bluuebunny/crossref_metadata_2025 huggingface dataset:
Murine and human TSPYL genes: novel members of the TSPY-SET-NAP1L1 family
Authors: Vogel T. , Dittrich O. , Mehraein Y. , Dechend F. , Schnieders F. , Schmidtke J.
Published: April 2003

Using expressed sequence tag (EST) sequence information, novel genes related to the Y chromosome gene family TSPY were isolated and characterized. Because of a significant homology to TSPY, the novel genes were designated TSPY-Like (TSPYL) and were assigned as new members of the TSPY-SET-NAP1L1 family. A human TSPYL gene was localized on chromosome 6 and a murine Tspyl gene was localized on chromosome 10. Expression of TSPYL was observed in all tissues investigated, as well as early onset during development. Both the human and murine Tspyl homologs lack introns over the entire region so far investigated and are thought to have arisen by an ancient retroposition event. Retroposition of Tspyl genes is supported by the isolation of a murine Tspyl pseudogene on chromosome 12 which also lacks intronic sequences, and by its observed proximity to an R element, a family of dispersed repetitive DNA.
The INSL4 gene maps close to WI-5527 at 9p24.1→p23.3 clustered with two relaxin genes and outside the critical region for the monosomy 9p syndrome
Authors: Veitia R. , Laurent A. , Quintana-Murci L. , Ottolenghi C. , Fellous M. , Vidaud M. , McElreavey K.
Published: April 2003

The insulin like growth factor 4 (INSL4) gene belongs to the insulin gene superfamily and has been mapped by fluorescent in situ hybridization to 9p24. Expression of INSL4, of unknown function, has been recently detected in the perichondrium and ligaments of the human embryo. Here we have mapped INSL4 within the framework of a partial YAC contig covering the distal part of 9p to find out whether this gene lies within the critical region defined for the monosomy 9p syndrome. The gene was also located using a human-rodent radiation hybrid panel. INSL4 was found to be distal to the del(9p) critical region and excluded as a candidate for the syndrome. In addition, the positions of two relaxin genes (RLN1, RLN2) that belong to the same superfamily as INSL4 and which have also been mapped to chromosome 9, were refined. We have shown that the three genes are clustered in the same region.
Pathogenetics of 45,X/46,XY gonadal mosaicism
Authors: Reddy K.S. , Sulcova V.
Published: April 2003

Five patients with 45,X/46,XY mosaicism ranging from 8% to 66% of 46,XY lymphocytes in the peripheral blood were studied. Their age when chromosome studies were performed ranged from a few days to 37 yr. The phenotypic presentations were two females with gonadal dysgenesis and Turner syndrome features (cases 1 and 2), two males with ambiguous genitalia and mixed gonadal dysgenesis (cases 3 and 4), and an infertile male with an atrophic testis (case 5). Fluorescence in situ hybridization (FISH) using dual-color X and Y probes on paraffin-embedded sections of the gonads was performed to assess mosaicism. A mosaic cell line with a Y chromosome was present in the streak ovary, dysgenetic gonad, and testis. In the mixed gonadal dysgenesis cases (cases 3 and 4), the testis had a higher percentage (greater than two fold) of XY cells than the ovary had. However, the highest ratio of cells with a Y chromosome was in the atrophic testis of the infertile male (case 5). The distribution of mosaic clones in the different gonadal cell types was examined. Both females (cases 1 and 2) with dysgenetic gonads had scant ovarian stroma and nests of Leydig or hilus cells. In FISH studies, the coelomic epithelial cells were predominantly 46,XY; in comparison, the Leydig and hilus cells had a lower percentage and the ovarian stroma the least number of cells with a Y signal. A mixed gonadal dysgenesis case (case 3) possessed a right testis with an XY complement in ∼21% of Sertoli cells and ∼14% of Leydig cells. The infertile male had an atrophic testis with interstitial hyperplasia (case 5). His testis contained Sertoli cells but no evidence of spermatogenesis. FISH detected a Y signal in about 50–60% of the Sertoli and Leydig cells.
Position effect of translocations involving the inactive X chromosome: physical linkage to XIC/XIST does not lead to long-range de novo inactivation in human differentiated cells
Authors: Surrallés J. , Natarajan A.T.
Published: April 2003

Given the reported long-range cis-inactivating effect of the XIST gene in early embryonic development and the lack of requirement of X-chromosome-specific elements for propagating the inactive state, there exists the possibility of cis inactivation of autosomal material after de novo translocation to an inactive X chromosome (Xi) in differentiated cells. We have analyzed de novo radiation-induced translocations between the Xi and autosomes to study the maintenance and spreading of X-chromosome inactivation (X inactivation) in relation to the position of the X-inactivation center (XIC)/XIST in differentiated cells. Autosome/Xi translocations were detected by fluorescence in situ hybridization (FISH). The activation status of the chromosomes involved in the translocation was determined by simultaneous immunocytogenetic studies using antibodies against either BrdU incorporated at late S phase or acetylated histone H4. The position of XIC/XIST in the reciprocal products of the translocation was determined by XIST-specific FISH and computer enhancement. In other experiments, the Xq13 region carrying XIC/XIST was localized by computer enhancement of the DAPI banding pattern. Our study in differentiated cells provides a visual demonstration that physical separation from XIC/XIST does not result in reactivation of inactive X-chromosome material and that X inactivation is not spread to the translocated autosomes irrespective of the position of XIC/XIST. This observation suggests that physical linkage to XIC/XIST does not lead to de novo inactivation of autosomal material.
Structure and chromosome mapping of the human small maf genes MAFG and MAFK
Authors: Iwata T. , Kogame K. , Toki T. , Yokoyama M. , Yamamoto M. , Ito E.
Published: April 2003

