bluuebunny/crossref_metadata_2025 huggingface dataset:
An interstitial nucleolus organizer region in the long arm of human chromosome 7: cytogenetic characterization and familial segregation
Authors: Guttenbach M. , Nassar N. , Feichtinger W. , Steinlein C. , Nanda I. , Wanner G. , Kerem B. , Schmid M.
Published: April 2003

An unusual NOR-bearing chromosome 7 was detected in a phenotypically normal, healthy 29-year-old male proband. Differential banding techniques as well as in situ hybridization employing various DNA-probes were performed in order to characterize the chromosome in detail. The nucleolus organizer region was found to be located between bands 7q21.3 and 7q22.1. No further rearrangements were detected in this chromosome. Analysis of spontaneously occurring micronuclei revealed 9% of them to contain a 7q fragment distal to (or including) the inserted NOR, suggesting that the inserted secondary constriction represents a potential hot spot for chromosomal breakage and rearrangement. Segregation analysis of the variant chromosome 7 in 51 members of the probands’ family showed transmission in a Mendelian fashion. 27 individuals were found to be heterozygous for the inserted chromosome. A three-year-old child in the consanguineous marriage of two heterozygous carriers exhibited the NOR-insertion in both of his chromosome 7 homologues. To our knowledge, this is the first report on a homozygous carrier of a non-acrocentric NOR-bearing chromosome.
Translocation breakpoint possibly predisposes to nonrandom X-chromosome inactivation in mouse embryos bearing Searle’s T(X;16)16H translocation
Authors: Ogura H. , Takada S. , Mise N. , Sugimoto M. , Tan, S.-S. , Takagi N.
Published: April 2003

To clarify the sequence of events that ultimately achieves the nonrandom inactivation of the paternally inherited X chromosome in postpartum female mice heterozygous for T(X;16)16H, we set out to examine the expression of Xist alleles and the X-linked HMG-lacZ transgene in embryos recovered at the egg cylinder stage. Lack of expression of the Xistb allele on the 16X translocation chromosome in the embryonic region of 7.5 d postcoitum (dpc) X16/XnXista;16XXistb/16 embryos strongly suggested the occurrence of nonrandom inactivation in favor of the normal X chromosome. The simplest explanation would be biased choice, followed by postinactivation selection against genetically unbalanced cells. However, the frequency and distribution of β-galactosidase-positive cells in X16/XnlacZ;16X/16 embryos at 6.5 and 7.5 dpc, together with earlier cytogenetic data, raised an intriguing possibility that the majority of 16X chromosomes were prevented from completing the inactivation process, when they had been chosen to be silenced. Phenotypes of female mice carrying a spontaneous recombination between Xn and 16X in the segment defined by the T16H breakpoint and the X-linked Ta locus suggested that the nonrandomness was brought about by disruption of an X-chromosomal sequence or structure at the translocation breakpoint.
A molecular cytogenetic analysis of X chromosome repatterning in the Bovidae: transpositions, inversions, and phylogenetic inference
Authors: Robinson, T.J. , Harrison, W.R. , Ponce de León F.A. , Davis S.K. , Elder F.F.B.
Published: April 2003

Chromosomal homologies among the X chromosomes of species representative of eight bovid subfamilies and most of the recognized tribes were established using a combination of FISH and conventional G- and C-banding. Our analyses allowed for the delimitation of three X chromosome types represented, respectively, by cattle (Bovinae, tribe Bovini), the tragelaphines (Bovinae, tribe Tragelaphini), and a large assemblage comprising all the remaining subfamilies and their tribes (the Cephalophinae, Hippotraginae, Alcelaphinae, Antilopinae, Aepycerotinae, Peleinae, and Caprinae). The use of the bacterial artificial chromosome probe BAC 101 (which maps to Xp12 in cattle) and an Xp painting probe comprising sequences specific for the short arm of cattle Xp (Xp24→p12) allowed us to orient this region, which has moved as a conserved euchromatic block during the evolution of the bovid X chromosome. We show that the differences between the three chromosomal types are attributable to a transposition, two inversions, and heterochromatic additions/deletions. A paucity of comparative mapping data precludes the assignment of the sequences contained in cattle Xp to either the presumed conserved (XCR) or the recently added (XAR) region of the eutherian X chromosome, and the reasons for the retention of these sequences as an evolutionarily conserved unit in the intrachromosomal restructuring of the bovid X across lineages remain enigmatic.
Sex determination in Ellobius lutescens: The story of an enigma
Authors: Vogel W. , Jainta S. , Rau W. , Geerkens C. , Baumstark A. , Correa-Cerro L.-S. , Ebenhoch C. , Just W.
Published: April 2003

The unusual karyotype of Ellobius lutescens (2n = 17,X in males and females) has attracted permanent interest and prompted a series of hypotheses on sex determination in this species since its first description by Matthey (1953). The developing knowledge about the sex chromosomes and sex determination as well as the availability of new cytogenetic and molecular genetic techniques prompted studies to test the compatibility between current hypotheses and new findings and rendered modifications of the hypotheses necessary. After a long period dominated by the question what the sex chromosome constitution of this species might be and where the testis determining factor could be located, the presence of Sry had been eventually excluded and sex determination attributed to a hypothetical mutated gene acting downstream of Sry. An X-chromosomal or autosomal location of this gene can be assessed by cosegregation of sex with X-chromosome markers. Some preliminary results concerning X-chromosome dinucleotide repeat markers are reported. However, these markers were homomorphic in Ellobius lutescens. We now report evidence that Zfy is also missing in Ellobius lutescens and E. tancrei (males and females XX), a finding from which we conclude that the entire Y chromosome has been lost from these species. Perspectives concerning future studies are discussed.
The serologically detected H-Y antigen revisited
Authors: Wolf U.
Published: April 2003

