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Results for “Chromosome segmentation”

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PubMed1990

Partial trisomy of the distal segment 14q.

The case of a male infant with duplication of the distal segment of chromosome 14q is described. There was an extra chromosomal segment at the distal end of the long arm of chromosome 17. Banding techniques suggested that the extra segment might be the distal segment of chromosome 14q. DNA analysis using probes from distal 14q as well as from other parts of the genome confirmed that the extra segment consisted of the distal part of 14q. Both the proband's parents and his elder sister had normal karyotypes.

Abnormalities, Multiple↗

PubMed2002

Transmission of chromosomal abnormalities: participation of chromosomally unbalanced gametes in fertilization and early development of unbalanced embryos in the Chinese hamster.

Using 14 Chinese hamster stocks with various reciprocal translocations, chromosomally unbalanced gametes were produced and used to investigate the participation of the unbalanced gametes in fertilization and the development of unbalanced embryos. The selection of chromosomally abnormal gametes during fertilization was investigated by the chromosomal analysis of meiotic cells in heterozygotes for the 14 reciprocal translocations and pronuclei of fertilized ova obtained from crossing these heterozygotes. Compared with the expected frequencies from meiotic metaphase II (MII) scoring, the frequencies of male pronuclei having commonly a deficiency of chromosome 1 (q14-->q42) or chromosome 3 (p23-->q31) in one-cell embryos decreased significantly. However, the frequencies of male pronuclei with other abnormalities were all consistent with those expected from MII scoring. In contrast, the frequencies of female pronuclei with any karyotype including the same ones, as those decreased in male pronuclei from the translocation heterozygotes were all consistent with those estimated from MII scoring. These results suggest that gametes with nullisomies as well as disomies for any chromosomal segments may mostly participate in fertilization, whereas some sperm nullisomic for the specific segments of chromosomes 1 and 3 may fail to fertilize. On the other hand, the zygotic selection of chromosomal imbalance was investigated by direct analyses of pre-implantation embryos from crosses between chromosomally normal females and male heterozygotes from the 14 stocks with various reciprocal translocations. The chromosomal and morphological analysis revealed that some embryos were arrested in development at the two-cell stage and their common abnormality was partial monosomy for chromosome 1 or 2. Embryos with partial monosomy including chromosomes 1, 3 and 4 showed arrested development at four-eight-cell stages. Among day 4 embryos, some chromosomally unbalanced embryos, mainly with a deficiency of other segments, such as chromosomes 1p, 2q, 5q and 8, had fewer blastomeres than karyotypically normal and balanced embryos. The homology between the mouse and the Chinese hamster chromosomes relating to the developmental abnormalities at early stages was partially confirmed.

Animals↗

PubMed1997

Oat-maize chromosome addition lines: a new system for mapping the maize genome.

Novel plants with individual maize chromosomes added to a complete oat genome have been recovered via embryo rescue from oat (Avena sativa L., 2n = 6x = 42) x maize (Zea mays L., 2n = 20) crosses. An oat-maize disomic addition line possessing 21 pairs of oat chromosomes and one maize chromosome 9 pair was used to construct a cosmid library. A multiprobe (mixture of labeled fragments used as a probe) of highly repetitive maize-specific sequences was used to selectively isolate cosmid clones containing maize genomic DNA. Hybridization of individual maize cosmid clones or their subcloned fragments to maize and oat genomic DNA revealed that most high, middle, or low copy number DNA sequences are maize-specific. Such DNA markers allow the identification of maize genomic DNA in an oat genomic background. Chimeric cosmid clones were not found; apparently, significant exchanges of genetic material had not occurred between the maize-addition chromosome and the oat genome in these novel plants or in the cloning process. About 95% of clones selected at random from a maize genomic cosmid library could be detected by the multiprobe. The ability to selectively detect maize sequences in an oat background enables us to consider oat as a host for the cloning of specific maize chromosomes or maize chromosome segments. Introgressing maize chromosome segments into the oat genome via irradiation should allow the construction of a library of overlapping fragments for each maize chromosome to be used for developing a physical map of the maize genome.

Chromosome Mapping↗

PubMed1982

Analysis of chromosomal homologies between two species of the subgenus Sophophora: D. miranda and D. melanogaster using cloned DNA segments.