The newly emerged Maf family proteins possess a highly conserved basic leucine zipper (bZip) domain in common and are subdivided into large and small Maf proteins. The Maf family proteins appear to regulate cell differentiation processes and also cellular functions as partner molecules of CNC family proteins. To facilitate understanding of the function of small Maf proteins, we isolated the genes (MAFG and MAFK) encoding human small Maf proteins MafG and MafK and characterized their structures and organization by means of restriction enzyme mapping, Southern blot hybridization and nucleotide sequence analysis. Organization of the small maf genes are highly conserved in vertebrates, suggesting an important functional contribution of the gene products. We also examined the location of these genes within the human genome by fluorescence in situ hybridization (FISH) analysis. Human MAFG and MAFK are located at 17q25 and 7p22, respectively. Thus, small maf genes are not clustered in a single locus.
Autosomal-dominant, prelingual, nonprogressive sensorineural hearing loss: localization of the gene (DFNA8) to chromosome 11q by linkage in an Austrian family
Authors: Kirschhofer K. , Kenyon J.B. , Hoover D.M. , Franz P. , Weipoltshammer K. , Wachtler F. , Kimberling W.J.
Published: April 2003

A four-generation family suffering from an autosomal-dominant, congenital, nonprogressive, nonsyndromic hearing loss was found in a rural region of Austria. The hearing loss was moderate to severe, a pure tone audiogram showing a U-shaped form with maximum loss at 2,000 Hz. An initial genome search led to a lod score of 3.01 with markers on chromosome 15. This locus was registered as DFNA8 in the HUGO data base. Further sampling of the family, however, yielded data that reduced the maximal lod score with chromosome 15 markers to 1.81. The genome search was restarted using an ABITM genotyper, which eventually detected several positive two-point lod scores with markers from the long arm of chromosome 11. The highest value was 3.6, which was seen with the marker D11S934. Haplotype analysis excluded the gene from the chromosomal region proximal from D11S898 and distal to D11S1309. These results place the gene in the region of the hearing loss gene DFNA12. Recent evidence suggests that the somewhat different phenotypes found in these two families are due to two different mutations in the human α-tectorine gene (Verhoeven et al., 1998).
Identification and characterization of STK12/Aik2: a human gene related to aurora of Drosophila and yeast IPL1
Authors: Kimura M. , Matsuda Y. , Yoshioka T. , Sumi N. , Okano Y.
Published: April 2003

Mutations in aurora of Drosophila and related Saccharomyces cerevisiae IPL1 protein kinases are known to cause abnormal chromosome segregation. We earlier isolated a cDNA encoding a novel human protein kinase Aik which shares high amino acid identity with the Aurora/Ipl1 protein kinase family. In the present study, a second human cDNA highly homologous to aurora/IPL1 (Aik2) was identified and the nucleotide sequence was determined (gene symbol STK12). The C-terminal kinase domain of the STK12 encoded protein shares high amino acid sequence identity with those of mouse STK-1 (90%), rat AIM-1 (90%), human Aik (69%), mouse IAK1/Ayk1 (69%), Xenopus pEg2 (68%), Drosophila Aurora (62%), and yeast Ipl1 (45%), whereas the N-terminal domain of the STK12 protein shares little homology with those of Aurora/Ipl1 family members except for AIM-1 and STK-1. Northern blotting analyses revealed that STK12 expression was high in thymus, while low level expression was detected in small intestine, testis, colon, spleen, and brain. The STK12 protein content in HeLa cells is low in S phase, but it accumulates during M phase. STK12 was mapped to human chromosome 17p13.1 by fluorescence in situ hybridization. The chromosome location of STK12 was further defined using a radiation hybrid panel (Stanford G3), that showed a linkage with marker WI-7901 (LOD Score 7.83) located between D17S938 and D17S786.
Molecular cytogenetic mapping of 24 CEPH YACs and 24 gene-specific large insert probes to chromosome 17
Authors: Bärlund M. , Nupponen N.N. , Karhu R. , Tanner M.M. , Paavola P. , Kallioniemi O.-P. , Kallioniemi A.
Published: April 2003

Defining boundaries of chromosomal rearrangements at the molecular level would benefit from landmarks that link the cytogenetic map to physical, genetic, and transcript maps, as well as from large-insert FISH probes for such loci to detect numerical and structural rearrangements in metaphase or interphase cells. Here, we determined the locations of 24 genetically mapped CEPH-Mega YACs along the FLpter scale (fractional length from p-telomere) by quantitative fluorescence in situ hybridization analysis. This generated a set of cytogenetically mapped probes for chromosome 17 with an average spacing of about 5 cM. We then developed large-insert YAC, BAC, PAC, or P1 clones to the following 24 known genes, and determined refined map locations along the same FLpter scale: pter–TP53–TOP3–cen–TNFAIP1–ERBB2–TOP2A–BRCA1–TCF11–NME1–HLF–ZNF147/CLN80–BCL5/MPO/SFRS1–TBX2–PECAM1–DDX5/PRKCA–ICAM2–GH1/PRKAR1A–GRB2–CDK3/FKHL13–qter. Taken together, these 48 cytogenetically mapped large-insert probes provide tools for the molecular analysis of chromosome 17 rearrangements, such as mapping amplification, deletion, and translocation breakpoints in this chromosome, in cancer and other diseases.
Evidence of a differential organization of chromatin containing terminal or interstitial (TTAGGG)n repeats by in situ digestion with nucleases
Authors: Fernández J.L. , Goyanes V.J. , Ramiro-Díaz J. , Gosálvez J.
Published: April 2003

