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Results for “Chromosome segmentation”

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PubMed1995

Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting.

By comparative gene mapping, extended conservation of synteny between different mammalian species has become apparent. Mapping in these species could be accelerated by exact visualization of the chromosomal segments that exhibit conserved synteny. We have hybridized human chromosome-specific DNA libraries onto porcine metaphase spreads to examine the extent of conservation of synteny between the two species. The hybridization signals on pig chromosomes are of variable quality, but the analysis allowed us to assign for all human autosomes homologous chromosomal segments in the pig karyotype. Extended conservation of synteny was observed, often comprising whole chromosomes. In our analysis 47 segments of conserved synteny common to the human and pig karyotype were identified. Intrachromosomal rearrangements by inversion within and between these segments are described. These rearrangements are common events during evolution. Our analysis shows that conservation of synteny between human and pig is three times more than between humans and mice and, consequently, is characterized by fewer, but larger conserved segments.

Animals↗

PubMed2003

Comparative chromosome painting defines the karyotypic relationships among the domestic dog, Chinese raccoon dog and Japanese raccoon dog.

The Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54 + 2-3 B) and Japanese raccoon dog (Nyctereutes p. viverrinus, 2n = 38 + 3-4 B) are two subspecies of the same species. The genome-wide comparative chromosome map between the Japanese raccoon dog and domestic dog (Canis familiaris) has been established by fluorescence in-situ hybridization with a set of domestic dog painting probes. In this study, we established the comparative chromosome map for the Chinese raccoon dog and domestic dog. In total, dog probes specific for the 38 autosomes delineated 41 conserved chromosomal segments in the Chinese raccoon dog. Probes from dog chromosomes 1, 13 and 19 each painted two Chinese raccoon dog chromosome segments. Fifteen dog autosomal probes each hybridized to one Chinese raccoon dog chromosome, while each of the other dog autosomal probes painted to a single Chinese raccoon dog chromosomal arm. Dog X chromosome probe delineated the entire X chromosome of the Chinese raccoon dog; the dog Y chromosome probe hybridized to the pseudoautosomal region at the Xpter as well as the entire Y chromosome of the Chinese raccoon dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in the genomes of the Chinese and Japanese raccoon dogs demonstrates that their differences in the karyotypes of these two subspecies could have resulted from eight Robertsonian translocations. The large difference in chromosome number between the Chinese and Japanese raccoon dogs suggests that they should be considered as two distinct species.

Animals↗

PubMed2006

Single nucleotide polymorphic marker enabling rapid and early screening for the homoeolocus of beta-amylase-R1: a gene linked to copper efficiency on 5RL.

This study describes the development of a PCR marker to detect the beta-amylase-R1 gene of rye. It provides an easy and rapid means for the identification of plants containing the beta-amylase-R1. Because rye chromosome segments do not normally recombine with wheat chromosomes, this marker provides a means for tracking all linked genes on that alien 5RL chromosome segment. Reaction conditions were optimised for an annealing temperature of 60 degrees C for a high stringency. The reaction was also optimised for low reaction volumes reducing the cost of the reagents required for the reaction. This PCR test can be used in breeding or mapping programs for the rapid screening of progeny containing translocations of 5RL and hence select for the copper efficiency trait of rye.

Base Sequence↗

PubMed1995

Comparative mapping in grasses. Wheat relationships.

Conventionally, the genetics of species of the family Gramineae have been studied separately. Comparative mapping using DNA markers offers a method of combining the research efforts in each species. In this study, we developed consensus maps for members of the Triticeae tribe (Triticum aestivum, T. tauschii, and Hordeum spp.) and compared them to rice, maize and oat. The aneuploid stocks available in wheat are invaluable for comparative mapping because almost every DNA fragment can be allocated to a chromosome arm, thus preventing erroneous conclusions about probes that could not be mapped due to a lack of polymorphism between mapping parents. The orders of the markers detected by probes mapped in rice, maize and oat were conserved for 93, 92 and 94% of the length of Triticeae consensus maps, respectively. The chromosome segments duplicated within the maize genome by ancient polyploidization events were identified by homoeology of segments from two maize chromosomes to regions of one Triticeae chromosome. Homoeologous segments conserved across Triticeae species, rice, maize, and oat can be identified for each Triticeae chromosome. Putative orthologous loci for several simply inherited and quantitatively inherited traits in Gramineae species were identified.

Avena↗

PubMed1989

Molecular cloning of the breakpoint region on chromosome 6 in cutaneous malignant melanoma: evidence for deletion in the c-myb locus and translocation of a segment of chromosome 12.

