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Results for “Chromosome segmentation”

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PubMed1989

Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources.

Duplication-containing cells are selected when growth of Salmonella typhimurium is limited by the availability of any one of several carbon and energy sources. Under conditions of extreme starvation, growth occurs almost exclusively in the duplication-containing fraction of the population. Cells with duplications of one large segment of the chromosome are repeatedly selected regardless of which of these carbon sources limits growth. The duplicated chromosomal segment encodes the transport systems for all of these carbon sources. This duplication is not selected during growth on a carbon source for which the permease is not included within the duplication segment. This suggests that the growth advantage conferred by the duplication may be due to increased transport of the limiting carbon source. Inclusion of the permease alone is not sufficient to explain the growth advantage of the duplications, since other common duplications that include the permease are not selected.

Adaptation, Physiological↗

PubMed1993

Chromosome painting as a supplement to cytogenetic banding analysis in non-Hodgkin's lymphoma.

Chromosomal in situ suppression (CISS) hybridization with biotin labeled chromosome-specific libraries was performed on short-term cultures from five cases of non-Hodgkin's lymphoma (NHL). The painting analysis proceeded in three stages. First-stage CISS hybridization was done with libraries specific for chromosomes that seemed to be lost or rearranged as judged by banding analysis. Second-stage CISS included hybridization with probes specific for chromosomes that, because of banding pattern similarities, were considered to be likely candidates to have contributed unidentified chromatin blocks in the abnormal karyotype. The third and final stage was a confirmation hybridization with a library specific for the chromosome that, at the stage two analysis, was found to have donated the previously unknown chromosomal segment. The aberrant chromosomes were often more complex than the banding analysis had led us to believe. Among the rearrangements whose nature was determined by CISS hybridization were two add(1)(p36) which, in both cases, were shown to be a der(1)t(1;2)(p36;q31). This study illustrates the potential use of chromosome painting in resolving karyotypic uncertainties in NHL, and it shows that new cytogenetic subgroups may emerge when classical banding analysis is supplemented with fluorescence in situ hybridization techniques.

Biotin↗

PubMed1994

Genes encoding oleosins in maize kernel of inbreds Mo17 and B73.

We have investigated all three oleosin genes which are expressed in the kernel of maize (Zea mays L., Mo17). Oleosin genes, ole16, ole17, and ole18, encode OLE16, OLE17, and OLE18, respectively, in proportional amounts of approximately 2:1:1 in isolated oil bodies. None of the three genes has an intron or a sequence encoding an N-terminal signal peptide. The three genes are expressed coordinately during seed maturation, and their encoded oleosins are present in similar proportional amounts in oil bodies isolated from the embryonic axis, scutellum, and aleurone layer. OLE16 represents one oleosin isoform, whereas OLE17 and OLE18 are close members of another oleosin isoform. ole16 and ole18 have been mapped to single loci on chromosomes 2 (near b1 gene) and 5S (near phya2), respectively. We predict that ole17 is located on chromosome 1 (near phya1), in a chromosomal segment duplicated on chromosome 5.

Amino Acid Sequence↗

PubMed2005

The expression of several Cbf genes at the Fr-A2 locus is linked to frost resistance in wheat.

The C-repeat binding factor (Cbf) gene family has been shown to have a critical role in the regulation of low-temperature stress response in Arabidopsis. In Triticum monococcum, a locus carrying a family of Cbf-like genes, orthologs of Arabidopsis Cbf genes, is tightly linked to the frost tolerance locus Fr-A ( m ) 2, representing candidates for the differences in frost tolerance mapped at this locus. In this work we show that several Cbf genes have dramatically different levels of induction after cold exposure in hexaploid wheat. The Cbf-transcription levels differ between substitution and single chromosome recombinant lines carrying different 5A chromosomes or chromosome segments of the chromosome 5A from frost-tolerant and frost-sensitive wheat varieties. When the expression of eight Cbf genes, previously mapped at the Fr-A2 locus was investigated with gene specific primers using real-time RT-PCR, three Cbf sequences (Cbf1A, Cbf1C, Cbf7) showed a significantly higher relative transcription level (more than fourfold change) in lines differing for the Fr-A2 region. Differences in Cbf expression were also associated with a variation in frost tolerance. These results suggest that the amount of some Cbf mRNAs might be a critical factor for determining the level of frost tolerance in wheat.

Adaptation, Physiological↗

PubMed1995

Structural characterization, chromosomal localization and phylogenetic evaluation of two pairs of AGAMOUS-like MADS-box genes from maize.