(TTAGGG)n sequence repeats in human telomeres and in Chinese hamster interstitial centromeric areas were digested in situ with exonuclease III (ExoIII) and exonuclease Bal 31. Incubation with AluI was performed beforehand to increase DNA breaks near telomere sequence areas. DNA removal at these specific regions was quantified by digital image analysis of the fluorescence in situ hybridization signal produced by a telomeric probe. Exonuclease III was 2.6 times more active in interstitial than in terminal telomeric sequence areas. Exonuclease Bal 31 was 2.3 times more effective in terminal than in interstitial telomeric sequence regions. These results support the hypothesis that chromatin is differentially organized in both telomeric sequence areas, despite their similar DNA composition.
Identification of the sex chromosomes of the medaka, Oryzias latipes, by fluorescence in situ hybridization
Authors: Matsuda M. , Matsuda C. , Hamaguchi S. , Sakaizumi M.
Published: April 2003

In the medaka, Oryzias latipes, which does not have cytologically recognizable sex chromosomes, the sex is genetically determined and the mechanism of sex determination (XX/XY) can be revealed by genetic crosses using a particular pigment gene. In a previous study, we isolated a sex-linked DNA marker (SL1) using the genomic differences between inbred strains of medaka. In the present paper, we further isolated another sex-linked clone (pHO5.110). The pHO5.110-related sequences were tightly linked to sex in O. latipes. We designated the locus of the pHO5.110-related sequence on sex chromosomes of medaka as Sex-Linked 2 (SL2). Southern blot analyses suggested that the pHO5.110-related sequence was tandemly repetitive in the medaka genome. Using the clone as a probe for FISH analysis, strong hybridization signals were obtained in a couple of chromosomes that formed one of two large submetacentric chromosome pairs. The pHO5.110-related sequences were repetitive in the genomes of other species of Oryzias (O. curvinotus, O. luzonensis and O. mekongensis) that are karyologically related to O. latipes (all are members of the so-called biarmed group). By contrast, the sequences were not detected as repetitive in other Oryzias species. Hence, it is thought that pHO5.110-related sequences were amplified in the genome of a common ancestor of the biarmed group.
Karyotype evolution of marsupials: from higher to lower diploid numbers
Authors: Svartman M. , Vianna-Morgante A.M.
Published: April 2003

A basic 2n = 14 ancestral marsupial karyotype giving rise to higher diploid numbers through chromosome fissions has been widely accepted for the last three decades. Our finding of interstitial telomeres in two South American species, one with the 2n = 14 “ancestral karyotype” and the other with 2n = 18, indicates that these complements evolved from a karyotype with a higher diploid number. A new scenario for the karyotype evolution in the group is put forward. In this scenario an ancestral karyotype with at least 22 chromosomes would have originated the basic karyotype with 2n = 14 before the radiation of marsupials.
Comparative genomic hybridization and its application to Wilms’ tumorigenesis
Authors: Getman M.E. , Houseal T.W. , Miller G.A. , Grundy P.E. , Cowell J.K. , Landes G.M.
Published: April 2003

Eighty sporadic Wilms’ tumor samples were analyzed by comparative genomic hybridization (CGH) to identify chromosomal regions involved in the etiology of the disease. Twenty percent of the samples showed chromosomal gains or losses. The majority of chromosomal gains and losses were similar to those identified through molecular and cytogenetic studies. Gains were observed on chromosomes 1q, 7q, 8, and 12, whereas losses were found on chromosomes 1p, 4p, 4q, 7p, 16q, 18q, 21q, and 22q. Other genetic aberrations identified in this study included deletions of chromosomes 5p and 15q, as well as gains of discrete loci on chromosomes 3p and 3q. These latter regions have not been previously implicated in Wilms’ tumorigenesis and may contain novel genes relevant to the development and/or progression of this disease.
Differential destabilization of repetitive sequence hybrids in fluorescence in situ hybridization
Authors: Hozier J.C. , Scalzi J.M. , Clase A.C. , Davis L.M. , Liechty M.C.
Published: April 2003

A method for painting a chromosome or chromosome region by fluorescence in situ hybridization (FISH) without blocking DNA is described. Both unique sequence and repetitive sequence components of a fluorescently labeled probe are hybridized under low-stringency conditions, but the chromosomes are washed in such a manner that repetitive sequences are differentially removed, while region-specific unique sequence fragments remain bound to the target chromosomes. We refer to this differential retention and removal of probe components as differential stability FISH.
Transcription factor effects on chromosome constitution of cell hybrids
Authors: Hines M.D. , Radomska H.S. , Eckhardt L.A.
Published: April 2003

When immunoglobulin (Ig)-secreting plasmacytomas are fused to a T-cell lymphoma, Ig gene expression ceases in greater than 95% of the resulting hybrids. In the rare hybrids that continue to express Ig, all other tested B lymphocyte-specific genes also remain active. The low frequency with which these Ig-expressing hybrids are recovered, along with the fact that cell fusions can lead to chromosome loss, led us to propose that this rare phenotype was due to loss of a T-cell-derived chromosome encoding a factor or factors with gene silencing activity. To identify the relevant chromosome, we have used a polymerase chain reaction (PCR)-assisted method of chromosome mapping to analyze both Ig-silenced (common) and Ig-expressing (rare) hybrids. Although no single chromosome was found to correlate with Ig gene silencing, we discovered that the two types of hybrids had undergone distinct patterns of chromosome loss. Moreover, we found that ectopic expression of a B-cell-specific transcription factor (Oct-2) dramatically altered both the phenotype and chromosome constitution of hybrids arising in these cell fusions.
Characterization and chromosome location of the gene GSTZ1 encoding the human Zeta class glutathione transferase and maleylacetoacetate isomerase
Authors: Blackburn A.C. , Woollatt E. , Sutherland G.R. , Board P.G.
Published: April 2003

