrangement of the integrated virus. Based on the predicted span of 0.34 nm per base pair for relaxed DNA, length measurements of 30 images showed a good correlation between the mean physical length of hybridized EBV DNA of 52.8 µm (158 kb) without the terminal repeats, and the EBV genomic length of 172 kb, including the terminal repeats. This DNA mapping procedure represents a useful tool for studying the structural organization of integrated viral genomes, and its application will have implications for the understanding of integration processes.
FISH localization of human cytoplasmic actin genes ACTB to 7p22 and ACTG1 to 17q25 and characterization of related pseudogenes
Authors: Ueyama H. , Inazawa J. , Nishino H. , Ohkubo I. , Miwa T.
Published: May 2008

Human β- and γ-cytoplasmic actin genes (ACTB and ACTG1) were mapped to chromosomes 7p22 and 17q25, respectively, by fluorescence in situ hybridization (FISH). Four processed pseudogenes, β-actin-related ACTBP9 and γ-actin-related ACTGPl, ACTGP3, and ACTGP9, were isolated from human libraries. By PCR of somatic cell hybrid DNAs, ACTBP9 and two β-actin-related pseudogenes (ACTBP7 and ACTBP8) were mapped to human chromosomes 18, 15, and 6, respectively. The γ-actin-related pseudogenes were mapped by FISH to chromosomes 3q23 (ACTGPl), 20pl3 (ACTGP3), and 6p21.1 (ACTGP9).
Chromosome mapping of the mouse Akt2 gene and Akt2 pseudogene
Authors: Altomare D.A. , Kozak C.A. , Sonoda G. , Testa J.R.
Published: May 2008

We previously reported the cloning of a murine cDNA encoding the protein-serine/threonine kinase Akt2, and we used this clone to map the Akt2 gene to mouse chromosome (MMU) 7B1 by fluorescence in situ hybridization. We now have cloned and partially sequenced a mouse Akt2 pseudogene. An analysis of two sets of multilocus crosses revealed that the Akt2 gene is closely linked to the Cyp2a locus in proximal MMU7. The Akt2 pseudogene was mapped to proximal MMU11 by both multilocus mapping and fluorescence in situ hybridization.
Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase
Authors: Matsushima M. , Inazawa J. , Takahashi E. , Suzumori K. , Nakamura Y.
Published: May 2008

We have isolated a human cDNA clone homologous to fungal ERG3, a gene encoding sterol C-5 desaturase. The full nucleotide sequence of this human cDNA revealed a 708-bp open reading frame that encodes a 236-amino-acid polypeptide. The gene was expressed in all normal human tissues examined. We determined its location to chromosome 11q23.3 by fluorescence in situ hybridization.
Standardization of cattle karyotype nomenclature: Report of the committee for the standardization of the cattle karyotype
Authors: Popescu C.P. , Long S. , Riggs P. , Womack J. , Schmutz S. , Fries R. , Gallagher D.S.
Published: May 2008

The purpose of this paper is to publish a table which correlates the previous nomenclature with marker genes mapped on cattle chromosomes. This table also presents the human correspondences and the chromosome measurements expressed as relative lengths.
Characterization of a flow-sorted human chromosome 10 cosmid library by FISH
Authors: Ma N.S.-F. , Zheng C. , Benchekroun Y. , Deaven L.L. , Longmire J.L. , Moir D.T. , Mao J.
Published: May 2008

Fluoresence in situ hybridization (FISH) was used to localize cosmids to regions of human chromosome 10. A total of 301 cosmids were selected randomly from a flow-sorted human chromosome 10 cosmid library constructed from human × hamster cell line 762–8A and arrayed in microtiter storage dishes. Over 70% (211/301) of the cosmids mapped to unique regions of chromosome 10. About 7% (22/301) produced multiple hybridization signals indicative of chimeric clones or sequences repeated at low copy number. Three cosmids (3/301, or 1 %) hybridized to the centromeric regions of chromosome 10 and one or more other human chromosomes. About 19% (59/301) consisted mostly or entirely of hamster DNA inserts, and about 2% (6/301) appeared to be nonrecombinants.
Cloning and chromosomal localization of the rat Stat5 and Yγ1 genes
Authors: Chen K.-S. , Paladugu A. , Aldaz C.M. , Gould M.N.
Published: May 2008