H-Y antigen has been defined by various immunological methods including graft rejection, T-cell mediated cytolysis, and antiserum cytotoxicity. The H-Y phenotype is normally associated with the male sex in mammals. Using specific T-cell clones, two Y-linked genes coding for H-Y epitopes have been identified in the mouse, Smcy and Uty, and one of these genes, SMCY, is also present on the human Y chromosome. Anti-H-Y antisera detect a membrane bound antigen associated with β2-microglobulin, and a soluble protein secreted by testicular Sertoli cells. The membrane bound antigen appears to be different from the peptides detected by cytotoxic T-cells, and for the soluble antigen evidence was provided that, in mammals it may be identical with anti-Müllerian hormone. In non-mammalian vertebrates, serological H-Y antigen is associated with the heterogametic sex, and sex-reversal of the homogametic sex results in the occurrence of H-Y antigen. Originally, H-Y antigen was believed to be responsible for sex determination, thus representing the testis-determining factor (TDF) in mammals, but this hypothesis has been disproved by showing that male gonadal differentiation can also occur (in the mouse) in the absence of H-Y antigen. In the meantime, SRY is considered to be TDF. Although it was revealed that the H-Y antigens as detected by different assays are genetically heterogeneous, they are probably involved in male-specific functions in mammals, and possibly in the differentiation of the heterogametic sex in non-mammalian vertebrates.
Asynchronous replication of homologous α-satellite DNA loci in man is associated with nondisjunction
Authors: Litmanovitch T. , Altaras M.M. , Dotan A. , Avivi L.
Published: April 2003

We tested the hypothesis that loss of replication control of DNA loci associated with human centromeres affects the main centromere function, namely, ensuring proper sister chromatid separation and accurate chromosomal segregation during cell division. Applying one-color fluorescence in situ hybridization (FISH) to interphase nuclei, we studied the replication patterns of homologous DNA loci associated with human centromeres (α-satellite sequences) of chromosome pairs 10, 11, 17, and X in PHA-stimulated lymphocytes of female cancer patients with a familial predisposition to malignancy and normal, healthy women. Concomitantly, we measured the rates of aneuploidy for these chromosomes in the same cells. To elucidate the replication patterns of the various centromeric loci, we analyzed the replication-dependent configuration signals obtained following FISH with four chromosome-specific α-satellite probes. Our data showed an association between replication timing of α-satellite sequences and centromeric function. Chromosome pairs whose homologous α-satellite loci replicated highly synchronously revealed low rates of aneuploidy, whereas chromosome pairs with a slightly asynchronous replication pattern (i.e., short intervals between early- and late-replicating loci) revealed intermediate rates of aneuploidy, and chromosome pairs exhibiting asynchrony with long-time intervals between early- and late-replicating loci showed the highest rate of aneuploidy.
Karyotype and chromosomal polymorphism of an undescribed Akodon from Central Brazil, a species with the lowest known diploid chromosome number in rodents
Authors: J. de Silva M.J. , Yonenaga-Yassuda Y.
Published: April 2003

The diploid chromosome number of 2n = 10 found in a new species of Akodon (Cricetidae, Rodentia) from two localities of the state of Mato Grosso, Central Brazil, represents the lowest chromosome number known for rodents. One female with nine chromosomes due to sex chromosome monosomy (2n = 9,XO) was also found. The karyotype comprises two large metacentric pairs (1 and 2); one large polymorphic pair (3), which could be acrocentric, submetacentric, or heterozygous as a result of a pericentric inversion; and one minute metacentric pair (4). The sex determination is of the XX/XY type. CBG, GTG, and RBG banding patterns, Ag-NORs, and meiotic data are presented. Fluorescence in situ hybridization with a (TTAGGG)7 repeat as a probe revealed interstitial telomeric bands (ITBs) in two of the large pairs.
Sex-chromosome elimination in the bandicoot Isoodon macrourus using Y-linked markers
Authors: Watson C.M. , Margan S.H. , Johnston P.G.
Published: April 2003

Cytogenetic studies have shown that the Y chromosome is eliminated from many somatic cell types of the bandicoot Isoodon macrourus, an Australian marsupial. Molecular techniques allow examination of a greater range of tissue types than that possible using cytogenetic techniques. The presence or absence of the Y chromosome was established using partial sequences of the Y-linked SRY and UBE1Y genes in I. macrourus, with the X-linked gene G6PD as a control. We show that a very small proportion of cells comprising hematopoietic tissues, and even fewer cells in peripheral blood, retain the Y chromosome. The Y chromosome is retained in most brain, liver, kidney, and lung cells and in cardiac and skeletal muscle. We also show that the bandicoot Y chromosome is retained in some cell types within tissues previously believed to completely eliminate the Y chromosome.
Human serine/threonine protein kinase EMK1: genomic structure and cDNA cloning of isoforms produced by alternative splicing
Authors: Espinosa L. , Navarro E.
Published: April 2003