The Zeta class of cytosolic glutathione-S-transferases (GSTs) has recently been identified and spans a range of species from plants to humans. The cDNA and protein of a human member of this class have been previously characterised in our laboratory. This cDNA has also been described as maleylacetoacetate isomerase (MAAI), an enzyme of the phenylalanine catabolism pathway (Fernandez-Canon and Penalva, 1998). The present study has determined the structure and chromosome location of the gene encoding human GSTZ1/MAAI. The gene spans approximately 10.9 kb and is composed of 9 exons. Three intron positions of GSTZ1 were precisely conserved compared to the carnation and Caenorhabditis elegans Zeta GST genes. Fluorescent in situ hybridization mapped the gene to a single locus on chromosome 14q24.3, which is in agreement with an independent localization between the Genethon markers D14S263 and D14S67. The coding region of the gene differed from the GSTZ1 cDNA at two nucleotide positions in exon 3, resulting in Lys-32→Glu and Arg-42→ Gly substitutions. This gene structure information will allow analysis of the polymorphism in genomic DNA samples, and enables further investigations into genetic defects in this step of the phenylalanine catabolism pathway.
High resolution RBA-banding comparison between early prometaphase chromosomes of cattle (Bos taurus L.) and goat (Capra hircus L.) at 700 band level
Authors: Di Berardino D. , Burguete I.
Published: April 2003

High resolution RBA-banded early prometaphase chromosomes of cattle (Bos taurus L.) and goat (Capra hircus L.), from thymidine synchronized lymphocyte cultures, are compared at a level of 700 bands per haploid genome, with the purpose of detecting the extent of banding homologies between the two species and improving the resolution level of the ISCNDA (1989) standardized RBA-banded karyotypes. The results demonstrate that, at this level of resolution, at least 10 autosomes can be fully homologized between the two species, namely chromosomes 11, 16, 17, 18, 20, 21, 22, 23, 24 and 26, whereas the remaining autosomes show variations in some regions which require further investigations on more elongated chromosomes. Such investigations should also involve the use of GTG, GBG and RBG-banding techniques. These variations concern basically the relative distance of the bands from the centromeres or telomeres, appearance of subbands, and clustering of some positive bands.
Centrosome amplification as a possible mechanism for numerical chromosome aberrations in cerebral primitive neuroectodermal tumors with TP53 mutations
Authors: Weber R.G. , Bridger J.M. , Benner A. , Weisenberger D. , Ehemann V. , Reifenberger G. , Lichter P.
Published: April 2003

Although alterations in chromosome number have frequently been detected in human tumor cells and associated with tumor initiation and progression, the causal mechanisms are still not understood. One protein known to be involved in maintaining genetic stability is tumor suppressor p53. In mice, p53 has been implicated in the maintenance of diploidy (Cross et al., 1995) and the regulation of centrosome duplication (Fukasawa et al., 1996). Here we report on cerebral primitive neuroectodermal tumors that lacked the wild-type p53 gene (TP53) and showed multiple numerical chromosome aberrations, as detected by comparative genomic hybridization. In these tumors, the centrosome number was significantly higher than in a control tumor without a detected TP53 mutation and with few chromosomal imbalances. These findings indicate that abnormal centrosome amplification can occur in human tumors lacking wild-type TP53 and may be a mechanism by which numerical chromosome aberrations are generated.
FISH on sperm heads allows the analysis of chromosome segregation and interchromosomal effects in carriers of structural rearrangements: results in a translocation carrier, t(5;8)(q33;q13)
Authors: Blanco J. , Egozcue J. , Clusellas N. , Vidal F.
Published: April 2003

Using three-color fluorescence in situ hybridization (FISH) with specific DNA probes, we have determined the chromosome segregation pattern of the translocated chromosomes in a human male carrier of a reciprocal translocation, t(5;8)(q33;q13). At the same time, we have assessed the possible interchromosomal effect on pair 21 using dual-color FISH. The segregation results showed that a 45.12% of the spermatozoa analyzed resulted from alternate segregation, 38.31% resulted from adjacent I, 6.97% from adjacent II, and 6.56% from 3:1 segregation. Finally, 1.23% could be either diploid sperm or 4:0 segregation. In both types of adjacent segregations, an excess of products containing short translocated segments (adjacent I) and interstitial regions (adjacent II) were found. Products resulting from the presence of an interstitial chiasma in pair 5 (1.26%), were found much more frequently (P < 0.0001) than those resulting from an interstitial chiasma in pair 8 (0.13%) (evaluated after adjacent II segregation). In 3:1 segregation, the products containing one chromosome were observed more frequently than those containing three chromosomes (P < 0.0001). No evidence of an interchromosomal effect on chromosome 21 was detected, the percentage of disomy 21 being similar to that in the controls (0.23% vs. 0.37%). However, the percentage of diploid sperm (1.18%) was significantly higher (P < 0.0001) than that in the controls (0.27%). FISH therefore appears to be a useful technique for assessing the percentage of abnormal sperm in translocation carriers. Their application in assisted reproduction centers could offer patients more accurate genetic counseling.
Molecular cloning, expression, and chromosomal localization of a ubiquitously expressed human 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase gene (PFKFB3)
Authors: Manzano A. , Rosa J.L. , Ventura F. , Pérez J.X. , Nadal M. , Estivill X. , Ambrosio S. , Gil J. , Bartrons R.
Published: April 2003