In order to gain a better understanding of the development and evolution of cereal flowers, we have cloned and sequenced two MADS-box genes from maize and the partial cDNA of a third one. One of the genomic clones was identified as ZAG2 (Zea AGAMOUS 2), while the other has a very similar structure and the potential to encode a protein which shares 94% sequence identity with the putative ZAG2 gene product. The cDNA reveals considerable similarity to ZAG1. Phylogenetic evaluation of the sequence information, as well as chromosomal localization, both suggest that we have identified two pairs of AGAMOUS-like MADS-box genes which were created during duplication of chromosomal segments or complete chromosomes.

AGAMOUS Protein, Arabidopsis↗

PubMed1990

Assignment of the growth hormone gene locus to 19q26-qter in cattle and to 11q25-qter in sheep by in situ hybridization.

The growth hormone gene locus (GH) of cattle and sheep was mapped to a chromosomal region in each species by using in situ hybridization. The probe employed was an 830-bp cDNA sequence from the ovine growth hormone gene. Based on QFQ chromosome preparations, our results show that the GH locus is on cattle chromosome 19 in the region of bands q26-qter and in sheep on chromosome region 11q25-qter. The GH assignments together with previous localizations of type I cytokeratin genes (KRTA) and one homeobox (HOX2) gene in cattle and one type I cytokeratin gene (KRTA) in sheep identify a strongly conserved chromosomal segment on human chromosome 17, bovine chromosome 19, and sheep chromosome 11.

Animals↗

PubMed1992

Expression and chromosome localization of the murine cystic fibrosis transmembrane conductance regulator.

A 13.5-kb genomic fragment of the mouse cystic fibrosis transmembrane conductance regulator (CFTR) gene was isolated from a C57BL/6J liver DNA library, using a human CFTR exon 10 probe. This region of the human gene includes the most common cystic fibrosis mutation (deletion of the Phe508 residue) in the first nucleotide binding domain of CFTR. Sequence analysis demonstrated 87% identity between the predicted mouse and the normal human CFTR exon 10 sequences, including conservation of the Phe508 residue. Northern analysis revealed that the mouse gene is expressed in intestine, lung, stomach, kidney, and salivary gland. In contrast to human CFTR, murine CFTR transcripts were not detectable by Northern analysis in the liver or pancreas. More sensitive PCR analysis, however, revealed that the mouse CFTR gene is weakly expressed in other tissues, including liver and pancreas. During development, mouse CFTR transcripts were observed as early as Embryonic Day 13. Southern analysis of mouse x Chinese hamster somatic cell hybrid DNAs mapped the mouse CFTR locus (Cftr) to Chromosome 6 (Chr 6). Subsequent typing of the progeny of an interspecies backcross revealed that Cftr is closely linked to the proto-oncogene c-met locus (Met) in the centromeric region of mouse Chr 6, consistent with the observation that there is a conserved chromosomal segment on human chromosome 7 and mouse Chr 6.

Amino Acid Sequence↗

PubMedDate not supplied

MAPH: from gels to microarrays.

The development of accurate and sensitive methodologies to detect small chromosomal imbalances (<3 Mb) is extremely important in clinical diagnostics and research in human genetics. The technique of array-comparative genomic hybridization (CGH) using BAC and PAC clones is very sensitive methodology and is rapidly becoming the method of choice for high-resolution screening of genomic copy-number changes. An alternative methodology to CGH is the multiplex amplifiable probe hybridization (MAPH) methodology, a DNA based method that allows the accurate and reliable determination of changes in copy number in "known" or "unknown locations" in the human genome. MAPH uses probes of 100-500 bp in size, that can be specifically designed for any gene or locus in the genome and cover any gene exons, the subtelomeric or subcentromeric regions, any chromosomal segment, a whole chromosome or the total human genome. MAPH can provide extremely high resolution and enable the sensitive detection of loss or gain of genomic DNA sequences as small as 150 bp. Very recently we succeeded in the advancement of MAPH from gel and capillary analyses to microarrays. The array-MAPH methodology offers an alternative methodology to array-CGH and provides a new sensitive microarray-based method including several advantages for the detection of copy number changes in the human genome.

DNA↗

PubMed2004

The evolution of eutherian chromosomes.