The EMK (e̲LKL m̲otif K̲inase) is a small family of ser/thr protein kinases involved in the control of cell polarity, microtubule stability and cancer. We have isolated several cDNA clones that encoded two isoforms of the human ser/thr protein kinase EMK1 (GDB symbol EMK1, alias ELKL motif kinase 1, and MARK2). These isoforms were characterized by the presence of a 162-bp alternative exon that gave rise to two forms, one containing the exon and the other one lacking it. Both forms were found to be coexpressed in a number of selected cell lines and tissue samples when analyzed by RT-PCR. By Northern blot, human EMK1 was shown to be encoded by a single mRNA ubiquitously expressed. We have reconstructed most of the genomic structure of EMK1 from the sequence of two human chromosome 11 cosmids deposited in databases, and showed that the gene is composed of a minimum of 16 small exons.
An optimized, fully automated system for fast and accurate identification of chromosomal rearrangements by multiplex-FISH (M-FISH)
Authors: Eils R. , Uhrig S. , Saracoglu K. , Sätzler K. , Bolzer A. , Petersen I. , Chassery J.-M. , Ganser M. , Speicher M.R.
Published: April 2003

Multiplex-FISH (M-FISH) is a recently developed technique by which each of the two dozen human chromosomes—the 22 autosomes and the X and Y sex chromosomes—can be stained or “painted” with uniquely distinctive colors. Using a combinatorial labeling technique and a specially designed filter set, each DNA probe can be identified by its unique spectral signature. Here we present several significant optimizations of the M-FISH technology. First, a new strategy for labeling the probes is described which allows for easy and fast production of the complex M-FISH probe mix. Second, a newly developed, completely motorized microscope equipped with an eight-position filter wheel and a new generation of filter sets is presented that allows fully automatic imaging of a complete metaphase spread within seconds. Third, to determine the characteristic spectral signatures for all different combinations of fluorochromes, we developed a novel multichannel image analysis method. The spectral analysis is solely guided by the image information itself and does not require any user interaction. A complete analysis of a metaphase spread can be accomplished in less than 3 min. Sophisticated built-in quality controls were developed, and the value of visual inspection of M-FISH images as a simple means of controlling the computer-generated chromosome classification are illustrated. In addition, we discuss advantages of adding new fluorochromes to the traditionally used five fluorochromes.
Optimized mitogen stimulation induces proliferation of neoplastic B cells in chronic lymphocytic leukemia: significance for cytogenetic analysis
Authors: Larramendy M.L. , Siitonen S.M. , Zhu Y. , Hurme M. , Vilpo L. , Vilpo J.A. , Knuutila S.
Published: April 2003

We tested the effects of interleukin-2 (IL-2), human recombinant tumor necrosis factor alpha (TNF-α), Staphylococcus aureus Cowan I (SAC), TPA, and their combinations, using a standard thymidine incorporation assay, in order to identify an optimal mitogen combination (OMC) for 24 consecutive patients with B-cell chronic lymphocytic leukemia (B-CLL). The combination that induced the highest thymidine incorporation was chosen as the OMC for each patient. Among 14 mitogen combinations tested, there were six different OMCs, of which the most frequent was TNF-α + IL-2. It was the OMC in 9 of 24 cases. The other OMCs were TNF-α + TPA1 (5/24), SAC + IL-2 (5/24), TPA1 + IL-2 (3/24), TPA10 + IL-2 (1/24), and TNF-α + TPA10 + IL-1 (1/24). The mitogenic power of the selected OMC in each case was then evaluated both by the combination of immunophenotyping and molecular cytogenetic techniques known as MAC (Morphology, Antibody, Chromosomes) and standard chromosome analysis. After OMC stimulation, the levels of DNA synthesis and B-cell proliferation (mitotic index) were, on average, 10-fold higher than those observed after standard TPA stimulation (P < 0.0001). The proportion of mitotic B cells exceeded the proportion of mitotic T cells in 70.1% of the cases after OMC stimulation. After TPA stimulation, 7.7% ± 2.5% of all mitoses were B-cell mitoses, whereas after OMC stimulation this proportion rose to 57.9% ± 5.3%. The frequency of clonal chromosomal aberrations increased from 46% after TPA stimulation to 79% after OMC stimulation. The clonal aberrations del(6q), del(11q), and/or del(13q) were observed in 26%, 32%, and 42% of the patients with the respective clonal chromosomal aberrations, whereas the corresponding frequencies after TPA stimulation were only 4%, 21%, and 17%. When the lineage involvement of cells with clonal chromosomal aberrations from three patients was analyzed, the aberrations were found to be restricted to B cells only, and in one patient to a minor subset of B cells. The results demonstrate that an individually chosen OMC induces a high rate of proliferation in neoplastic B cells. We found deletions in 6q, 11q, and 13q at higher frequencies than reported previously, most probably as a result of an improved mitogenic response. The identification of an optimal mitogen stimulation for each patient, prior to chromosome analysis, can well be expected to reduce the rate of false-normal results in the future. This is essential for accurate evaluation of the prognostic significance of chromosomal aberrations in B-CLL.
Characteristics of chromosomes in polarized normal human bronchial cells provide a blueprint for nuclear organization
Authors: Koss L.G.
Published: April 2003