We report the identification of a human 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase gene (PFKFB3) isolated from a human fetal brain cDNA library. The gene was localized to 10p15→p14 by fluorescence in situ hybridization. The entire cDNA (4,322 bp) codes for a polypeptide of 520 amino acid residues (molecular weight, 59.571 kDa). Structural analysis showed the presence of a kinase domain located at the amino terminus and a bisphosphatase domain at the carboxy terminus, characteristic of previously described 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase isozymes. In addition, a phosphorylation site for cAMP-dependent protein kinase was found at the carboxy terminus. Northern blot analysis showed the presence of a unique 4.8-kb mRNA expressed in the different tissues studied. In mammalian COS-1 cells, this cDNA drives the expression of an active isozyme. Taken together, these results identify the presence of a gene coding for a human 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase isozyme which is ubiquitously expressed.
Integrated genetic and physical map of the 1q31→q32.1 region, encompassing the RP12 locus, the F13B and HF1 genes, and the EEF1AL11 and RPL30 pseudogenes
Authors: van Soest S. , van Rossem M.J. , Heckenlively J.R. , van den Born L.I. , de Meulemeester T.M.A.M.O. , Vliex S. , de Jong P.T.V.M. , Bleeker-Wagemakers E.M. , Westerveld A. , Bergen A.A.B.
Published: April 2003

The gene for autosomal recessive retinitis pigmentosa (RP12) with preserved para-arteriolar retinal pigment epithelium was previously mapped close to the F13B gene in region 1q31→q32.1. A 4-Mb yeast artificial chromosome contig spanning this interval was constructed to facilitate cloning of the RP12 gene. The contig comprises 25 sequence-tagged sites, polymorphic markers, and single-copy probes, including five newly obtained probes. The contig orders the F13B and HF1 genes, as well as five expressed sequence tags, with respect to the integrated genetic map of this region. Homozygosity mapping resulted in refinement of the candidate gene locus for RP12 to a 1.3-cM region. Currently, approximately 1 Mb of the contig is represented in P1-derived artificial chromosome (PAC) clones. Direct screening of a cDNA library derived from neural retina with PACs resulted in identification of the human elongation factor 1α pseudogene (EEF1AL11) and a human ribosomal protein L30 pseudogene (RPL30). A physical and genetic map covering the entire RP12 candidate gene region was constructed.
Chromosomal localization of zebrafish AluI repeats by primed in situ (PRINS) labeling
Authors: Sola, L. , Gabrielli I. , De Innocentiis S. , Gornung E.
Published: April 2003

Two zebrafish AluI repeats were localized in metaphase chromosomes by means of the primed in situ (PRINS) labeling technique, using oligonucleotide primers based on published sequences. An AT-rich, tandemly repeated, long AluI restriction fragment (RFAL1) labeled the (peri)centromeric regions of all chromosomes. The GC-rich short frag- ment (RFAS) was found to be localized in the paracentromeric regions of 17 chromosome pairs, which were mostly subtelocentric. The RFAS labeling pattern generally fits the previously described chromomycin A3 (CMA3) staining pattern. The differential composition of heterochromatin in zebrafish chromosomes is discussed.
Molecular cloning of a SALL1-related pseudogene and mapping to chromosome Xp11.2
Authors: Kohlhase J. , Köhler A. , Jäckle H. , Engel W. , Stick R.
Published: April 2003

SALL1 and SALL2 have been identified as two human homologs of the region-specific homeotic gene spalt (sal) of Drosophila, which encodes a zinc finger protein of characteristic structure. SALL1 has recently been found to be mutated in patients with Townes-Brocks syndrome (TBS, OMIM No. 107480). Here we report the isolation and mapping of another sal-like human gene, named SALL1P, on chromosome Xp11.2. This intronless gene closely resembles SALL1 but displays several mutations, suggesting that SALL1P represents a sal-related pseudogene. The high similarity of SALL1P to SALL1 is of considerable importance for mutation analysis of SALL1 in TBS.
Physical mapping of the CXC chemokine locus on human chromosome 4
Authors: O’Donovan N. , Galvin M. , Morgan J.G.
Published: April 2003

A physical map of the CXC chemokine locus on chromosome 4 has been constructed by PCR analysis and PFGE mapping of YAC clones. The genes for IL8, GRO1, PPBP, PF4, SCYB5 (ENA-78) and SCYB6 (GCP-2) have been co-localized on a 335-kb genomic fragment. The GRO2 and GRO3 genes did not map within this region and based on analysis of a YAC contig overlapping IL8 we speculate that GRO2 and GRO3 map downstream of this region. We have also assigned the novel CXC chemokine gene, SCYB9B (alias H174/βR1) to chromosome 4q21, upstream and within 12 kb of INP10. Like INP10 and MIG, INP10 and SCYB9B are arranged in a head to tail manner. The chromosomal arrangement of these genes appears to reflect the evolution of this multigene family and supports the theory that it arose by gene duplication.
Identification of BAIAP2 (BAI-associated protein 2), a novel human homologue of hamster IRSp53, whose SH3 domain interacts with the cytoplasmic domain of BAI1
Authors: Oda K. , Shiratsuchi T. , Nishimori H. , Inazawa J. , Yoshikawa H. , Taketani Y. , Nakamura Y. , Tokino T.
Published: April 2003

BAI1 (brain-specific angiogenesis inhibitor 1) was originally isolated as a p53-target gene specifically expressed in brain. To clarify its function, we have been searching for cellular proteins that associate with the cytoplasmic domain of BAI1. Using its intracellular carboxyl terminus as “bait” in a yeast two-hybrid system, we isolated a cDNA clone named BAIAP2 whose nucleotide sequence would encode a 521-amino acid protein showing significant homology to a 58/53-kDa substrate of insulin-receptor kinase in the hamster. As the expression profile of BAIAP2 examined by Northern blot analysis was almost identical to that of BAI1, BAIAP2 appears to be active mainly in neurons. In vitro binding assays confirmed that a proline-rich cytoplasmic fragment of BAI1 interacted with the Src homology 3 (SH3) domain of BAIAP2. Double-color immunofluorescent analysis revealed that BAIAP2 was localized at the cytoplasmic membrane when it was coexpressed with BAI1 in COS-7 cells; BAIAP2 not associated with BAI1 was diffused in the cytoplasm. Predominant localization of BAI1 protein in a sub-cellular fraction enriched in growth cones indicated a possible role of BAI1 as a cell adhesion molecule inducing growth cone guidance. As a protein partner of BAI1, BAIAP2 may represent an important link between membrane and cytoskeleton in the process of neuronal growth.
Assignment of a novel bifurcated SET domain gene, SETDB1, to human chromosome band 1q21 by in situ hybridization and radiation hybrids
Authors: Harte P.J. , Wu W. , Carrasquillo M.M. , Matera A.G.
Published: April 2003

