SEARCH · PubMed Health

Results for “Chromosome segmentation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources

PubMed1997

Genetic isolation of a chromosome 1 region affecting blood pressure in the spontaneously hypertensive rat.

Recent linkage studies in the spontaneously hypertensive rat (SHR) suggest that a blood pressure regulatory gene or genes may be located on rat chromosome 1q. To investigate this possibility, we replaced a region of chromosome 1 in the SHR (defined by the markers D1Mit3 and Igf2) with the corresponding chromosome segment from the normotensive Brown-Norway (BN) strain. In male SHR congenic rats carrying the transferred BN chromosome segment, 24-hour average systolic and diastolic blood pressures were significantly lower than in male progenitor SHR. Polymerase chain reaction genotyping using 60 polymorphic microsatellite markers dispersed throughout the genome confirmed the congenic status of the new strain designated SHR.BN-D1Mit3/Igf2. These findings provide direct evidence that a blood pressure regulatory gene exists on the differential segment of chromosome 1 that is sufficient to decrease blood pressure in the SHR. The SHR.BN-D1Mit3/Igf2 congenic strain represents an important new model for fine mapping and characterization of genes on chromosome 1 involved in the pathogenesis of spontaneous hypertension.

Animals↗

PubMed2006

Chromosome painting between human and lorisiform prosimians: evidence for the HSA 7/16 synteny in the primate ancestral karyotype.

Multidirectional chromosome painting with probes derived from flow-sorted chromosomes of humans (Homo sapiens, HSA, 2n = 46) and galagos (Galago moholi, GMO, 2n = 38) allowed us to map evolutionarily conserved chromosomal segments among humans, galagos, and slow lorises (Nycticebus coucang, NCO, 2n = 50). In total, the 22 human autosomal painting probes detected 40 homologous chromosomal segments in the slow loris genome. The genome of the slow loris contains 16 sytenic associations of human homologues. The ancient syntenic associations of human chromosomes such as HSA 3/21, 7/16, 12/22 (twice), and 14/15, reported in most mammalian species, were also present in the slow loris genome. Six associations (HSA 1a/19a, 2a/12a, 6a/14b, 7a/12c, 9/15b, and 10a/19b) were shared by the slow loris and galago. Five associations (HSA 1b/6b, 4a/5a, 11b/15a, 12b/19b, and 15b/16b) were unique to the slow loris. In contrast, 30 homologous chromosome segments were identified in the slow loris genome when using galago chromosome painting probes. The data showed that the karyotypic differences between these two species were mainly due to Robertsonian translocations. Reverse painting, using galago painting probes onto human chromosomes, confirmed most of the chromosome homologies between humans and galagos established previously, and documented the HSA 7/16 association in galagos, which was not reported previously. The presence of the HSA 7/16 association in the slow loris and galago suggests that the 7/16 association is an ancestral synteny for primates. Based on our results and the published homology maps between humans and other primate species, we propose an ancestral karyotype (2n = 60) for lorisiform primates.

Animals↗

PubMed1983

Evidence showing that the nucleolus-envelope region is located on the nor-bearing chromosomes in Aotus trivirgatus.

We investigated whether the existence of the Nucleolus-Envelope Region observed in dividing animal cells is related to the Nucleolus Organizer Region or to other chromosome segments of the NOR-bearing chromosomes, since NORs are usually adjacent to the chromosome segments attached to the nuclear envelope such as the centromere, telomere or heterochromatin region. We used Aotus Trivirgatus fibroblasts whose karyotype is characterized by a single pair of NORs located on the long arm of the third pair of chromosomes, far from the centromere, the telomere and any obvious heterochromatin region. All the nucleoli were seen to be clearly associated with the nuclear envelope but separated from it by the outermost layer of chromatin. These results further support the hypothesis that the NOR is a site of attachment of the chromatin to the nuclear envelope by means of the Nucleolus-Envelope Region. They show that genetically active chromatin is also attached to the nuclear envelope. A model of the arrangement of chromatin during interphase is proposed which provides a functional interpretation of the currently available data.

Animals↗

PubMed2004

Agropyron elongatum chromatin localization on the wheat chromosomes in an introgression line.