Chromosomal homology between two species of the subgenus Sophophora, D. miranda and D. melanogaster, belonging to the obscura and the melanogaster group respectively, was probed by DNA in situ cross hybridizations. A set of recombinant plasmids with inserts derived from the D. melanogaster genome were cross hybridized to the D. miranda karyotype. Vice versa, recombinant Lambda phages isolated from a genomic D. miranda library were localized in D. miranda and probed for localization in D. melanogaster. In the main, the results support the homology relations proposed on the basis of cytogenetic data. However, the location of both tandemly repetitive genes tested, 5S RNA genes and the histone genes, is not in accordance with expectation. The 5S RNA genes, when probed with the D. melanogaster plasmid 12D8 (Artavanis-Tsakonas et al., 1977), were found to occur at two sites in both, D. miranda and D. pseudoobscura.

Animals↗

PubMed2001

Location and incidence of chromosome and chromatid breaks in patients with Hodgkin's disease or testicular tumors.

In 90 patients aged 17 to 35 who suffered from Hodgkin's disease (HD) or had testicular tumors (TT), the location of chromosome and chromatid breaks on individual chromosome segments was reviewed using an adapted Funes-Cravioto scheme, in addition to examining the percentage of structural chromosomal aberrations. On the basis of an analysis of 1121 breaks in patients with HD or TT, the results were presented graphically as multiples of the expected number of breaks for the normal population. Before the beginning of treatment, the number of structural chromosomal aberrations (SCA) in patients with TT or HD was equal to that in a control group of subjects with malignant diseases. This, however, does not apply to the location of chromosome and chromatid breaks. In patients with HD, the dominant unstable sites are located on group A2 chromosomes, segments 2 and 5, and on group B chromosomes, segment 5. In patients with TT, the number of chromosome and chromatid breaks is also increased on group A2 chromosomes, segments 2 and 5, and in addition, also on group B chromosomes, segment 4.

Adolescent↗

PubMed1996

Comparative analysis of the cattle and human genomes: detection of ZOO-FISH and gene mapping-based chromosomal homologies.

Comparative chromosome painting with individual human chromosome-specific libraries (CSLs) on cattle metaphase chromosomes delineated 46 homologous chromosomal segments between the two species. Continuous arrangement of these segments on individual cattle chromosomes demonstrates a nearly complete coverage of the bovine karyotype and shows physical boundaries of bovine chromosomal segments homologous to individual human chromosomes. Alignment of the available comparative gene mapping data with the homologous segments strongly supports the detected gross homologies between the karyotypes of the two species. In addition to cattle, four human CSLs were hybridized to sheep metaphase chromosomes also, to further verify the known karyotype homology within the Bovidae. Besides its application to karyotype evolution research, the comparative knowledge provides for rapid expansion of the much needed Type I locus-based bovine gene map.

Animals↗

PubMed1972

The T6 translocation in the mouse: its use in trisomy mapping, centromere localization, and cytological identification of linkage group 3.

The occurrence of hairless piebald mice trisomic for the chromosome segments of the T6M chromosome has shown that the LG III loci hr and s are not located on T6M. The T6 breakpoint in LG III is therefore in the position hr-s-T6. T6M must carry the gene Fkl, which is located on the far side of the T6 breakpoint from hr in LG III.-T6 reduces recombination in the hr-s region.-Trisomy for the chromosome segments of the T6M chromosome appears to severely reduce viability.-The gene hr has been shown to lie between the centromere and the T6 breakpoint. The order of loci in LG III is therefore: centromere-hr-s-T6.-Equations are given for the relation between the frequency of adjacent-2 segregation and the frequency of recovery of complementation zygotes for the case in which the translocation heterozygote can form either quadrivalent or univalent-trivalent configurations at meiosis.-Linkage Group III is carried on chromosome 14. LG VI is the other linkage group involved in T6, and is carried on chromosome 15.

Animals↗

PubMed1978

RNA transcription and chromatin structure during meiotic and postmeiotic stages of spermatogenesis.