In normal human terminally differentiated and polarized bronchial cells, the fluorescent “painting” technique (FISH) for all chromosomes (except Y) documented that each homologue of each chromosome occupies a distinct, separate domain within the nucleus. The homologues are distributed along the nuclear membrane. In most cells and chromosomes studied, the two homologues were not identical: one was usually more “compact” than the other which was more “open,” displaying fiber-shaped extensions. The differences between the territories of homologues 1 and 7 were shown to be statistically valid (P < 0.0001 by Wilcoxon sign rank test), as has been previously documented for the two X chromosomes (Eils et al., 1996).In some parallel arrays of bronchial cells, the position of the chromosomes in the nuclei was either identical or formed a mirror image, suggesting that the position of the chromosomes in polarized nuclei may be constant. To confirm this observation, the angles formed by the two homologues in the polarized oval nuclei were measured for chromosomes 1, X, and 7. The measurements disclosed that, in about two-thirds of the nuclei, the two homologues formed angles of 150°, 157° and 148°, nearly identical to those formed by the same three chromosomes in prometaphase rosettes of cultured diploid human fibroblasts (Nagele et al., 1995). In about one third of the nuclei, the same homologues formed angles of 89°, 72°, and 94°, and occasionally an angle of 180°. A three-dimensional computer reconstruction of the nuclei was performed using the data for the X chromosomes. By cinematographic technique, it could be documented that the angles separating the two homologues depended on the rotation of the nucleus along the axes X, Y, and Z. The cause of the rotation is speculative at this time. Because of the concordance of these data in terminally differentiated epithelial cells with prior observations on prometaphases of human diploid fibroblasts, it is suggested that the position of chromosomes in all human cells is constant throughout the cell cycle. The possible significance of these observations is discussed.
Application of FISH for in situ detection and quantification of DNA breakage
Authors: Fernández J.L. , Goyanes V.J. , Ramiro-Díaz J. , Gosálvez J.
Published: April 2003

We describe a simple procedure that allows the use of fluorescence in situ hybridization (FISH) for in situ detection of DNA strand breaks in single cells (DBD-FISH: DNA Breakage Detection-FISH). After trapping within an agarose microgel, cells are incubated in an unwinding alkaline solution, deproteinized and dehydrated. Areas of single-stranded DNA are generated by the alkaline solution in proportion to the degree of DNA strand breakage. These then act as targets for FISH of whole genomic or region-specific probes (telomeric, human chromosome 8 painting, human alphoid DXZ1 locus, and human c-erbB-2 cosmid probes). Measurement of the amount and surface of FISH signals provides information on the breakage level in probed areas, permitting the assessment of possible intragenomic differences in sensitivity as well as intercellular heterogeneity in DNA damage induction or repair.
Rat tenascin-R gene: structure, chromosome location and transcriptional activity of promoter and exon 1
Authors: Leprini A. , Gherzi R. , Vecchi E. , Borsi L. , Zardi L. , Siri A.
Published: April 2003

Tenascin-R is an extracellular matrix protein expressed exclusively in the central nervous system where it is thought to play a relevant role in regulating neurite outgrowth. We have i) cloned the cDNA of the rat tenascin-R 5′ region; ii) defined its genomic organization, obtaining the sequence of two novel untranslated exons; iii) mapped the gene to rat chromosome 13q23 and suggested a previously unreported synteny between rat chromosome 13q23, human chromosome 1q24, and mouse chromosome 4E; and iv) sequenced and characterized the elements responsible for its neural cell-restricted transcription. We found that two discrete regions of the rat gene (the first in the proximal promoter, the second in the first exon) are independently able to activate to a high degree the transcription of a reporter gene in either human or rat neuroblastoma cell lines but not in other cell lines. Based on this observation, we re-evaluated the arrangement of transcriptionally active regions in the human tenascin-R gene we recently cloned and found that the human gene also contains an exon sequence able to initiate and sustain transcription independently of promoter sequences.
Characterisation and mapping of the human SOX14 gene
Authors: Arsic N. , Rajic T. , Stanojcic S. , Goodfellow P.N. , Stevanovic M.
Published: April 2003

SOX genes comprise a family of genes that are related to the mammalian sex determining gene SRY in the region that encodes the HMG-box domain responsible for the sequence-specific DNA-binding activity. SOX genes encode putative transcriptional regulators implicated in the decision of cell fates during development and the control of diverse developmental processes. We have cloned and characterised SOX14, a novel member of the human SOX gene family. Based on the HMG-box sequence, human SOX14 is a member of the B subfamily. SOX14 is expressed in human foetal brain, spinal cord and thymus, and like other members of the B subfamily, it might have a role in regulation of nervous system development. While other members of the B subfamily show similarity outside the HMG-box, the regions flanking the HMG box of the human SOX14 gene are unique. SOX14 has been mapped to human chromosome 3q22→ q23, close to the marker D3S1549. This location places SOX14 within a chromosome interval associated with two distinct syndromes that affect craniofacial development: Blepharophimosis-ptosis-epicantus inversus syndrome and Möbius syndrome.
Alternative splicing, genomic structure, and fine chromosome localization of REV3L
Authors: Morelli C. , Mungall A.J. , Negrini M. , Barbanti-Brodano G. , Croce C.M.
Published: April 2003

We have localized a human homolog, REV3L, of the Saccharomyces cerevisiae REV3 gene on chromosome region 6q21. The full-length cDNA consists of 10,919 nucleotides, with a putative open reading frame of 9,159 bp for a predicted protein of 3,053 amino acids. The gene contains 33 exons in about 200 kb of genomic DNA. In contrast to the previously reported sequence, an additional exon and an alternative splicing site are demonstrated.
Comparative gene mapping: cytogenetic localization of PROC, EN1, ALPI, TNP1, and IL1B in cattle and sheep reveals a conserved rearrangement relative to the human genome
Authors: Lòpez-Corrales N.L. , Sonstegard T.S. , Smith T.P.L.
Published: April 2003