The introgressed small-chromosome segment of Agropyron elongatum (Host.) Neviski (Thinopyrum ponticum Podp.) in F5 line II-1-3 of somatic hybrid between common wheat (Triticum aestivum L.) and A. elongatum was localized by sequential fluorescence in situ hybridization (FISH), genomic in situ hybridization (GISH) and karyotype data. Karyotype analysis offered basic data of arm ratios and relative lengths of 21 pairs of chromosomes in parent wheat Jinan177 and hybrid II-1-3. Using special high repetitive sequences pSc119.2 and pAs1 for FISH, the entire B- and D-genome chromosomes were detected. The FISH pattern of hybrid II-1-3 was the same as that of parent wheat. GISH using whole genomic DNA from A. elongatum as probe determined the alien chromatin. Sequential GISH and FISH, in combination with some of the karyotype data, localized the small chromosome segments of A. elongatum on the specific sites of wheat chromosomes 2AL, 1BL, 5BS, 1DL, 2DL and 6DS. FISH with probe OPF-03(1296) from randomly amplified polymorphic DNA (RAPD) detected E-genome chromatin of A. elongatum, which existed in all of the small chromosome segments introgressed. Microsatellite primers characteristic for the chromosome arms above were used to check the localization and reveal the genetic identity. These methods are complementary and provide comprehensive information about the genomic constitution of the hybrid. The relationship between hybrid traits and alien chromatin was discussed.

Agropyron↗

PubMed1989

A genetic method to quantitate induced chromosome breaks using a mouse/human monochromosomal hybrid cell line: identification of potential clastogenic agents.

A genetic assay to detect the clastogenic potential of environmental agents is described. This assay is based on the cloning efficiency of cells in a medium that permits the growth of cells following loss of a specific chromosome segment resulting from a chromosome break. For this purpose a mouse/human hybrid cell line R12-2 containing a dominantly marked chromosome 5 as the only human component has been constructed. This chromosome 5 carries two dominant selectable markers, Ecogpt and the gene for sensitivity to diphtheria toxin (DTs). Ecogpt codes for the enzyme xanthine-guanine phosphoribosyltransferase which allows selection for cells containing chromosome 5 or the segment carrying Ecogpt as judged by growth in medium supplemented with mycophenolic acid and xanthine (MX medium). Human cells are sensitive to 10(-13) M DT, whereas mouse cells are resistant to 10(-7) M DT and DTs is expressed as a dominant phenotype. Cultivation of R12-2 cells in the medium containing 10(-13) M DT permit the selection of cells that have lost chromosome 5 or the segment carrying DTs. The presence of two selectable markers on the same chromosome permits the identification and quantitation of cells for the selective loss of a specific chromosome segment. Growth of R12-2 cells in MX medium containing 10(-13) M DT therefore, provides a convenient method to determine the frequency of clastogen induced breaks in chromosome 5. The utility of the proposed genetic assay is assessed using X-irradiation as a model clastogen. Our results clearly show a dose related response that is consistent with cytogenetic observations.

Animals↗

PubMed2005

Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.

Genome-wide copy number changes were analyzed in 70 primary human lung carcinoma specimens and 31 cell lines derived from human lung carcinomas, with high-density arrays representing approximately 115,000 single nucleotide polymorphism loci. In addition to previously characterized loci, two regions of homozygous deletion were found, one near the PTPRD locus on chromosome segment 9p23 in four samples representing both small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC) and the second on chromosome segment 3q25 in one sample each of NSCLC and SCLC. High-level amplifications were identified within chromosome segment 8q12-13 in two SCLC specimens, 12p11 in two NSCLC specimens and 22q11 in four NSCLC specimens. Systematic copy number analysis of tyrosine kinase genes identified high-level amplification of EGFR in three NSCLC specimens, FGFR1 in two specimens and ERBB2 and MET in one specimen each. EGFR amplification was shown to be independent of kinase domain mutational status.

Carcinoma, Non-Small-Cell Lung↗

PubMed1984

Isolation and regional localization by in situ hybridization of a unique gene segment to chromosome 21.

V chromosome 21 (ch. 21) flow-sorted library was screened for the presence of unique DNA segments which are specific for the 21st chromosome. By combining the techniques of somatic cell genetics and in situ hybridization, we have identified several of these recombinant probes and have regionally mapped one of them to the distal half of the long arm of chromosome 21 (q22.1- greater than qter). This represents the first report of the sublocalization of a unique DNA segment to chromosome 21 by in situ hybridization.