Nonrandom involvement of chromosome 6 in cutaneous malignant melanoma have been noted by several investigators. Recently an alteration in the c-myb locus (6q22-23) has been identified by Southern analysis in the WM983A cell line which was derived from a primary melanoma of the vertical growth phase. In the present study, the nature of this rearrangement in the WM983A cell line has been further characterized by molecular cloning and nucleotide sequence analysis of the break-point region in the c-myb locus. The results of this investigation demonstrate that the rearrangement in the 6q22-23 region results in deletion of the 3'-end of the c-myb locus with the concomitant translocation of a portion of chromosome 12 to chromosome 6.

Base Sequence↗

PubMed2005

Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation.

The current study is the first installment of an effort to explore the secondary gene pool for the enhancement of Upland cotton (Gossypium hirsutum L.) germplasm. We developed advanced-generation backcross populations by first crossing G. hirsutum cv. Tamcot 2111 and G. barbadense cv. Pima S6, then independently backcrossing F(1) plants to the G. hirsutum parent for three cycles. Genome-wide mapping revealed introgressed alleles at an average of 7.3% of loci in each BC(3)F(1) plant, collectively representing G. barbadense introgression over about 70% of the genome. Twenty-four BC(3)F(1) plants were selfed to generate 24 BC(3)F(2) families of 22-172 plants per family (totaling 2,976 plants), which were field-tested for fiber elongation and genetically mapped. One-way analysis of variance detected 22 non-overlapping quantitative trail loci (QTLs) distributed over 15 different chromosomes. The percentage of variance explained by individual loci ranged from 8% to 28%. Although the G. barbadense parent has lower fiber elongation than the G. hirsutum parent, the G. barbadense allele contributed to increased fiber elongation at 64% of the QTLs. Two-way analysis of variance detected significant (P<0.001) among-family genotype effects and genotypexfamily interactions in two and eight regions, respectively, suggesting that the phenotypic effects of some introgressed chromosomal segments are dependent upon the presence/absence of other chromosomal segments.

Analysis of Variance↗

PubMed1994

Quantitative resistance to Phytophthora infestans in potato: a case study for QTL mapping in an allogamous plant species.

Phytophthora infestans is the most important fungal pathogen in the cultivated potato (Solanum tuberosum). Dominant, race-specific resistance alleles and quantitative resistance--the latter being more important for potato breeding--are found in the germplasm of cultivated and wild potato species. Quantitative trait loci (QTLs) for resistance to two races of P. infestans have been mapped in an F1 progeny of a cross between non-inbred diploid potato parents with multiple alleles. Interval mapping methods based on highly informative restriction fragment length polymorphism markers revealed 11 chromosome segments on 9 potato chromosomes showing significant contrasts between marker genotypic classes. Whereas phenotypically no difference in quantitative resistance response was observed between the two fungal races, QTL mapping identified at least one race specific QT locus. Two QT regions coincided with two small segments on chromosomes V and XII to which the dominant alleles R1, conferring race specific resistance to P. infestans, Rx1 and Rx2, both inducing extreme resistance to potato virus X, have been allocated in independent mapping experiments. Some minor QTLs were correlated with genetic loci for specific proteins related to pathogenesis, the expression of which is induced after infection with P. infestans.

Alleles↗

PubMed1997

Chromosome painting: a method for testing chromosomal changes in lemur evolution.

Chromosome painting using commercially available human chromosome-specific DNA libraries was performed to elucidate chromosomal rearrangements in lemur evolution. Human-specific probes for chromosomes 3, 14, 15, and 21 were used to paint chromosomes of six species: Eulemur fulvus mayottensis, Varecia variegata, Lemur catta, Hapalemur simus, H. griseus griseus, and H. aureus. All human chromosome libraries hybridized specifically to chromosome segments of varying length or to whole arms of Lemur chromosomes. The labeling was clearly visualized and permitted precise delineation of the hybridized Lemur chromosomal segments. The use of commercial probes of human chromosomes for chromosome painting appears efficient enough to investigate homology in different species of Lemur. In general, the results obtained by chromosome painting in this study confirm results previously obtained by the R-banding technique but modify the location of some chromosomal rearrangements on different branches of the evolutionary tree of the Lemuridae and reveal some new rearrangements that were not detectable with banding techniques. These results show that chromosome painting with human chromosome-specific DNA libraries can provide useful information in comparative studies on karyotypes of distantly related mammalian species, providing a powerful tool for evolutionary studies, especially in phylogeny.

Animals↗

PubMed1992

Molecular cloning and physical analysis of an 8.2 kb segment of chromosome XI of Saccharomyces cerevisiae reveals five tightly linked genes.