We have identified a human gene encoding an unusual bifurcated SET domain protein containing a large “insertion” between the most highly conserved parts of the SET domain. The existence of an evolutionarily related C. elegans gene encoding a similarly bifurcated SET domain suggests that SET domains may generally be composed of two functionally distinct subdomains. We mapped this gene, called SETDB1, to human chromosome 1q21. This region is targeted by a large number of recurrent translocations, suggesting that like the SET domain protein MLL, mutant forms of SETDB1 may be associated with human neoplasias.
cDNA cloning, characterization, and chromosome mapping of UBE2E3 (alias UbcH9), encoding an N-terminally extended human ubiquitin-conjugating enzyme
Authors: Ito K. , Kato S. , Matsuda Y. , Kimura M. , Okano Y.
Published: April 2003

A cDNA encoding a third member of human class III ubiquitin-conjugating enzymes (E2s), UBE2E3, was cloned from a human gastric adenocarcinoma cDNA library. The deduced 207-amino acid protein shares over 94% amino acid identity with the UBC domains of class III E2s, UbcH6, UBE2E2, UbcM2, UbcM3, and UbcD2. But the N-terminal extension exhibited little homology among these, except for UbcM2, which showed 100% identity, and which is thought to be a mouse counterpart. Northern hybridization analysis exhibited a strong 1.9-kb band of UBE2E3 in skeletal muscle. Recombinant fusion protein of GST-UBE2E3 was found to form a thioester bond with ubiquitin (Ub) in an E1-dependent manner, demonstrating that the cDNA encodes a functional E2. In addition, a UBE2E3 mutant of cysteine-145 to serine failed in UBE2E3-Ub complex formation, indicating that the cysteine is essential for E2 function. Using FISH and PCR analysis of radiation hybrid and somatic cell hybrid panels the UBE2E3 gene was mapped to human chromosome 2q32.1 and showed strong linkage to SHGC-8506 (LOD = 11.52) between D2S1302 and D2S364.
High resolution multicolor-banding: a new technique for refined FISH analysis of human chromosomes
Authors: Chudoba I. , Plesch A. , Lörch T. , Lemke J. , Claussen U. , Senger G.
Published: April 2003

A new multicolor-banding technique has been developed which allows the differentiation of chromosome region specific areas at the band level. This technique is based on the use of differently labeled overlapping microdissection libraries. The changing fluorescence intensity ratios along the chromosomes are used to assign different pseudo-colors to specific chromosome regions. The multicolor banding of human chromosome 5 is presented as an example.
Comparative genomic in situ hybridization discloses recurrent gain of chromosome 4 in experimental gliomas of the rat
Authors: Kappler R. , Schlegel J. , Kindler-Röhrborn A. , Mennel H.-D. , Scherthan H.
Published: April 2003

The genetic characterization of experimental tumors is essential in order to evaluate their relevance as appropriate animal models for human neoplasms. We have used flow cytometry and a recently established Comparative Genomic in situ Hybridization (CGH) protocol for the rat (Kappler et al., 1998) to investigate chromosome copy number changes in five ethylnitrosourea induced gliomas of the rat. Flow cytometry showed aneuploid DNA indices in three of the tumors investigated. CGH analysis of primary tumors revealed whole chromosome and subchromosomal gains of rat chromosomes (RNO) 1, 2, 4, 6, 7, 10, 11, 12, and 13. Loss of RNO 5q23→q35 was apparent in one tumor. High level copy number gains were not observed using CGH as well as semiquantitative PCR with Tgfa, Met and Hbb primers. Low copy number gain of RNO 4 represents the most common aberration, since it was detected in four of five tumors investigated. Three tumors showed gain of RNO 7, while two tumors showed gains of RNO 10q31→qter and RNO 12q. Deletion of RNO 5q23→q35 and gain of RNO 4 occurred mutually exclusively. Therefore, we conclude that these two alterations may represent different pathways in the pathogenesis of experimental gliomas in the rat. Findings are discussed in analogy to human gliomas.
Human and mouse GPAA1 (Glycosylphosphatidylinositol anchor attachment 1) genes: genomic structures, chromosome loci and the presence of a minor class intron
Authors: Inoue N. , Ohishi K. , Endo Y. , Fujita T. , Takeda J. , Kinoshita T.
Published: April 2003

Many eukaryotic cell surface proteins are anchored to the membrane with glycosylphosphatidylinositol (GPI) that is covalently linked to the carboxyl-terminus. A Saccharomyces cerevisiae gaa1 mutant is defective in posttranslational attachment of GPI to proteins. A recent report demonstrated that the GPAA1 gene encodes a component of a transamidase that mediates GPI-anchor attachment. Here, we report structures and chromosome loci of human and mouse GPAA1 genes. Both genes consist of twelve exons that span about 4 kb. Human and mouse GPAA1s are located at 8q24.3 and 15E, respectively. There is a human pseudo GPAA1 gene (GPAA1P1) that is located at 2q12→q14. Introns 8 of human and mouse GPAA1s were minor class introns bearing AT at the 5′ splice sites and AC and AT at the 3′ splice sites, respectively. The 3′ splice sites of corresponding introns of African green monkey, Chinese hamster, dog and rat were AC, AT, AT and AA, respectively. The mouse GPAA1 gene (Gpaa1) bearing AG at the 3′ splice site prepared by site-directed mutagenesis was functional, indicating that any nucleotide is allowed at the 3′ end of a minor class intron.
The structural organization of the human aldehyde reductase gene, AKR1A1, and mapping to chromosome 1p33→p32
Authors: Fujii J. , Hamaoka R. , Matsumoto A. , Fujii T. , Yamaguchi Y. , Egashira M. , Miyoshi O. , Niikawa N. , Taniguchi N.
Published: April 2003