Animals↗

PubMed2006

Epistatic kinship a new measure of genetic diversity for short-term phylogenetic structures--theoretical investigations.

The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full-sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered.

Algorithms↗

PubMed2006

GISH/FISH mapping of genes for freezing tolerance transferred from Festuca pratensis to Lolium multiflorum.

The first backcross breeding programme for the transfer of freezing-tolerance genes from winter hardy Festuca pratensis to winter-sensitive Lolium multiflorum is described. A partly fertile, triploid F(1) hybrid F. pratensis (2n=2x=14) x L. multiflorum (2n=4x=28) was employed initially, and after two backcrosses to L. multiflorum (2x) a total of 242 backcross two (BC(2)) plants were generated. Genomic in situ hybridisation (GISH) was performed on 61 BC(2) plants selected for their good growth and winter survival characters in the spring following one Polish winter (2000-2001). Among the winter survivors, diploid chromosome numbers were present in 80% of plants. An appropriate single Festuca introgression in an otherwise undisturbed Lolium genome could provide increased freezing tolerance without compromise to the good growth and plant vigour found in Lolium. Among all the diploids, a total of 20 individuals were identified, each with a single F. pratensis chromosome segment. Another diploid plant contained 13 Lolium chromosomes and a large metacentric F. pratensis chromosome, identified as chromosome 4, with two large distal Lolium introgressions on each chromosome arm. Three of the diploid BC(2), including the genotype with Festuca chromosome 4 DNA sequences, were found to have freezing tolerance in excess of that of L. multiflorum, and in one case in excess of the F. pratensis used as control. A detailed cytological analysis combining GISH and fluorescence in situ hybridisation analyses with rDNA probes revealed that the other two freezing-tolerant genotypes carried a Festuca chromosome segment at the same terminal location on the non-satellite arm of Lolium chromosome 2.

Acclimatization↗

PubMed1993

A 'zebra' chromosome arising from multiple translocations involving non-homologous chromosomes.

An alloplasmic wheat line carrying a 'zebra' chromosome z5A was isolated from the derivatives of an Elymus trachycaulus x Triticum aestivum cv Chinese Spring hybrid. Chromosome z5A was named zebra because of its striped genomic in situ hybridization pattern. z5A consists of four chromosome segments derived from E. trachycaulus and four chromosome segments, including the centromere, from wheat. The short arm of z5A paired with the telocentric chromosome 1H(t)S of E. trachycaulus and the long arm with the long arm of normal 5A. z5A also carried several genetic markers derived from 1H(t)S. Chromosome 1H(t) was the only E. trachycaulus chromosome found in the sib plants of a previous generation from which z5A was derived. Monosomic 5A and telocentric chromosome 5AL were also found in most of the sib plants. The zebra chromosome most probably originated from spontaneous multiple translocations between chromosomes 5A and 1H(t)S or 5A and 1H(t).

Chromosome Banding↗

PubMed1999

Chromosomal mapping of quantitative trait loci that influence renal hemodynamic functions.

BACKGROUND: Impaired renal hemodynamic function has been suspected to be responsible for hypertension in the spontaneously hypertensive rat (SHR). METHODS AND RESULTS: We measured renal hemodynamic functions, including the glomerular filtration rate, renal plasma flow, and renal vascular resistance, in an F2 rat population derived from spontaneously hypertensive and Wistar-Kyoto (WKY) rats and performed a genome-wide screening to map quantitative trait loci that influence these functions to gain insight into the relationship between renal hemodynamic functions and blood pressure control. The D1 Mit7 locus was identified as a major locus that influenced renal hemodynamic functions, and we transferred the SHR chromosomal segment around the D1 Mit7 locus into the WKY strain. The congenic rats exhibited impaired renal hemodynamic functions. The systolic blood pressure of the congenic rats was significantly higher than that of age-matched WKY rats, but only at nighttime. No significant differences in systolic blood pressure during daytime or diastolic blood pressure were observed between the 2 strains. CONCLUSIONS: We have identified a chromosome segment that influences renal hemodynamic function. The SHR chromosome segment around the D1 Mit7 locus had significant, but not dramatic, effects in increasing blood pressure in the WKY genetic background. However, further studies will be necessary to determine the significance of this locus in SHR hypertension.