The nucleotide sequence of 6472 base pairs of an 8.2 kb segment of Saccharomyces cerevisiae chromosome XI has been determined. The sequence contains a cluster of four long open reading frames (ORF) designated YKL2, YKL3, YKL4 and TGL1 in the same orientation, flanked at the 5'-end by a divergent incomplete ORF (YKL1). Transcription and Southern analysis of the four complete ORFs showed that all are expressed and are present in single copy on the haploid genome. The average codon adaptation index of the coding regions is approximately 0.2, suggesting that these genes are lowly expressed. The upstream regions of all four genes as well as the YKL1 ORF contain putative promoter elements previously found to be characteristic of nuclear genes encoding mitochondrial proteins. Significant sequence similarities were found between the YKL3 protein and Escherichia coli ribosomal protein S2 as well as between the TGL1 protein and triglyceride lipases from rat salivary gland and human gastric tissue. The 3'-end of the 6472 bp nucleotide sequence overlaps with the upstream region of the previously identified CTK1 gene, encoding the largest subunit of CTD kinase (Lee, J.M. and Greenleaf, A.L., 1991, Gene Expression 2, 149-167), thereby increasing the number of genes on the 8.2 kb fragment to at least five. The transcripts of these genes represent approximately 83% of the DNA fragment, making it one of the most highly transcribed regions of the yeast chromosome analysed to date.

Amino Acid Sequence↗

PubMed2006

Localization of a prostate cancer predisposition gene to an 880-kb region on chromosome 22q12.3 in Utah high-risk pedigrees.

Chromosome 22q has become recently a region of interest for prostate cancer. We identified previously a logarithm of odds (LOD) of 2.42 at chromosome 22q12.3. Additionally, this region has been noted by eight other studies, with linkage evidence ranging from LOD of 1.50 to 3.57. Here, we do fine mapping and localization of the region using a pedigree-specific recombinant mapping approach in 14 informative, high-risk Utah pedigrees. These 14 pedigrees were chosen because they were either "linked" or "haplotype-sharing" pedigrees or both. "Linked" pedigrees were those with significant pedigree-specific linkage evidence (LOD, >0.588; P < 0.05) to the 22q12.3 region, regardless of the number of prostate cancer cases sharing the segregating haplotype. "Haplotype-sharing" pedigrees were those with at least five prostate cancer cases sharing a segregating haplotype in the 22q12.3 region, regardless of the linkage evidence. In each pedigree, the most likely haplotype configuration (in addition to the multipoint LOD graph for linked pedigrees) was used to infer the position of recombinant events and delimit the segregating chromosomal segment in each pedigree. These pedigree-specific chromosomal segments were then overlaid to form a consensus recombinant map across all 14 pedigrees. Using this method, we identified a 881,538-bp interval at 22q12.3, between D22S1265 and D22S277, which is the most likely region that contains the 22q prostate cancer predisposition gene. The unique Utah extended high-risk pedigree resource allows this powerful localization approach in pedigrees with evidence for segregating predisposition to prostate cancer. We are mutation screening candidate genes in this region to identify specific genetic variants segregating in these pedigrees.

Aged↗

PubMed1997

Chromosomal imbalance maps of malignant solid tumors: a cytogenetic survey of 3185 neoplasms.

To assess the distribution of gains and losses of genetic material in malignant solid neoplasms, 11 tumor types for which at least 100 short-term cultured cases with clonal chromosome aberrations had been reported in the literature were selected. The study was based on cytogenetic information from 508 breast carcinomas, 447 malignant neuroglial tumors, 435 kidney carcinomas, 333 colon carcinomas, 304 ovarian carcinomas, 303 lung carcinomas, 209 testicular germ cell tumors, 206 head and neck carcinomas, 172 malignant melanomas, 142 Wilms' tumors, and 126 neuroblastomas. In each case, the net imbalances were calculated for each chromosome band. The profiles of gains and losses revealed that all tumor types display unique combinations of imbalances. However, there is also considerable overlap among the profiles of the different diagnostic entities, indicating that similar molecular mechanisms may be operative in the development of many types of neoplasia. Deletions were more common than gains in all tumor types, with chromosomes X, Y, 4, 10, 13-15, 18, and 22 and chromosome segments 1p22-pter, 3p13-pter, 6q14-qter, 8p, 9p, and 11p being particularly often deleted in the majority of tumors. To better delineate critical lost segments, deletion profiles based only on structural rearrangements were made for chromosomes 1, 3-12, and 17, which all had on average at least four registered deletions per band. The relative distribution of losses indicated that different bands/regions are affected in different tumor types and that, often, several distinct candidate tumor suppressor gene loci can be discerned within the same chromosome arm, e.g., 1p12-13, 1p22, 1p34, and 1p36 on the short arm of chromosome 1 and 7q22, 7q32, and 7q36 on the long arm of chromosome 7. The only chromosomes or chromosome segments more often gained than deleted were chromosomes 7 and 20 and the long arms of chromosomes 1 and 12, suggesting the presence there of dominantly acting growth-regulatory genes. The data presented in this study should be valuable as a guide for molecular genetic studies on allelic imbalances and for the interpretation of results from studies using comparative genomic hybridization.