Autoradiographic procedures for the study of RNA and protein synthesis during spermatogenesis have been complemented with electron microscope techniques for visualization of gene activity. These procedures have enabled us to determine that RNA transcription is highly selective with respect to RNA species, timing of synthesis, types of chromosomes (autosomes and sex chromosomes), segments of chromosomes (i.e., the lampbrush segment), and chromatin structure. In mouse and human spermatocytes, a peak production of ribosomal RNA (rRNA) occurs during leptotene-zygotene, preceding nonnucleolar RNA synthesis, which is at a peak in middle pachytene. Transcription in late spermatids decreases in coincidence with changes in chromatin structure and high incorporation rates of [3H]arginine. In these cells, a particulate repeating pattern of chromatin is replaced by chromatin fibers of uniform diameter as highly arginine-rich proteins replace somatic histones. In spermatogonia, spermatocytes and Sertoli cells, the products of transcription are mainly heterogeneous nuclear RNA (hnRNA) and rRNA, whereas spermatids transcribe predominantly hnRNA during early spermiogenesis. Persistent long-lived [3H]-uridine-labeled RNA species in pachytene spermatocyte nuclei contrast with a fast turnover of [3H]uridine-labeled RNA in Sertoli cells as detected at the same pulse labeling time (8--12 days). From these results one can postulate a still undefined control mechanism of gene expression during spermatogenesis for modulating a cascade of events required for male gamete formation.

Animals↗

PubMed1994

Human immunoglobulin VH and D segments on chromosomes 15q11.2 and 16p11.2.

In addition to the major human immunoglobulin heavy-chain locus on chromosome 14q32.3, VH and D segments are known to be present on chromosomes 15 and 16. We have now amplified and sequenced 24 such VH segments from somatic cell hybrids and have assigned them to 15q11.2 and 16p11.2 using cosmid and yeast artificial chromosome clones. In addition, we have located a cluster of D segments on 15q11.2, previously thought to be located on 14q32.3. We propose that the segments on chromosome 16 arose by an interchromosomal duplication and identify the corresponding region on chromosome 14. Taken together with the completion of a map of the human VH locus on 14q32.3, the total number of VH segments now identified is 117. We can now account for most, if not all human germ-line VH segments.

Base Sequence↗

PubMed1976

Further delineation of the clinical picture of trisomy for the distal segment of chromosome 13: report of three cases.

Three cases of partial trisomy for the distal segment of chromosome 13 are reported. Common clinical features included normal birth weight, postnatal asphyxia, convulsions, severe psychomotor retardation, normal growth, and a distinct pattern of dysmorphias consisting of trigonocephalic head with prominent metopic suture, long and markedly curved eyelashes, a stubby nose, increased distance between nose and upper lip, high-arched palate, misshapen ears with virtually absent lobules and prominent anthelices which are curved in a sharp angle, and hemangiomata. Features present in 2 cases were microcephaly, long and narrow fingers with convex nails, and hexadactyly. Two cousins were unbalanced offspring of a large family of carriers of a 9/13 translocation, whereas the third case exhibited a 13p+ chromosome which was formed de novo. The clinical features in the 3 patients are typical of the syndrome due to partial trisomy for the distal segment of chromosome 13 which shows selected and mitigated signs of full trisomy 13.

Abnormalities, Multiple↗

PubMed1991

A proximal mouse chromosome 9 linkage map that further defines linkage groups homologous with segments of human chromosomes 11, 15, and 19.

A 42-cM map of proximal mouse chromosome 9, including eight loci defined by restriction fragment length variants, has been generated. Linkage was established by haplotype analyses of 114 interspecific backcross mice and indicated the following gene order: (centromere) Pvs-5.3 cM-Icam-1/Ldlr-18.4 cM-Thy-1-1.8 cM-Ncam-0.9 cM-Hexa-7.9 cM-Gsta-7.9 cM-Trf. Three of these loci, Pvs, Icam-1, and Hexa, have not been mapped previously. Together with previous mapping studies the current results suggested that chromosomal segments of mouse chromosomes 7 and 9 and chromosomal segments of human chromosomes 11, 15, and 19 derive from a single putative primordial chromosome. The studies support the postulate that detailed analysis of chromosome organization will be useful in defining events in mammalian evolution.

Animals↗

PubMed2005

Efficient inference of haplotypes from genotypes on a large animal pedigree.

We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes. The rate of haplotype resolution for the simulated data was >91% with a standard deviation of 2%. With 20% missing data, the rate of haplotype resolution was 67.5% with a standard deviation of 1.3%. In both cases all recovered haplotypes were correct. In the real data, allele origin was resolved for 22% of the heterozygous genotypes, even though 70% of the genotypes were missing. Haplotypes were resolved for 36% of the males. Computing time was insignificant for both data sets. Despite the intricacy of large-scale real pedigree genotypes, the proposed algorithm provides a practical rule-based solution for resolving haplotypes for small chromosomal segments in commercial animal populations.

Algorithms↗

PubMed1998

Identification of NFIB as recurrent translocation partner gene of HMGIC in pleomorphic adenomas.