Rat β-casein gene expression is controlled in part by the positively acting factor Stat5 and the negatively acting factor Yy1. Partial cDNAs encoding the SH2 domain of rat Stat5a and Stat5b and the zinc finger domain of rat Yy1 have been cloned by an RT-PCR based approach. The nucleotide sequences encoding the SH2 domain of rat Stat5a and Stat5b are 75% homologous. The rat Yy1 cDNA is 95% homologous to its human and mouse counterparts in the zinc finger domain-encoding region. Using fluorescence in situ hybridization, we have localized Stαî5a to rat chromosome band 10q32.1 and Yy1 to rat chromosome band 6q32.
Cloning, expression pattern and mapping to Xq of NAP1L3, a gene encoding a peptide homologous to human and yeast nucleosome assembly proteins
Authors: Watanabe T.K. , Fujiwara T. , Nakamura Y. , Hirai Y. , Maekawa H. , Takahashi E.
Published: May 2008

From a human fetal brain cDNA library, we isolated a novel gene sharing significant homology with the genes of nucleosome assembly proteins (NAPs). This cDNA clone, designated NAP1L3 (nucleosome assembly protein 1-like 3), contained an open reading frame of 1518 nucleotides encoding 506 amino acids. Its predicted amino acid sequence showed 46% identity and 65% similarity with NAP1L. In its C-terminal half NAP1L3 contained several characteristic motifs strictly conserved with NAP 1L and yeast NAP1 but the N-terminal half showed little conservation. Northern-blot analysis revealed strong expression of a 3.0-kb transcript in human adult brain and weak expression in heart. NAP1L3 was closely linked to a marker (DXS990) mapped to chromosome bands Xq21.3→q22, where genes responsible for several X-linked mental retardation syndromes have been localized.
Molecular cloning of a novel receptor (CMKLR1) with homology to the chemotactic factor receptors
Authors: Gantz I. , Konda Y. , Yang Y.-K. , Miller D.E. , Dierick H.A. , Yamada T.
Published: May 2008

We report the cloning of a novel human gene, CMKLR1, which encodes a protein that has notable sequence and structural homology to the seven transmembrane G-protein linked chemokine receptors. This gene has 55 % nucleotide sequence homology to the IL-8 type 1 receptor and 53% to the N-formyl peptide related receptor 1 genes. The mRNA of this receptor is expressed in a broad array of tissues associated with hematopoietic and immune function including, spleen, thymus, appendix, lymph node, bone marrow, and fetal liver. Using fluorescence in situ hybridization the gene encoding CMLKR1 (chemokine-like receptor 1) was localized to human chromosome 12q24.1.
3p21 is a recurrent treatment-related breakpoint in myelodysplastic syndrome and acute myeloid leukemia
Authors: Shi G. , Weh H.J. , Martensen S. , Seeger D. , Hossfeld D.K.
Published: May 2008

In this study we report 11 cases with chromosome abnormalities involving 3p21. Nine cases were diagnosed as myelodysplastic syndrome (MDS), and two as acute myeloid leukemia (AML). Six of nine MDS cases were secondary to a primary malignant disease. In two patients, AML was secondary to breast cancer and polycythemia vera (PV). Seven of eleven patients had a history of intensive polychemotherapy and/or radiation therapy for 3.5 to 5 years. The mean interval from initial therapy to secondary disease was 13.2 years. Complex chromosomal aberrations were found in all 11 cases. Band 3p21 was involved in translocations in 9 patients and in deletions in 2 patients. A t(3;16)(p21;pl3) was found in two cases. Additional abnormalities frequently included a –5, –7, as well as deletions or rearrangements of these 2 chromosomes. Data reported in this paper suggest that 3p21 is a recurrent treatment-related breakpoint in MDS and AML and is likely to contain a gene involved in the pathogenesis of this disease.
Molecular cloning of the papillary renal cell carcinoma-associated translocation (X;1)(p11;q21) breakpoint
Authors: Weterman M.A.J. , Wilbrink M. , Janssen I. , Janssen H.A.P. , van den Berg E. , Fisher S.E. , Craig I. , Geurts van Kessel A.
Published: May 2008