The cytogenetic locations of the genes for protein C (PROC), transition protein 1 (TNP1), intestinal alkaline phosphatase (ALPI), engrailed (EN1), and human protointerleukin β (IL1B) have been compared between cattle (Bos taurus, BTA) and sheep (Ovis aries, OAR). Bovine YAC and cosmid clones were used as FISH probes to determine the order (centromere to telomere) of four of these genes on OAR 2q, as well as the location of IL1B on OAR 3p. In cattle, IL1B and EN1 were assigned to BTA 11 and BTA 2, respectively. Alignment of the ovine, bovine, and human physical maps based on these data shows that segments of conserved synteny and chromosomal rearrangements detected between cattle and human are also found in sheep, where the order in cattle is conserved.
Meiotic drive favors Robertsonian metacentric chromosomes in the common shrew (Sorex araneus, Insectivora, Mammalia)
Authors: Wyttenbach A. , Borodin P. , Hausser J.
Published: April 2003

Meiotic drive has attracted much interest because it concerns the robustness of Mendelian segregation and its genetic and evolutionary stability. We studied chromosomal meiotic drive in the common shrew (Sorex araneus, Insectivora, Mammalia), which exhibits one of the most remarkable chromosomal polymorphisms within mammalian species. The open question of the evolutionary success of metacentric chromosomes (Robertsonian fusions) versus acrocentrics in the common shrew prompted us to test whether a segregation distortion in favor of metacentrics is present in female and/or male meiosis. Performing crosses under controlled laboratory conditions with animals from natural populations, we found a clear trend toward a segregation distortion in favor of metacentrics during male meiosis, two chromosome combinations (gm and jl) being significantly preferred over their acrocentric homologs. Apart for one Robertsonian fusion (hi), this trend was absent in female meiosis. We propose a model based on recombination events between twin acrocentrics to explain the difference in transmission ratios of the same metacentric in different sexes and unequal drive of particular metacentrics in the same sex. Pooled data for female and male meiosis revealed a trend toward stronger segregation distortion for larger metacentrics. This is partially in agreement with the frequency of metacentrics occurring in natural populations of a chromosome race showing a high degree of chromosomal polymorphism.
Human outer dense fiber gene, ODF2, localizes to chromosome 9q34
Authors: Shao X. , Murthy S. , Demetrick D.J. , van der Hoorn F.A.
Published: April 2003

We have isolated the human homolog of the rat Odf2 gene. In rat, Odf2, the 84-kDa major outer dense fiber protein, interacts strongly and specifically with Odf1, the 27-kDa major outer dense fiber protein. The interaction is mediated by leucine zippers during ODF assembly along the sperm axoneme. We compared homology and genomic structure to rat and mouse Odf2 genes. Using fluorescence in situ hybridization, we mapped the human Odf2 gene (ODF2) to chromosome 9q34.
Conservation of pericentromeric duplications of a 200-kb part of the human 21q22.1 region in primates
Authors: Orti R. , Potier M.C. , Maunoury C. , Prieur M. , Créau N. , Delabar J.M.
Published: April 2003

We analyzed the conservation of large paralogous regions (more than 200 kb) on human chromosome regions 21q22.1 and 21q11.2 and on pericentromeric regions of chromosomes 2, 13, and 18 in three nonhuman primate species. Orthologous regions were found by FISH analysis of metaphase chromosomes from Gorilla gorilla, Pan troglodytes, and Pongo pygmaeus. Only one orthologous region was detected in chromosomes of P. pygmaeus, showing that the original locus was at 21q22.1 and that the duplication arose after the separation of Asian orangutans from the other hominoids. Surprisingly, the paralogous regions were more highly conserved in gorilla than in chimpanzee. PCR amplification of STSs derived from sequences of the chromosome 21 loci and low-stringency FISH analysis showed that this duplication occurred recently in the evolution of the genome. Different rates of sequence evolution through substitutions or deletions, after the duplication, may have resulted in diversity between closely related primates.
GCMB, a second human homolog of the fly glide/gcm gene
Authors: Kammerer M. , Pirola B. , Giglio S. , Giangrande A.
Published: April 2003

Glial cells play fundamental roles in neurogenesis. In addition, defective or abnormal gliogenesis is associated with severe diseases. To understand the molecular basis of such diseases, it is crucial to identify the genes promoting normal gliogenesis. Here we identify GCMB, which encodes a human protein homologous to the fly glial promoting factor glial cell deficient/glial cell missing (glide/gcm).
HOX11L1, a gene involved in peripheral nervous system development, maps to human chromosome 2p13.1→p12 and mouse chromosome 6C3–D1
Authors: Puliti A. , Cinti R. , Betsos N. , Romeo G. , Ceccherini I.
Published: April 2003

HOX11L1 is a homeobox gene involved in peripheral nervous system development as confirmed by knockout mice exhibiting megacolon with enteric ganglia, a phenotype associated in human with Intestinal Neuronal Dysplasia (IND). Using FISH and radiation hybrids we have localized HOX11L1 to human chromosome 2p13.1→p12, in a 14-cR interval between WI-5987 (D2S2088) and GCT1B4 (D2S2497), and confirmed the synteny between mouse 6C3–D1 and human 2p13.1→p12 chromosomes by mapping an EST cDNA clone corresponding to mouse HOX11L1 (Tlx2).
Comparative FISH-mapping of six expressed gene loci to river buffalo and sheep chromosomes
Authors: Iannuzzi L. , Gallagher Jr. D.S. , Di Meo G.P. , Yang Y. , Womack J.E. , Davis S.K. , Taylor J.F.
Published: April 2003