Approximately 12% of all pleomorphic adenomas of the salivary glands are characterized by chromosome aberrations involving the chromosome segment 12q13-15. Several chromosomes have been found as translocation partners of chromosome 12, and some of these recurrently. Recently, the HMGIC gene was identified as the target gene affected by the 12q13-15 aberrations. Here, we report the identification and characterization of a new translocation partner gene of HMGIC in pleomorphic adenomas. 3'-RACE analysis of a primary adenoma with an apparently normal karyotype revealed an HMGIC fusion transcript containing ectopic sequences derived from the human NFIB gene, previously mapped to chromosome band 9p24.1. The HMGIC NFIB fusion transcript was also confirmed by RT-PCR. Since the chromosome segment 9p12-24 is repeatedly involved as translocation partner of chromosome 12q13-15 in pleomorphic adenomas, we tested whether NFIB might be a recurrent partner of HMGIC. RT-PCR analysis of a second adenoma with an ins(9;12)(p23;q12q15) as the sole anomaly, revealed that also in this tumor an HMGIC/NFIB hybrid transcript was present. The reciprocal NFIB/HMGIC fusion transcript, however, could not be detected in any of these tumors. Nucleotide sequence analysis of the fusion transcripts indicated that the genetic aberration in both tumors resulted in the replacement of a carboxy-terminal segment of HMGIC by the last five amino acids of NFIB. In conclusion, our results reveal the recurrent involvement of the NFIB gene as translocation partner gene of HMGIC in pleomorphic adenomas.

Adenoma↗

PubMed1990

Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato.

Quantitative trait loci (QTLs) have been mapped to small intervals along the chromosomes of tomato (Lycopersicon esculentum), by a method we call substitution mapping. The size of the interval to which a QTL can be mapped is determined primarily by the number and spacing of previously mapped genetic markers in the region surrounding the QTL. We demonstrate the method using tomato genotypes carrying chromosomal segments from Lycopersicon chmielewskii, a wild relative of tomato with high soluble solids concentration but small fruit and low yield. Different L. chmielewskii chromosomal segments carrying a common restriction fragment length polymorphism were identified, and their regions of overlap determined using all available genetic markers. The effect of these chromosomal segments on soluble solids concentration, fruit mass, yield, and pH, was determined in the field. Many overlapping chromosomal segments had very different phenotypic effects, indicating QTLs affecting the phenotype(s) to lie in intervals of as little as 3 cM by which the segments differed. Some associations between different traits were attributed to close linkage between two or more QTLs, rather than pleiotropic effects of a single QTL: in such cases, recombination should separate desirable QTLs from genes with undesirable effects. The prominence of such trait associations in wide crosses appears partly due to infrequent reciprocal recombination between heterozygous chromosomal segments flanked by homozygous regions. Substitution mapping is particularly applicable to gene introgression from wild to domestic species, and generally useful in narrowing the gap between linkage mapping and physical mapping of QTLs.

Alleles↗

PubMed1982

Regional localization on the human X of DNA segments cloned from flow sorted chromosomes.

Fluorescence activated sorting of chromosomes from 49,XXXXY human lymphoblasts has been used to obtain DNA enriched for the human X. This DNA was cloned in lambda phage Charon 21A to obtain a library of approximately 60,000 pfu. Phage inserts free of human highly repeated DNA sequences are localized to different regions of the human X by two independent hybridization analyses. The first utilized comparative hybridization to rodent-human hybrid cell DNA samples containing all or known portions of the human X, while the second was based on hybridization dosage to DNA samples from human cell lines differing in the number of X chromosomes or X chromosome segments. Of five unique sequence inserts tested, three were X chromosome specific and were localized to regions Xpter leads to Xcen, Xql leads to Xq22 and Xq24 leads to Xqter, respectively. The library presented here represents a highly enriched source of human X chromosome-specific DNA sequences.

Animals↗

PubMed1996

Interchange of the active and silent S-layer protein genes of Lactobacillus acidophilus by inversion of the chromosomal slp segment.