Genomic DNA encoding for human aldehyde reductase (AKR1A1), a member of the aldo-keto reductase superfamily, was isolated and characterized. The genomic DNA is approximately 16 kb in length and contains eight exons which encode the entire coding region and the 3′-untranslated sequences. AKR1A1 was localized on chromosome 1p33→p32 by fluorescence in situ hybridization.
Chinese hamster telomeres are comparable in size to mouse telomeres
Authors: Slijepcevic P. , Hande M.P.
Published: April 2003

We report here the results of a telomere length analysis in four male Chinese hamsters by quantitative fluorescence in situ hybridization (Q-FISH). We were able to measure telomere length of 64 (73%) of 88 Chinese hamster telomeres. We could not measure telomere length in chromosome 10 or in the short arms of chromosomes 5, 6, 7 and 8 because of the overlaps between the interstitial and terminal telomeric signals. Our analysis in the 73% of Chinese hamster telomeres indicate that their average length is ∼38 kb. Therefore, Chinese hamster telomeres are comparable in length to mouse telomeres, but are much longer than human telomeres. Similar to previous Q-FISH studies on human and mouse chromosomes, our results indicate that individual Chinese hamster chromosomes may have specific telomere lengths, suggesting that chromosome-specific factors may be involved in telomere length regulation.
Genomic organization of human JAK2 and mutation analysis of its JH2-domain in leukemia
Authors: Cools J. , Peeters P. , Voet T. , Aventin A. , Mecucci C. , Grandchamp B. , Marynen P.
Published: April 2003

The Janus kinase family of proteins, with four mammalian members (JAK1, JAK2, JAK3 and TYK2), plays an essential role in the signal transduction pathway from non-catalytic cytokine receptors to the nucleus. We recently reported the involvement of ETV6-JAK2 fusion genes in the development of leukemia of both lymphoid and myeloid origin. Dominant missense mutations of hopscotch, a Drosophila JAK homologue, causing leukemia-like defects were described. One of these mutations affected a conserved residue of the kinase- like JH2 domain and the introduction of this mutation in murine Jak2 resulted in the constitutional activation of its kinase activity. In order to further analyze its role in leukemogenesis, we cloned human JAK2 and determined its genomic organization. Twenty-four exons spanning a region of approximately 150 kb were identified. A mutation analysis of the exons 13 to 19, encoding the kinase-like JH2 domain failed to detect activating mutations in leukemia samples, suggesting that this is a rare event in human leukemia.
Human chromosome 3 and pig chromosome 13 show complete synteny conservation but extensive gene-order differences
Authors: Sun H.-F.S. , Ernst C.W. , Yerle M. , Pinton P. , Rothschild M.F. , Chardon P. , Rogel-Gaillard C. , Tuggle C.K.
Published: April 2003

A comparative map of human chromosome 3 (HSA 3) and pig chromosome 13 (SSC 13) was constructed using physically assigned pig sequence-tagged sites (STSs). Pig STSs representing 11 HSA 3 genes, including v-Raf-1 murine leukemia viral oncogene homolog 1 (RAF1), retinoic acid β receptor (RARB), cholecystokinin (CCK), pituitary transcription factor 1 (POU1F1), ceruloplasmin (CP), guanine nucleotide binding protein, α-inhibiting polypeptide 2 (GNAI2), sucrase-isomaltase (SI), rhodopsin (RHO), dopamine receptor D3 (DRD3), growth-associated protein 43 (GAP43), and somatostatin (SST), were developed. Ten pig STSs were regionally mapped using a somatic cell hybrid panel (SCHP) to SSC 13 with 80–100% concordance. Large-insert probes were obtained by screening a pig yeast artificial chromosome (YAC) library with primers for each STS. Several YACs were identified for DRD3, GAP43, POU1F1, RHO, SI, and SST for fluorescence in situ hybridization (FISH) mapping. Single gene and bi-color FISH with each pairwise combination were used to further define the gene order on SSC 13. While these data confirm chromosome painting results showing that HSA 3 probes hybridize to a major portion of SSC 13, they also demonstrate extensive gene-order differences between man and pig within this large conserved synteny group. Interestingly, several conserved chromosomal regions have been detected between pig and mouse that are not conserved between man and mouse, suggesting that the SSC 13 gene arrangement may be the closest to that of the ancestral eutherian chromosome.
Identification and characterization of a mouse homolog to yeast Cdc6p
Authors: Berger C. , Strub A. , Staib C. , Lepke M. , Zisimopoulou P. , Hoehn K. , Nanda I. , Schmid M. , Grummt F.
Published: April 2003