Breast Neoplasms↗

PubMed1994

Interchromosomal exchange of a large subtelomeric segment in a Plasmodium falciparum cross.

Duplications and interchromosomal transpositions of chromosome segments are implicated in the genetic variability of Plasmodium falciparum malaria parasites. One parasite clone, HB3, was shown to lack a subtelomeric region of chromosome 13 that normally carries a PfHRPIII gene. We show here that the chromosome 13 segment carrying PfHRPIII was replaced in HB3 by a duplicated terminal segment from chromosome 11. Mapping results indicate that the segment includes at least 100-200 kb of subtelomeric DNA and contains duplicated copies of the Pf332 and RESA-2 genes. We followed inheritance of this duplication in a genetic cross between the HB3 and another P.falciparum clone, Dd2, that is euploid for the Pf332, RESA-2 and PfHRPIII genes. Three types of progeny from the cross showed expected inheritance forms: a Dd2 euploid parent type, an HB3 aneuploid parent type, and a recombinant euploid type that carried PfHRPIII from Dd2 chromosome 13 and Pf332 from HB3 chromosome 11. However, a fourth euploid progeny type was also observed, in which the chromosome 13 segment from HB3 was transposed back to replace the terminus of chromosome 11. Three of 14 individual progeny were of this type. These findings suggest a mechanism of recombination from subtelomeric pairing and exchange between non-homologous chromosomes in meiosis.

Alleles↗

PubMed1998

Comparative FISH mapping of mouse and rat homologues of twenty-five human X-linked genes.

We constructed a comparative cytogenetic map of 25 functional genes in mouse and rat X chromosomes by direct R-banding fluorescence in situ hybridization. Nineteen and 22 out of the 25 genes, which have been mapped on the human X chromosome, were newly localized to mouse and rat X chromosomes, respectively. Twenty-two additional genes were integrated in the rat-mouse-human comparative map of the X chromosome in this study. Comparison of the gene order indicated the presence of four chromosome segments with conserved linkage homology between mouse and rat X chromosomes, suggesting that a minimum of four chromosomal inversion events occurred between mouse and rat X chromosomes during the evolution of the two species. Four chromosome segments with conserved linkage homology were found between human and rat X chromosomes.

Animals↗

PubMed1995

An 8.2 kb DNA segment from chromosome XIV carries the RPD3 and PAS8 genes as well as the Saccharomyces cerevisiae homologue of the thiamine-repressed nmt1 gene and a chromosome III-duplicated gene for a putative aryl-alcohol dehydrogenase.

A 8.2 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome XIV (GenBank/EMBL accession number: X83226) encompasses four open reading frames (ORFs) longer than 100 residues. The ORF N0295 is highly similar to the Aspergillus parasiticus and Schizosaccharomyces pombe nmt1 gene products, which are involved in thiamine biosynthesis and are strongly repressed by thiamine. N0300 is 76% identical to YCR107w, a hypothetical protein of yeast chromosome III, and 55% identical to a ligninolytic aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium. In addition, this fragment encodes Rpd3, a pleiotropic transcription factor (Vidal and Gaber, 1991), and part of Pas8, a protein essential for the biogenesis of peroxisomes (Voorn-Brouwer et al., 1993).

Alcohol Oxidoreductases↗

PubMed1989

Mapping RFLP loci in maize using B-A translocations.

Plants hypoploid for specific segments of each of the maize (Zea mays L.) chromosomes were generated using 24 different B-A translocations. Plants carrying each of the B-A translocations were crossed as male parents to inbreds, and sibling progeny hypoploid or not hypoploid for specific chromosomal segments were recovered. Genomic DNAs from the parents, hypoploid progeny, and nonhypoploid (euploid or hyperploid) progeny for each of these B-A translocations were digested with restriction enzymes, electrophoresed in agarose gels, blotted onto reusable nylon membranes, and probed with nick-translated, cloned DNA fragments which had been mapped previously by restriction fragment length polymorphism (RFLP) analysis to the chromosome involved in the B-A translocation. The chromosomal segment on our RFLP map which was uncovered by each of the B-A translocations was determined. This work unequivocally identified the short and long arms of each chromosome on this map, and it also identified the region on each chromosome which contains the centromere. Because the breakpoints of the B-a translocations were previously known on the cytological and the conventional genetic maps, this study also allowed this RFLP map to be more highly correlated with these maps.