The gross organization of the genome of Eutheria (placental mammals) into chromosomes follows a simple architecture that, with some minor changes, is almost completely conserved for more than 100 million years in various species of almost all extant mammalian orders. Recent molecular cytogenetic results--especially those from the assumed oldest clade, the Afrotheria--suggest an ancestral karyotype that would calculate the "default" frequency of gross rearrangements to less than two changes within 10 million years of mammalian evolution. The main changes are the fission, movement and subsequent fusion of large chromosome segments or of chromosome arms. Reciprocal translocations are the exception. Chromosome numbers may have increased or decreased significantly in this fusion/fission process but, in most instances, the main architecture still remains evident. There are, however, some exceptions in mammals with extremely derived karyotypes.

Animals↗

PubMed2003

Highly conserved chromosomes in an Asian squirrel (Menetes berdmorei, Rodentia: Sciuridae) as demonstrated by ZOO-FISH with human probes.

The chromosomes of Menetes berdmorei (Rodentia, Sciuridae, Sciurinae) were studied by ZOO-FISH using whole human chromosome probes. All homoeologies between M. berdmorei and human chromosomes were determined, except for two small chromosome segments. Twelve human chromosomes are conserved in a unique block of synteny; ten are split into two and one into three blocks. Thus, a small number of interchromosomal rearrangements, about twenty, separates human from this squirrel karyotype. Homoeologies between human and the presumed ancestral chromosomes of Sciurinae could also be deduced, as well as those with the presumed ancestral chromosomes of eutherian mammals. Sciurinae chromosomes appear to be much closer to those of non-rodent mammals than those of Muridae and Cricetidae species studied so far. Thus, they provide an interesting tool to link the rodent genome to those of other mammals.

Animals↗

PubMed2001

Chromosome painting in Arabidopsis thaliana.

Chromosome painting, that is visualisation of chromosome segments or whole chromosomes based on fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes is widely used for chromosome studies in mammals, birds, reptiles and insects. Attempts to establish chromosome painting in euploid plants have failed so far. Here, we report on chromosome painting in Arabidopsis thaliana (n = 5, 125 Mb C(-1)). Pools of contiguous 113-139 BAC clones spanning 2.6 and 13.3 Mb of the short and the long arm of chromosome 4 (17.5 Mb) were used to paint this entire chromosome during mitotic and meiotic divisions as well as in interphase nuclei. The possibility of identifying any particular chromosome region on pachytene chromosomes and within interphase nuclei using selected BACs is demonstrated by differential labelling. This approach allows us, for the first time, to paint an entire autosome of an euploid plant to study chromosome rearrangements, homologue association, interphase chromosome territories, as well as to identify homeologous chromosomes of related species.

Arabidopsis↗

PubMed1984

Hereditary persistence of fetal haemoglobin (HPFH) in conjunction with a chromosomal translocation involving the haemoglobin beta locus.

An HPFH syndrome was found in a woman and her daughter who also carry a 'balanced' cyclic translocation of chromosome segments involving four chromosomes, with one break point located in the region of the Hb beta locus. This HPFH is characterized by 5% and 8% Hb F in peripheral blood, uneven distribution of Hb F in the red cells, and a G gamma/G gamma + A gamma ratio of 0.4. The mapping of the non alpha gene cluster shows no detectable deletion in the entire gamma-delta-beta-globin gene region.

Adult↗

PubMed2006

Direct labelling of BAC-DNA by rolling-circle amplification.

Efficient amplification and labelling of probes are crucial for successful sequence detection by fluorescent in situ hybridization (FISH). In particular, chromosome painting to visualize chromosome segments or entire chromosomes by FISH requires large amounts of probes derived from extended templates. There are a number of techniques for probe labelling. The most widespread is nick translation, based on the replicational incorporation of modified nucleotides. Here we demonstrate successful rolling-circle amplification (RCA) of very low amounts of long circular template sequences (single bacterial artificial chromosomes (BACs) or pools of BACs). The amplicons were suitable for labelling by nick translation and subsequent FISH. A novel achievement is the use of RCA for simultaneous amplification and labelling of single BACs or BAC pools in a labour- and cost-effective manner.

Arabidopsis↗

PubMed1975

An unstable strain of Aspergillus foetidus segregating proline auxotrophs.