Periodic expression of the Cdc6 protein is essential for the entry of budding yeast cells into S phase, and also for participating in checkpoint controls that ensure that DNA replication is completed before mitosis is initiated. We have identified a mouse protein closely related to Cdc6p (MmCdc6p) as well as to its human and Xenopus homologs. The gene coding for MmCdc6p (Cdc6) is located at band D on murine chromosome 11. Analysis of its genomic region revealed that the 13-kb Cdc6 gene is divided into 12 exons by 11 introns. MmCdc6p has putative cyclin-dependent phosphorylation sites, a destruction box, nuclear localization signals, a nucleotide triphosphate-binding motif, and a potential leucine zipper. None of these consensus motifs except the leucine-zipper and the destruction box overlaps an intron. Expression of MmCdc6 mRNA and protein is suppressed in mouse NIH3T3 fibroblasts made quiescent by serum starvation. Upon replenishment of the medium, transcript and protein levels increase during progression through G1, peaking as cells enter S phase. MmCdc6p is phosphorylated in vitro by cdk1/cyclin B, cdk4/cyclin D, cdk2/cyclin E, and cdk2/cyclin A, respectively at serine-residues. In vivo however, phosphorylation of MmCdc6p is carried out by cdk2/cyclin A at serine-residues exclusively. Conservation of structures among members of the Cdc6-related proteins suggests that these proteins play a key role in the regulation of DNA replication during the cell cycle in all eukaryotes. These results strongly suggest, that Cdc6p plays an important role in cell cycle regulation and replication licensing.
Targeted integration of a dominant neoR marker into a 2- to 3-Mb human minichromosome and transfer between cells
Authors: Au H.C. , Mascarello J.T. , Scheffler I.E.
Published: April 2003

The physical and genetic characterization of a stable human minichromosome in a Chinese hamster hybrid cell is described. The minichromosome is 2–3 Mb in size, is linear, and contains a complementing SDHC gene. It is derived from a human chromosome 1, including the centromere, some pericentric heterochromatin from 1q12, and 1–2 Mb of 1q21. Genomic DNA surrounding the SDHC gene was used to construct a targeting vector with a selectable drug resistance marker (neoR); the marker was then successfully integrated into the minichromosome. With the new selectable marker, the 8.2.3 minichromosome could be transferred into mouse LMTK– and 3T3 TK– cells.
Identification of two paralogous regions mapping to the short and long arms of human chromosome 2 comprising LIS1 pseudogenes
Authors: Fogli A. , Giglio S. , Arrigo G. , Lo Nigro C. , Zollo M. , Viggiano L. , Rocchi M. , Archidiacono N. , Zuffardi O. , Carrozzo R.
Published: April 2003

Reiner et al. (1995b) reported on the existence of a gene with a coding region virtually identical to LIS1, the gene responsible for Miller-Dieker lissencephaly. This gene, LIS2, was mapped to chromosome 2p11.2, and a related pseudogene, LIS2P, was mapped to 2q13→q14. By sequencing genomic clones that were mapped by means of 2p and 2q-only hybrids, we now demonstrate the existence of two LIS1 processed pseudogenes mapping to 2p11.2 and 2q13 (PAFAH1P1 and PAFAH1P2, respectively). The two sequences appear to lie within larger paralogous regions and share a 98.6% degree of identity. Comparative mapping data by cytogenetic analysis on great apes indicate that the duplication of the genomic region comprising the LIS1 pseudogenes occurred in humans. We also demonstrate that the cDNA sequence shown as part of the LIS2 gene and marking its chromosome 2 specificity belongs to the 3′ untranslated region of a different gene (C1orf6) that we mapped to 1q21 by FISH analysis.
Rabbit calcium-sensing receptor (CASR) gene: chromosome location and evidence for related genes
Authors: Martin-DeLeon P.A. , Canaff L. , Korstanje R. , Bhide V. , Selkirk M. , Hendy G.N.
Published: April 2003

Abstract. Diverse cellular functions are regulated by the calcium-sensing receptor, encoded by the CASR gene, which plays an important role in calcium homeostasis. Here we provide the sequence for exon VII of the rabbit CASR gene and show that it is 91% identical to the human gene at the nucleotide level, and 95% identical at the amino acid level. The gene was mapped by fluorescence in situ hybridization, using a cosmid isolated from a genomic library, to chromosome 14q11 and this was confirmed independently by PCR amplification of flow sorted chromosomes. In addition, the cosmid detected sites with lower frequencies on four other chromosomes: 3q, 5p, 8p, and 13p. Two of these sites (5p and 13p) were also detected by a related but unidentical cosmid, and map to regions that are homologous to the mouse calcium-sensing receptor related sequences (Casr-rs); suggesting that they may represent CASR-related sequences in the rabbit. The data support the presence of a family of genes related to the calcium-sensing receptor in the G-protein coupled receptor (GPCR) superfamily, as well as extend the existing knowledge of homology for several human and rabbit chromosomes.
Structural organization and chromosome location of the mouse Elongin A gene (Tceb3)
Authors: Aso T. , Amimoto K. , Takebayashi S. , Okumura K. , Hatakeyama M.
Published: April 2003

Elongin A is the transcriptionally active subunit of the Elongin complex, which strongly increases the rate of elongation by RNA polymerase II by suppressing the transient pausing of the polymerase at many sites within transcription units. In the present study, we obtained the cDNA sequence of the mouse Elongin A gene (Tceb3) and characterized its genomic structure. The deduced 773-amino acid sequence of mouse Elongin A shows 91% and 81% identity with rat and human Elongin A, respectively. The Elongin A gene was mapped to mouse chromosome 4D3 by fluorescence in situ hybridization.
Transcriptional map of chromosome region 6q16→q21
Authors: Karayianni E. , Magnanini C. , Orphanos V. , Negrini M. , Maniatis G.M. , Spathas D.H. , Barbanti-Brodano G. , Morelli C.
Published: April 2003

We present the transcription map of chromosome region 6q16→q21 by mapping fifteen known genes within this region. Five genes lay in the subregion containing a tumor suppressor gene, eight genes are located in the subregion harboring a senescence gene, and two genes are distal to the latter region. The precise location of the genes was obtained using a previously described translocation and deletion mouse/human hybrid panel. An even more accurate definition was possible for the genes spanning the senescence gene region, since a previously described YAC contig with its restriction map was available. From this transcription map it is possible to derive a large region of synteny with mouse chromosome 10.