Centromere↗

PubMed1981

Evidence for double replication of chromosomal DNA segments as a general consequence of DNA replication inhibition.

We have previously presented evidence that a transient inhibition of DNA synthesis by a pulse of 1-beta-D-arabinofuranosylcytosine (ara-C) results in a disruption of the pattern of replication of the chromosomal DNA of cultured human cells, resulting in some DNA segments being replicated more than once in a single S phase. Further evidence is presented in this paper that this effect is not a specific property of the ara-C molecule in that a similar effect is produced in cells by a pulse of 9-beta-D-arabinofuranosyladenine (ara-A) and also by a pulse of cycloheximide. The activated form of ara-A and ara-C (the triphosphates) both inhibit DNA synthesis at the level of the polymerase. Double replication following an ara-A pulse demonstrates that double replication after an ara-C pulse is not caused by some specific property of the ara-C molecule which might be unrelated to any effect on DNA synthesis. However, cycloheximide is an inhibitor of mammalian protein synthesis and inhibits DNA synthesis only indirectly, probably through a consequent deficiency of DNA-packaging proteins. Hence, the occurrence of double replication of chromosomal DNA segments following a pulse of cycloheximide is consistent with this phenomenon being a general and nonspecific consequence of the freezing of DNA replication forks.

Cell Line↗

PubMed1989

A 6000 kb segment of chromosome 1 is conserved in human and mouse.

A murine linkage map generated from analyses of 428 meiotic events in an interspecific cross and pulsed field gel electrophoresis allowed examination of the genomic organization of a 6000 kb segment of mouse and human chromosome 1. Analysis of five genes within this syntenic segment of both species revealed striking conservation of gene order, intergenic distance and, to a lesser extent, CpG dinucleotides. In the mouse, meiotic crossover events were not evenly distributed; a hot spot for meiotic recombination was coincident with a CpG-island. These studies provide a practical approach to aid physical mapping of the human genome and a model for determining the molecular principles that govern meiotic recombination. In addition, these findings demonstrate profound conservation of genomic organization over mammalian evolution.

Animals↗

PubMed1981

Studies of mammalian chromosome replication. II. Evidence for the existence of defined chromosome replicating units.

Sister chromatids of metaphase chromosomes can be differentially stained if the cells have replicated their DNA semiconservatively for two cell cycles in a medium containing 5-bromodeoxyuridine (BrdU). When prematurely condensed chromosomes (PCC) are induced in cells during the second S phase after BrdU is added to the medium, the replicated chromosome segments show sister chromatid differential (SCD) staining. Employing this PCC-SCD system on synchronous and asynchronous Chinese hamster ovary (CHO) cells, we have demonstrated that the replication patterns of the CHO cells can be categorized into G1/S, early, early-mid, mid-late, and late S phase patterns according to the amount of replicated chromosomes. During the first 4 h of the S phase, the replication patterns show SCD staining in chains of small chromosome segments. The amount of replicated chromosomes increase during the mid-late and late S categories (last 4 h). Significantly, small SCD segments are also present during these later intervals of the S phase. Measurements of these replicated segments indicate the presence of characteristic chromosome fragment sizes between 0.2 to 1.2 micrometers in all S phase cells except those at G1/S which contain no SCD fragments. These small segments are operationally defined as chromosome replicating units of chromosomal replicons. They are interpreted to be composed of clusters of molecular DNA replicons. The larger SCD segments in the late S cells may arise by the joining of adjacent chromosomal replicons. Further application of this PCC-SCD method to study the chromosome replication process of two other rodents, Peromyscus eremicus and Microtus agrestis, with peculiar chromosomal locations of heterochromatin has demonstrated an ordered sequence of chromosome replication. The euchromatin and heterochromatin of the two species undergo two separate sequences of decondensation, replication, and condensation during the early-mid and mid-late intervals respectively of the S phase. Similar-sized chromosomal replicons are present in both types of chromatin. These data suggest that mammalian chromosomes are replicated in groups of replicating units, or chromosomal replicons, along their lengths. The organization and structure of these chromosomal replicons with respect to those of the interphase nucleus and metaphase chromosomes are discussed.

Animals↗