Six expressed gene loci (NF1, CRYB1, CHRNB1, TP53, P4HB and GH1), recently assigned to cattle chromosome 19 by both radiation hybrid analysis and FISH-mapping, were comparatively FISH-mapped to river buffalo chromosome (BBU) 3p and sheep chromosome (OAR) 11, extending the physical map in these two important bovids. The six loci mapped to the same homoeologous chromosome bands of BBU 3p and OAR 11, and their gene order was centromere–NF1–CRYB1–CHNRB1–TP53–(GH1, P4HB).
Characterization of the human laminin β2 chain locus (LAMB2): linkage to a gene containing a nonprocessed, transcribed LAMB2-like pseudogene (LAMB2L) and to the gene encoding glutaminyl tRNA synthetase (QARS)
Authors: Durkin M.E. , Jäger A.C. , Khurana T.S. , Nielsen F.C. , Albrechtsen R. , Wewer U.M.
Published: April 2003

The laminin β2 chain is an important constituent of certain kidney and muscle basement membranes. We have generated a detailed physical map of a 110-kb genomic DNA segment surrounding the human laminin β2 chain gene (LAMB2) on chromosome 3p21.3→p21.2, a region paralogous with the chromosome 7q22→q31 region that contains the laminin β1 chain gene locus (LAMB1). Several CpG islands and a novel polymorphic microsatellite marker (D3S4594) were identified. The 3′ end of LAMB2 lies 16 kb from the 5′ end of the glutaminyl tRNA synthetase gene (QARS). About 20 kb upstream of LAMB2 we found a gene encoding a transcribed, non-processed LAMB2-like pseudogene (LAMB2L). The sequence of 1.75 kb of genomic DNA at the 3′ end of LAMB2L was similar to exons 8–12 of the laminin β2 chain gene. The LAMB2L–LAMB2–QARS cluster lies telomeric to the gene encoding the laminin-binding protein dystroglycan (DAG1).
Molecular cloning and characterization of the tumor transforming gene (TUTR1): a novel gene in human tumorigenesis
Authors: Kakar S.S. , Jennes L.
Published: April 2003

We cloned and sequenced the cDNA of a potent tumor transforming gene (TUTR1) from human testis and determined its primary structure. The TUTR1 cDNA is composed of 656 nucleotides and encodes a novel protein of 202 amino acids. The predicted TUTR1 protein is extremely hydrophilic and contains two proline-rich motifs at its C-terminus. Northern blot analysis of the mRNA from various human tissues and tumors revealed that TUTR1 mRNA is highly expressed in tumors of the pituitary gland, adrenal gland, ovary, endometrium, liver, uterus, and kidney as well as in cell lines derived from tumors of the pituitary, breast, endometrium, and ovary. With the exception of the testis, the levels of TUTR1 mRNA were either very low or undetectable in normal human tissues. Overexpression of TUTR1 in mouse fibroblasts (NIH 3T3) cells resulted in an increase in cell proliferation, induced cellular transformation in vitro, and promoted tumor formation in nude mice. These results suggest that TUTR1 is a novel and potent transforming gene, which may be involved in tumorigenesis in numerous different human tumors.
Comparative cytogenetic mapping of COL14A1, the gene for human and mouse collagen XIV
Authors: Imhof M. , Trueb B.
Published: April 2003

Utilizing the FISH technique, the gene for collagen XIV was mapped in the human and the mouse genome. The human gene (COL14A1) was assigned to chromosome bands 8q23→q24.1. This assignment is in agreement with the localization of the undulin gene (UND), whose product has been suggested to be a variant of collagen XIV. The mouse gene (Col14a1) was assigned to chromosome 15 band D. Thus, collagen XIV represents another example of a gene that belongs to human/mouse homology group 90.
Abnormal methylation does not prevent X inactivation in ICF patients
Authors: Bourc’his D. , Miniou P. , Jeanpierre M. , Molina Gomes D. , Dupont J.-M. , De Saint-Basile G. , Maraschio P. , Tiepolo L. , Viegas-Péquignot E.
Published: April 2003

DNA undermethylation is a characteristic feature of ICF syndrome and has been implicated in the formation of the juxtacentromeric chromosomal abnormalities of this rare syndrome. We have previously shown that in female ICF patients the inactive X chromosome (Xi) is also undermethylated. This result was unexpected since female ICF patients are not more severely affected than male patients. Here we show that CpG island methylation is abnormal in some ICF patients but in other ICF patients, the difference in methylation pattern between Xi and Xa (active X) is maintained. The consequences of Xi undermethylation on gene expression were investigated by enzyme assays. They showed that significant gene expression did not correlate with CpG island methylation status. The widespread Xi undermethylation does not affect overall Xi replication timing and does not prevent Barr body formation suggesting that a normal methylation pattern is not required for normal chromatin organization of Xi. Molecular investigation of some X-chromosome intron regions showed that the methylation changes in ICF female patients extend to non CpG islands sequences. Our results suggest that the genetic alteration of DNA methylation in ICF syndrome has little consequence on X chromosome gene expression and chromatin organization.
Standard G-, Q-, and R-banded ideograms of the domestic sheep (Ovis aries): homology with cattle (Bos taurus). Report of the committee for the standardization of the sheep karyotype
Authors: Ansari H.A. , Bosma A.A. , Broad T.E. , Bunch T.D. , Long S.E. , Maher D.W. , Pearce P.D. , Popescu C.P.
Published: April 2003