A combination of Southern blot analysis on a panel of tumor-derived somatic cell hybrids and fluorescence in situ hybridization techniques was used to map YACs, cosmids and DNA markers from the Xp11.2 region relative to the X chromosome breakpoint of the renal cell carcinoma-associated t(X; 1 )(p 11 ;q21). The position of the breakpoint could be determined as follows: Xcen-OATL2-DXS146-DXS255-SYP-t(X;1)-TFE3-OATL1-Xpter. Fluorescence in situ hybridization experiments using TFE3-containing YACs and cosmids revealed split signals indicating that the corresponding DNA inserts span the breakpoint region. Subsequent Southern blot analysis showed that a 2.3-kb EcoRl fragment which is present in all TFE3 cosmids identified, hybridizes to aberrant restriction fragments in three independent t(X;1)-positive renal cell carcinoma DNAs. The breakpoints in these tumors are not the same, but map within a region of approximately 6.5 kb. Through preparative gel electrophoresis an (X;1) chimaeric 4.4-kb EcoRl fragment could be isolated which encompasses the breakpoint region present on der(X). Preliminary characterization of this fragment revealed the presence of a 150-bp region with a strong homology to the 5’ end of the mouse TFE3 cDNA in the X-chromosome part, and a 48-bp segment in the chromosome 1-derived part identical to the 5’ end of a known EST (accession number R93849). These observations suggest that a fusion gene is formed between the two corresponding genes in t(X;1)(p11;q21)-positive papillary renal cell carcinomas.
Genetic mapping of GLCLC, the human gene encoding the catalytic subunit of γ-glutamylcysteine synthetase, to chromosome band 6p12 and characterization of a polymorphic trinucleotide repeat within its 5’ untranslated region
Authors: Walsh A.C. , Li W. , Rosen D.R. , Lawrence D.A.
Published: May 2008

The first and rate-limiting step in the formation of glutathione is catalyzed by γ-glutamylcysteine synthetase (glutamate-cysteine ligase, E.C. 6.3.2.2). Herein, we describe a trinucleotide repeat polymorphism located in the 5’ untranslated region of the human gene, GLCLC, that encodes the catalytic subunit of this enzyme, and we genetically map GLCLC to band 6pl2, 1.6 cM distal to D6S295.
Comparative mapping of Na+-phosphate cotransporter genes, NPT1 and NPT2, in human and rabbit
Authors: Kos C.H. , Tihy F. , Murer H. , Lemieux N. , Tenenhouse H.S.
Published: May 2008

The chromosome locations of the rabbit (Oryctolagus cuniculus) Na+-phosphate cotransporter genes NPT1 and NPT2 were determined by fluorescence in situ hybridization. Our results localize NPT1 to rabbit chromosome 12p11 and NPT2 to rabbit chromosome 3p 11. The corresponding genes in the human map to chromosome bands 6p22 and 5q35, respectively. These assignments agree with the previously reported homology between rabbit chromosome 12 and human chromosome 6 and provide the basis for the establishment of a conserved syntenic group between rabbit chromosome 3 and human chromosome 5.
Chromosome homology between the domestic pig and the babirusa (family Suidae) elucidated with the use of porcine painting probes
Authors: Bosma A.A. , de Haan N.A. , Mellink C.H.M. , Yerle M. , Zijlstra C.
Published: May 2008

Homology among three pairs of domestic pig (Sus scrofa) and five pairs of babirusa (Babyrousa babyrussa) autosomes has been demonstrated with the use of porcine painting probes. With the results of this study, in addition to data obtained earlier through the application of banding techniques, correspondence between all individual chromosomes of these two distantly related pigs has been identified.
Molecular characterization of the complex sex-chromosome heterochromatin in the rodent Microtus chrotorrhinus
Authors: Ivanov S.V. , Modi W.S.
Published: May 2008