Animals↗

PubMed1999

A major linkage region on distal chromosome 4 confers susceptibility to mouse autoimmune gastritis.

Although much is known about the pathology of human chronic atrophic (type A, autoimmune) gastritis, its cause is poorly understood. Mouse experimental autoimmune gastritis (EAG) is a CD4+ T cell-mediated organ-specific autoimmune disease of the stomach that is induced by neonatal thymectomy of BALB/c mice. It has many features similar to human autoimmune gastritis. To obtain a greater understanding of the genetic components predisposing to autoimmune gastritis, a linkage analysis study was performed on (BALB/cCrSlc x C57BL/6)F2 intercross mice using 126 microsatellite markers covering 95% of the autosomal genome. Two regions with linkage to EAG were identified on distal chromosome 4 and were designated Gasa1 and Gasa2. The Gasa1 gene maps within the same chromosomal segment as the type 1 diabetes and systemic lupus erythematosus susceptibility genes Idd11 and Nba1, respectively. Gasa2 is the more telomeric of the two genes and was mapped within the same chromosomal segment as the type 1 diabetes susceptibility gene Idd9. In addition, there was evidence of quantitative trait locus controlling autoantibody titer within the telomeric segment of chromosome 4. The clustering of genes conferring susceptibility to EAG with those conferring susceptibility to type 1 diabetes is consistent with the coinheritance of gastritis and diabetes within human families. This is the first linkage analysis study of autoimmune gastritis in any organism and as such makes an important and novel contribution to our understanding of the etiology of this disease.

Animals↗

PubMed1984

Metaphase chromosome transfer of introduced selectable markers.

A general method for creating somatic cell hybrids which maintain chromosome segments by selection is described. To extend the technique of metaphase chromosome transfer to regions of the genome which do not carry a selectable marker, a retroviral vector has been employed to introduce the dominant selectable neo gene at many genomic locations in a population of murine cells. We have used such cells as donors in metaphase chromosome transfer experiments in which hamster and monkey cells were used as recipients. Cells acquiring a transferred chromosomal segment containing the neo gene were selected by growth in the presence of the drug G418. Hybridization to cloned interspersed repeat DNA sequences of the mouse was used to estimate the proportion of mouse DNA in each transferent. These experiments indicate that transferents produced in this manner contain 0.01 to 1.0% of the mouse genome. To analyze the organization of the DNA transferred to each recipient, we used Southern transfer hybridization of DNA from each transferent to a cloned mouse interspersed repeated DNA probe which did not cross-hybridize to hamster or monkey DNA. We found that each primary transferent gave a unique pattern of restriction fragments hybridizing to this probe. Secondary transferents from two independent primary transferents were compared by this technique. Each set of secondary transferents exhibited a hybridization pattern which resembled closely that of the primary transferent from which it was derived. However, a number of hybridizing DNA segments present in each primary transferent were absent in some of the secondary transferents. These results are most compatible with the view that an intact segment of the mouse chromosome surrounding the integration site of the retroviral vector can be transferred by the techniques used in this study. We believe this technique will be generally applicable to cells from many species, and will allow the study of chromosome regions previously refractory to analysis by chromosome transfer techniques.

Animals↗

PubMed2003

Genome-level evolution of resistance genes in Arabidopsis thaliana.

Pathogen resistance genes represent some of the most abundant and diverse gene families found within plant genomes. However, evolutionary mechanisms generating resistance gene diversity at the genome level are not well understood. We used the complete Arabidopsis thaliana genome sequence to show that most duplication of individual NBS-LRR sequences occurs at close physical proximity to the parent sequence and generates clusters of closely related NBS-LRR sequences. Deploying the statistical strength of phylogeographic approaches and using chromosomal location as a proxy for spatial location, we show that apparent duplication of NBS-LRR genes to ectopic chromosomal locations is largely the consequence of segmental chromosome duplication and rearrangement, rather than the independent duplication of individual sequences. Although accounting for a smaller fraction of NBS-LRR gene duplications, segmental chromosome duplication and rearrangement events have a large impact on the evolution of this multigene family. Intergenic exchange is dramatically lower between NBS-LRR sequences located in different chromosome regions as compared to exchange between sequences within the same chromosome region. Consequently, once translocated to new chromosome locations, NBS-LRR gene copies have a greater likelihood of escaping intergenic exchange and adopting new functions than do gene copies located within the same chromosomal region. We propose an evolutionary model that relates processes of genome evolution to mechanisms of evolution for the large, diverse, NBS-LRR gene family.