Revised G-, Q- and R-banded karyotypes and ideograms for sheep chromosomes at the 420-band level of resolution are presented. The positions of landmark bands on the sheep chromosomes are defined by their distance relative to the centromere to facilitate comparison with equivalent cattle chromosomes. Chromosome-specific (reference) molecular markers that have been mapped to sheep chromosomes and their equivalent cattle chromosomes are proposed. Reference markers will facilitate genome comparisons between sheep and cattle and minimise confusion due to chromosome nomenclature. Numbering of the Robertsonian translocation chromosomes remains as previously reported.
Aneuploidy in pig sperm: multicolor fluorescence in situ hybridization using probes for chromosomes 1, 10, and Y
Authors: Rubeš J. , Vozdová M. , Kubíčková S.
Published: April 2003

The objective of this research was to develop chromosome-specific probes for use in evaluating aneuploidy in boar spermatozoa through the application of fluorescence in situ hybridization (FISH) technology. A multicolor FISH method was developed to detect aneuploidy in the sperm of boars using DNA probes specific for small regions of chromosomes 1, 10, and Y. The average frequencies of sperm with disomy for chromosomes 1, 10, and Y were 0.075%, 0.067%, and 0.094%, respectively. The incidence of disomy did not differ significantly by chromosome. The average frequencies of diploidy were 0.177% for 1-1-10-10 and 0.022% for Y-Y-10-10. Thus, the incidence of overall diploidy (1-1-10-10) was significantly higher than that of disomy for the chromosomes examined (P < 0.01 for disomy of the autosomes and P < 0.05 for disomy of the Y chromosome). No significant age or breed effects on disomy and diploidy rates and no significant interindividual variations in disomy or diploidy were found. The observed level of numerical chromosome aberrations in pig sperm appear to be within the range of the baseline frequencies reported so far in men.
Construction of a swine BAC library: application to the characterization and mapping of porcine type C endoviral elements
Authors: Rogel-Gaillard C. , Bourgeaux N. , Billault A. , Vaiman M. , Chardon P.
Published: April 2003

A porcine bacterial artificial chromosome (BAC) library was constructed using the pBeloBAC11 vector. It comprised 107,520 clones with an average insert size of 135 kb, representing an almost fivefold coverage of the swine haploid genome. Screening of the library allowed recovery of one to eight clones for 142 unique markers located all over the genome, while it failed for only one marker. About 4% chimeric clones were found. The library was also screened for the protease gene of type C porcine endoviral sequences (PERVs), and 62 clones were recovered, all but two of which contained one protease gene. We found 20 protease sequences (PERV-1 to PERV-20) which, despite differing by point mutations, were all coding sequences. The most frequent sequence, PERV-2, was 100% similar to a protease sequence expressed in the porcine PK-15 cell line. Most of the clones harbored envelope genes. Thirty-three BAC clones were mapped by fluorescence in situ hybridization to 22 distinct locations on 14 chromosomes, including the X and Y chromosomes. These overall results indicate that there is generally one PERV copy per integration site. Although PERV sequences were not tandemly arranged, clusters of integration sites were observed at positions 3p1.5 and 7p1.1. Southern blot experiments revealed 20–30 PERV copies in the Large White pig genome studied here, and variations in PERV content among pigs of different breeds were observed. In conclusion, this BAC collection represents a significant contribution to the swine large genomic DNA cloned insert resources and provides the first detailed map of PERV sequences in the swine genome. This work is the first step toward identification of potential active sites of PERV elements.
Physical assignment of the bovine MHC class IIa and class IIb genes
Authors: Heß M. , Goldammer T. , Gelhaus A. , Ried K. , Rappold G. , Eggen A. , Bishop M.D. , Schwerin M. , Horstmann R.D.
Published: April 2003

Screening of a bovine yeast artificial chromosome (YAC) library revealed two clones which contain most of the class II genes of the major histocompatibility complex (MHC) known to date. The YACs were mapped by fluorescence in situ hybridization (FISH) and characterized for the class II genes they contain. We found that the classic class II genes BoLA- DQA, -DQB, -DRA, and -DRB3 are located at BTA 23q21 and the non-classic class II genes DYA, DIB, LMP2, LMP7, TAP2, BoLA-DOB, -DMA, -DMB, and -DNA are located at BTA 23q12→q13. These two different mapping locations confirm and extend previous findings of a gross physical distance between classic and non-classic MHC class II genes in cattle.
Identification of GTF2IRD1, a putative transcription factor within the Williams-Beuren syndrome deletion at 7q11.23
Authors: Franke Y. , Peoples R.J. , Francke U.
Published: April 2003

Williams-Beuren syndrome (WBS) is a microdeletion syndrome caused by haploinsufficiency of genes at 7q11.23. Here we describe the identification and characterization of a novel gene named GTF2IRD1, for GTF2I-repeat domain 1, within the WBS deletion region. Northern blot analysis revealed ubiquitous expression during development with two transcripts of 3.6 kb and 5.0 kb generated by alternative splicing. GTF2IRD1 encodes a protein of 944 amino acids that contains a region of high similarity to a unique motif with helix-loop-helix forming potential occurring within the transcription factor GTF2I. Analogous to TFII-I, the product of GTF2IRD1 may have the ability to interact with other HLH-proteins and function as a transcription factor or as a negative transcriptional regulator. A recent report of the identification of a muscle-specific transcription factor, MusTRD1, supports this hypothesis (O’Mahoney et al., 1998). The open reading frame described for MusTRD1 is identical to that of GTF2IRD1; however, the putative MusTRD1-protein is 486 amino acids shorter than the predicted protein encoded by GTF2IRD1. A heterozygous deletion of GTF2IRD1 may contribute to the complex WBS phenotype.
Complete homology maps of the rabbit (Oryctolagus cuniculus) and human by reciprocal chromosome painting
Authors: Korstanje R. , O’Brien P.C.M. , Yang F. , Rens W. , Bosma A.A. , van Lith H.A. , van Zutphen L.F.M. , Ferguson-Smith M.A.
Published: April 2003