The sex chromosomes of Microtus chrotorrhinus are unusually large compared to those of other mammals, comprising about 20 % of the karyotype and containing substantial amounts of constitutive heterochromatin. Previous studies have described two highly repeated DNA families (MSAT-160 and MSAT-2570) that localize to this heterochromatin (Modi, 1992, 1993c). The present report describes a third satellite DNA family (termed MSAT-21) in M. chrotorrhinus that is also located in the sex heterochromatin. This repeat consists of diverged copies (average similarity = 75 %) of a tandemly repeated 21-mer. Southern blotting of MSAT-21 revealed that although some higher order (5–20 kb) repeats do exist, none has spread throughout an appreciable portion of the genome. Pulsed field gel experiments indicated that most of the larger arrays (50-700 kb) of all three satellite families are distributed across numerous size classes, suggesting that the three repeats are interspersed with one another in this heterochromatin. Analysis of a boundary between MSAT-21 and MSAT-160 showed that the junction monomers of each satellite are intact and that a pentanucleotide has apparently been transferred from MSAT-21 to MSAT-160 via recombination. Sequence comparisons of MSAT-160 with another rodent satellite and with the U3 region of the Rous sarcoma virus (RSV) long terminal repeat identified inverted repeats and similarities with viral enhancer domains in the rodent sequences. Additionally, the MSAT-21 consensus was found to be similar to the R region of RSV, suggesting a retroviral ancestor for these rodent repeated DNA families.
Development of DNA libraries specific for Chinese hamster chromosomes 3, 4, 9, 10, X, and Y by DOP-PCR
Authors: Xiao Y. , Slijepcevic P. , Arkesteijn G. , Darroudi F. , Natarajan A.T.
Published: May 2008

In a previous study of ours, DNA libraries specific for Chinese hamster chromosomes 1, 2, 3, 5, 6, 7, and 8 were constructed by single laser flow sorting and the linker adapter PCR method. Since a single laser flow sorting of chromosomes is based on chromosome size, it is difficult to separate chromosomes of equal size, such as chromosome 3 and the X chromosome. This problem can be circumvented by bivariate flow sorting. In the present study, we have used bivariate flow sorting of Chinese hamster chromosomes and the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) for generating DNA libraries specifically for chromosomes 3, 4, 9, 10, X, and Y. Fluorescence in situ hybridization (FISH) analyses indicate that the probe libraries are highly specific and can be applied to various cytogenetic studies.
Alterations of yeast artificial chromosome transgenic sequences in stretched embryonic stem-cell chromatin visualized by fluorescence in situ hybridization
Authors: Rosenberg C. , Voltz A.K. , Lawler A.M. , Lamb B.T. , Stetten G. , Gearhart J.D.
Published: May 2008

Transgenic mice have been generated from embryonic stem (ES) cells carrying functional genes cloned within yeast artificial chromosomes (YACs). Information on the integrity and organization of the inserted sequences, including the, number of copies and their orientation to each other, is still limited by current methods. We have applied fluorescence in situ hybridization to stretched chromatin preparations from YAC-transfected ES cells to analyze the organization and copy number of the integrated sequences
Human CLAPS2 encoding AP17, a small chain of the clathrin-associated protein complex: cDNA cloning and chromosomal assignment to 19q13.2→q13.3
Authors: Winterpacht A. , Endele S. , Enklaar T. , Fuhry M. , Zabel B.
Published: May 2008

We have cloned the cDNA for the human homolog of the rat AP17 gene, a small chain of the clathrin-associated protein complex AP-2. The cDNA is highly conserved between rat and human. Human AP17, gene symbol CLAPS2 (clathrin-associated/assembly/adaptor protein, small 3, 17 kDa), was assigned to chromosome region 19q13.2→q13.3.
Chromosome mapping of rat histone genes H1fv, H1d, H1t, Th2a and Th2b
Authors: Walter L. , Klinga-Levan K. , Helou K. , Albig W. , Drabent B. , Doenecke D. , Günther E. , Levan G.
Published: May 2008