Arabidopsis↗

PubMed2005

Evaluation of identity-by-descent probabilities for half-sibs on continuous genome.

A new method is provided for exact evaluation of the distribution of the amount of genetic material, from a chromosomal segment, shared identical-by-descent by a finite number of half-sibs. The interest in such distribution stems from its relation to the distribution of genetic material from chromosomal segments of an individual surviving to the next generation. The new method is superior to the existing one which has recently been suggested by Stefanov [V.T. Stefanov, Distribution of the amount of genetic material from a chromosomal segment surviving to the following generation. J. Appl. Probab. 41 (2004) 345]. It allows both faster computation and a large number of half-sibs. Relevant software codes are provided for automated implementation of such evaluations.

Animals↗

PubMed2002

MLL5, a homolog of Drosophila trithorax located within a segment of chromosome band 7q22 implicated in myeloid leukemia.

Proteins encoded by Polycomb and Trithorax-group (Pc-G and Trx-G) genes regulate developmental fates by maintaining or repressing HOX gene expression, respectively. In a search for candidate myeloid leukemia tumor suppressor genes from a approximately 2.5 Mb commonly-deleted segment within chromosome band 7q22, we identified a novel human Trithorax (Trx) family member named MLL5. Trx-G genes encode proteins that modulate transcriptional programs through protein-protein interactions that are mediated by PHD and SET domains, and by binding to DNA via A-T hooks and methyltransferase homology motifs. MLL5 is a homolog of the Drosophila gene CG9007; it encodes a 6.5 kb mRNA that is expressed widely. MLL5 includes a SET domain and a single PHD finger, but lacks A-T hooks and methyltransferase homology domains that are found in MLL. The leukemia cell line RCV-ACV-A carries a heterozygous missense mutation within the PHD domain; however, no mutations within the MLL5 coding region were detected in primary leukemias. MLL5 is a novel mammalian Trx-G gene that might modulate transcription by protein association.

Amino Acid Sequence↗

PubMed2003

Adenoma multiplicity in irradiated Apc(Min) mice is modified by chromosome 16 segments from BALB/c.

Ionizing radiation (IR) is a well-characterized carcinogen in humans and mice. The BALB/c mouse strain is unusually sensitive to IR-induced tissue damage and cancer development in a range of organs, suggestive of a partial defect in DNA damage response. This has been confirmed by finding BALB/c-specific functional polymorphism in Prkdc, a gene on mouse chromosome 16 that encodes the catalytic subunit of DNA-dependent protein kinase. Prkdc(BALB) has been associated with increased susceptibility to IR-induced mammary and lymphatic neoplasia. Here, we provide evidence that chromosome 16 segments from BALB/c interact with Apc(Min) (multiple intestinal neoplasia) and specifically enhance IR-induced adenoma development in the upper part of the small intestine.

Adenoma↗

PubMed1987

Localization of the Huntington's disease gene to a small segment of chromosome 4 flanked by D4S10 and the telomere.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder of late onset, characterized by progressive motor disturbance, psychological manifestations, and intellectual deterioration. The HD gene has been genetically mapped by linkage to the DNA marker D4S10, but the exact physical location of the HD defect has remained uncertain. To delineate critical recombination events revealing the physical position of the HD gene, we have identified restriction fragment length polymorphisms for two recently mapped chromosome 4 loci, RAF2 and D4S62, and determined the pattern of segregation of these markers in both reference and HD pedigrees. Multipoint linkage analysis of the new markers with D4S10 and HD establishes that the HD gene is located in a very small physical region at the tip of the chromosome, bordered by D4S10 and the telomere. A crossover within the D4S10 locus orients this segment on the chromosome, providing the necessary information for efficient application of directional cloning strategies for progressing toward, and eventually isolating, the HD gene.

Alleles↗