Fluorescence in situ hybridization (FISH) was used to construct a homology map to analyse the extent of evolutionary conservation of chromosome segments between human and rabbit (Oryctolagus cuniculus, 2n = 44). Chromosome-specific probes were established by bivariate fluorescence activated flow sorting followed by degenerate oligonucleotide-primed PCR (DOP-PCR). Painting of rabbit probes to human chromosomes and vice versa allowed a detailed analysis of the homology between these species. All rabbit chromosome paints, except for the Y paint, hybridized to human chromosomes. All human chromosome paints, except for the Y paint, hybridized to rabbit chromosomes. The results obtained revealed extensive genome conservation between the two species. Rabbit chromosomes 12, 19 and X were found to be completely homologous to human chromosomes 6, 17 and X, respectively. All other human chromosomes were homologous to two or sometimes three rabbit chromosomes. Many conserved chromosome segments found previously in other mammals (e.g. cat, pig, cattle, Indian muntjac) were also found to be conserved in rabbit chromosomes.
Familial adenomatous polyposis: from bedside to bench and vice versa
Authors: Griffioen, G. , Vasen, H.F.A. , Verspaget, H.W. , Lamers C.B.H.W.
Published: April 2003

Familial adenomatous polyposis (FAP) is characterized by the presence of numerous adenomatous polyps in the colorectum, as well as an autosomal dominant mode of inheritance. This syndrome will inevitably lead to colorectal cancer when left untreated, and it is estimated that 1% of all colorectal cancer cases are due to it. Over the past 20 years molecular genetic studies on FAP patients have laid down the basis for the elucidation of the genetic phenomena that ultimately result in the development of colorectal cancer. Professor P. Meera Khan was one of the leading authorities in the world of molecular genetics of colorectal cancer in general and of FAP in particular. His scientific contributions from the pre-DNA era up to the recent implementation of molecular genetic research in daily clinical practice have helped revolutionize our approach and management of FAP patients and their relatives.
Genome-wide allelotyping indicates increased loss of heterozygosity on 9p and 14q in early age of onset colorectal cancer
Authors: Weber T.K. , Conroy J. , Keitz B. , Rodriguez-Bigas M. , Petrelli N.J. , Stoler D.L. , Anderson G.R. , Shows T.B. , Nowak N.J.
Published: April 2003

Colorectal cancer remains a significant public health challenge, despite our increased understanding of the genetic mechanisms involved in the initiation and progression of this disorder. It has become clear that multiple mechanisms lead to the tumorigenic phenotype, with familial predisposition syndromes accounting for less than 15% of all colorectal cancers. A genome-wide scan for loss of heterozygosity (LOH) was carried out with 150 highly polymorphic markers in an effort to identify additional loci involved in colorectal tumorigenesis in DNA samples from 42 colorectal cancer patients. The results confirm earlier observations that tumor DNAs from patients with hereditary nonpolyposis colon cancer (HNPCC) either maintain heterozygosity or exhibit altered or additional alleles. DNAs from patients with early onset colorectal carcinomas (diagnosed prior to age 50) revealed a higher overall degree of LOH than DNAs from patients with sporadic colorectal cancers diagnosed later in life (after age 50). While regions on 1p, 10q and 14q are suggestive, statistical analysis of LOH at these regions failed to reach significance. However, LOH at 9p did reveal a statistically significant increase in the early onset patient group, compared to the greater than age 50 group. LOH on 9p may involve inactivation of p16/CDKN2 through aberrant DNA methylation on the remaining chromosome, resulting in a situation analogous to a homozygous deletion of p16 and providing a selective growth advantage to these cells. This marker may prove to be a useful prognostic indicator for patient stratification in the design of therapy for early onset colorectal cancer patients.
Genomic structure, alternative transcripts and chromosome location of the human LIM domain binding protein 1 gene LDB1
Authors: Drechsler M. , Schumacher V. , Friedrich S. , Wildhardt G. , Giesler S. , Schroth A. , Bodem J. , Royer-Pokora B.
Published: April 2003

By protein interaction screening using a radioactive LMO2 protein probe we have isolated a LIM domain binding protein. The gene shows high homology to independently isolated genes from mouse, Xenopus and Drosophila called Ldb1/Nli/Clim-2, Xldb1 and Chip, respectively. The human and mouse genes differ by only two amino acids, suggesting that the gene that we have isolated is the human homologue. Here we describe the genomic organization, alternative transcript forms and the chromosome mapping of the human gene LDB1 (alias NLI). The gene is spread over at least 12 kb and has 11 exons. Preceding the described ATG initiation site in the mouse a highly conserved region between mouse, chicken and human was detected with a second possible in frame initiation site coding for further 36 amino acids. An alternative splice site adding six nucleotides corresponding to the addition of two amino acids at the end of exon 10 was found. The gene was mapped to chromosome 10q24→q25 by in situ hybridization, a region frequently deleted in many types of cancer. Fine mapping with a radiation hybrid panel localized the gene in the interval between the markers D10S603 and D10S540.