Chromosome assignment of the rat histone genes H1t, H1d (H1.4), H1fv (H1⁰), Th2a and Th2b is described. The testicularly expressed histone genes H1t, Th2a and Th2b could be assigned to rat chromosome (RNO) 17 by PCR analysis of somatic cell hybrid DNAs. The Hid gene was mapped to RN017p12→p11 by FISH. These genes might form a histone gene cluster homologous to that found on HSA6p21.3 in humans and MMU13A2–3 in mice. The rat histone Hlfv gene was assigned to RN07 by PCR. This result allows the inclusion of rat Hlfv to an established conserved group of syntenic genes in rat, mouse and human on chromosomes RN07, MMU15 and HSA22, respectively.
Characterization and Mapping of the Xiphophorus maculatus (Teleostei: Poeciliidae) RPS15 gene
Authors: Walter R.B. , Obermoeller R.D. , Moore D.D. , Lacson J.M. , Della Coletta L. , McEntire B.B. , Morizot D.C. , Nairn R.S.
Published: May 2008

We have determined the nucleotide sequence and gene map location of the Xiphophorus mαculαtus homologue of RPS 15 (ribosomal protein S15, alias RIG). The Xiphophorus RPS15 cDNA encodes 145 amino acids, which show 94 % identity compared to deduced mammalian and avian RPS15 amino acid sequences. At the nucleotide level, 84% sequence identity is maintained between the fish and human gene, while homologous amphibian and avian sequences show about 80% nucleotide identity compared to the Xiphophorus sequence. Nucleotide identity substantially decreases when the fish gene is compared to Arabidopsis S15 (64%) and yeast S21 (55%) genes. Genetic linkage analysis of an RPS 15 restriction fragment length polymorphism in backcross hybrids generated from the cross X. hellerí × (X. maculatus Jp 163 B × X helleri) demonstrated linkage of Xiphophorus RPS 15 to the EGFR, UMPK and YES loci in Xiphophorus Linkage Group VI.
Sex chromosome linkage of 5S rDNA in rainbow trout (Oncorhynchus mykiss)
Authors: Moran P. , Martinez J.L. , Garcia-Vazquez E. , Pendas A.M.
Published: May 2008

The karyotype of the rainbow trout is characterized by a primitive XX/XY sex-determining chromosomal system. (Thorgaard et al., 1977). In the present study using FISH we have physically linked the 5S rRNA genes to the partially undifferentiated X chromosome pair. PCR amplified 5S rDNA was used for FISH and hybridization signals indicated that the genes were duplicated, present in one acrocentric and one metacentric pair of chromosomes. After analyzing several individuals, the female metaphases showed four fluorescent signals whereas males presented only three signals. Two of the three signals obtained in males corresponded to the metacentric pair whereas the single signal was mapped to the heterochromatin that cytologically differentiates the X chromosome from the Y chromosome. Double FISH experiments demonstrated that the 5S rDNA which is not sex linked is located at the NOR bearing arm close to the major ribosomal RNA genes (5.8S, 18S and 28S), similar to the situation observed in Atlantic salmon (Pendas et al., 1994a).
The Ag-NOR proteins present a crescent-shaped distribution at the secondary constrictions of metaphase PtK1 chromosomes
Authors: Suja J.A. , Hernandez-Verdun D.
Published: May 2008

The ultrastructural distribution of the proteins responsible for the silver staining of NORs was analyzed on serial thin sections of preembedded silver-stained rat kangaroo PtKi metaphase chromosomes. Our results show that the Ag-NOR proteins present a crescent-shaped distribution at the secondary constriction of each chromatid. Moreover, in somecases the crescent-shaped structures of both chromatids are not symmetrically arranged but show different orientations. These observations, together with our own and previously reported light microscopy results obtained on silver-stained mammalian chromosomes, lead us to suggest a mechanism for the formation of apparent secondary constrictions at NORs.