The most-dominant surface-exposed protein in many bacterial species is the S-protein. This protein crystallises into a regular monolayer on the outside surface of the bacteria: the S-layer. Lactobacillus acidophilus harbours two S-protein-encoding genes, slpA and slpB, only one of which (slpA) is expressed. In this study, we show by polymerase chain reaction (PCR) analysis that slpA and slpB are located on a 6 kb chromosomal segment, in opposite or orientations. In a small fraction of the bacterial population, this segment is inverted. The inversion leads to interchanging of the expressed and silent S-protein-encoding genes, and places the formerly silent gene behind the S-promoter which is located outside the inverted segment. A 26 bp sequence showing a high degree of similarity with the consensus sequence recognized by the Din family of invertases is present in the region where recombination occurs. Expression of the slpA gene seems to be favoured under laboratory growth conditions because 99.7% of the chromosomes of an L. acidophilus ATCC 4356 broth culture had the slpA gene present at the slp expression site.

Amino Acid Sequence↗

PubMed1997

Expression of HMGI-C and HMGI(Y) in ordinary lipoma and atypical lipomatous tumors: immunohistochemical reactivity correlates with karyotypic alterations.

The high mobility group proteins (HMGs) are a class of low molecular weight, nonhistone, nuclear proteins that bind DNA and function as transcription cofactors. This class includes the HMGI family members HMGI-C and HMGI(Y). Both are not significantly expressed in differentiated adult tissues, including fat, but their expression is induced in proliferating and transformed cells. Their involvement in the development of lipomatous tumors has been recently demonstrated for HMGI-C, which is encoded by a gene located at 12q15, the chromosomal segment often rearranged in ordinary lipomas. The same chromosomal segment is consistently amplified in the ring and giant marker chromosomes of atypical lipomatous tumors (ALTs), a term used to designate tumors previously labeled as well differentiated liposarcomas or atypical lipomas. The involvement of HMGI(Y) is strongly suspected as the gene coding for HMGI(Y) is located at 6p21, a chromosomal segment rearranged in a subset of ordinary lipomas. HMGI-C or HMGI(Y) protein expression was analyzed immunohistochemically in a group of 39 well differentiated adipose neoplasms (19 lipomas and 20 ALTs) of known karyotype using polyclonal antibodies raised against a recombinant protein (HMGI-C) and against a synthetic peptide (HMGI(Y)). The results of this study demonstrate that HMGI proteins are commonly expressed in well differentiated adipose neoplasms. Seventeen of twenty ALTS (85.0%), all of which had ring or giant marker chromosomes with amplification of 12q13-15, strongly expressed HMGI-C. HMGI-C expression was detected in 7 of 11 ordinary lipomas (63.6%) with alterations at 12q14-15 and in one case with an abnormal karyotype that included double minute chromosomes. HMGI-C immunoreactivity correlates with 12q13-15 chromosomal alterations (P = 0.001). HMGI(Y) reactivity was demonstrated in only two ordinary lipomas: one with 6p21 rearrangement and one with normal karyotype. No significant HMGI(Y) expression was found in the ALT group. The finding of aberrant expression of HMGI proteins in well differentiated adipose neoplasms in association with 12q13-15 and 6p21 chromosomal changes supports the proposed pathogenetic role of this group of proteins in the development of adipose tissue tumors.

Adult↗

PubMed1999

Endotoxin response in spontaneously hypertensive rats: a role of the TNFalpha-gene region.

We have shown previously that administration of endotoxin induces a smaller decrease of body temperature in spontaneously hypertensive rats (SHR) than in normotensive Brown Norway (BN) rats. Several studies have suggested that tumor necrosis factor alpha (TNFalpha) is one of the mediators of the body-temperature response to endotoxin. To test whether the TNFalpha gene could be involved in determination of the observed difference in the body-temperature response to endotoxin, we studied SHR (n = 6) and a congenic strain, SHR.1N (n = 5), which differs from SHR by a segment of chromosome 20 originating from BN and containing the TNFalpha gene. Body temperature was recorded continuously by means of radiotelemetry. We showed that, in both strains, an intraperitoneal injection of endotoxin (500 microg/kg of body weight) induces a rapid hyperthermic phase (20-40 minutes post-injection), which is followed, first, by a hypothermic phase (100-120 minutes post-injection) and, then, by a late hyperthermic phase (seven hours). Although both strains demonstrated a similar trend in the response, a significant difference was observed between the two response curves (P = 0.0001). Further analysis at each time point revealed that the two strains differed significantly at a peak of the hypothermic phase (P = 0.035) and the late hyperthermic phase (P = 0.035). In conclusion, these data indicate that the differential chromosomal segment of SHR.1N contains a gene(s) causally related to the body-temperature response to endotoxin. In the light of previously published data, the TNFalpha gene appears to be the most likely candidate gene within the segment.

Animals↗