Two basic colony types have been obtained through single conidial isolation from the Bode strain of Aspergillus foetidus as well as from mutants of this unstable strain. Type I is prototrophic whereas type II is an auxotroph requiring proline. When a type I strain is grown on complex medium it gradually becomes overwhelmed by type II sectors of growth. However, essentially pure cultures of type I can be maintained on minimal medium (lacking proline). The yield of glucoamylase from type II cultures is less than half that obtained with type I cultures. The instability of type I cultures when grown on complex medium can not be explained by heterokaryosis or the presence of virus-like particles found in the original Bode strain and its derivatives. The isolation of five stable prototrophic strains obtained as more rapidly growing sectors from type I subcultures grown on complex medium suggests that the instability most probably results from a duplicated chromosomal segment or other chromosomal aberration analogous to those described in A. nidulans.

Aspergillus↗

PubMed1981

A cloned gene that is turned on at an intermediate stage of spore formation in Bacillus subtilis.

Cells of Bacillus subtilis synthesize a relatively long-lived ribonucleic acid (RNA) of about 300 bases during the course of spore formation. This transcript does not appear until an intermediate stage (III or IV) of development but is the predominant sporulation-specific transcript among RNAs of discrete size in late (stages IV to VI) developing cells. Appearance of the 300-base RNA is under sporulation control as this transcript could not be detected in cells of an early-blocked sporulation mutant (Spo0A). We have located the coding sequence for the 300-base RNA within a cloned chromosomal segment from the purA-cysA region that was previously shown to contain a cluster of genes that are actively transcribed during sporulation. The coding sequence for the 300-base RNA (designated as the 0.3 kb gene) mapped between a gene (veg) that was actively transcribed during growth and development and a gene (0.4 kb) that was turned on at the onset of sporulation. Although clustered within a small segment of the chromosome, the veg, 0.3 kb, and 0.4 kb transcription units exhibited, therefore, distinct patterns of temporally programmed gene expression. Models for the activation of the 0.3 kb gene at an intermediate stage of development are discussed.

Bacillus subtilis↗

PubMed1996

The Lactobacillus acidophilus S-layer protein gene expression site comprises two consensus promoter sequences, one of which directs transcription of stable mRNA.

S-proteins are proteins which form a regular structure (S-layer) on the outside of the cell walls of many bacteria. Two S-protein-encoding genes are located in opposite directions on a 6.0-kb segment of the chromosome of Lactobacillus acidophilus ATCC 4356 bacteria. Inversion of this chromosomal segment occurs through recombination between two regions with identical sequences, thereby interchanging the expressed and the silent genes. In this study, we show that the region involved in recombination also has a function in efficient S-protein production. Two promoter sequences are present in the S-protein gene expression site, although only the most downstream promoter (P-1) is used to direct mRNA synthesis. S-protein mRNA directed by this promoter has a half-life of 15 min. Its untranslated leader can form a stable secondary structure in which the 5' end is base paired, whereas the ribosome-binding site is exposed. Truncation of this leader sequence results in a reduction in protein production, as shown by reporter gene analysis of Lactobacillus casei. The results obtained indicate that the untranslated leader sequence of S-protein mRNA is involved in efficient S-protein production.

Bacterial Outer Membrane Proteins↗

PubMed2004

Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER.

We analyzed 77 nonproductive and 574 productive human V(H)DJ(H) rearrangements with a newly developed program, JOINSOLVER. In the productive repertoire, the H chain complementarity determining region 3 (CDR3(H)) was significantly shorter (46.7 +/- 0.5 nucleotides) than in the nonproductive repertoire (53.8 +/- 1.9 nucleotides) because of the tendency to select rearrangements with less TdT activity and shorter D segments. Using criteria established by Monte Carlo simulations, D segments could be identified in 71.4% of nonproductive and 64.4% of productive rearrangements, with a mean of 17.6 +/- 0.7 and 14.6 +/- 0.2 retained germline nucleotides, respectively. Eight of 27 D segments were used more frequently than expected in the nonproductive repertoire, whereas 3 D segments were positively selected and 3 were negatively selected, indicating that both molecular mechanisms and selection biased the D segment usage. There was no bias for D segment reading frame (RF) use in the nonproductive repertoire, whereas negative selection of the RFs encoding stop codons and positive selection of RF2 that frequently encodes hydrophilic amino acids were noted in the productive repertoire. Except for serine, there was no consistent selection or expression of hydrophilic amino acids. A bias toward the pairing of 5' D segments with 3' J(H) segments was observed in the nonproductive but not the productive repertoire, whereas V(H) usage was random. Rearrangements using inverted D segments, DIR family segments, chromosome 15 D segments and multiple D segments were found infrequently. Analysis of the human CDR3(H) with JOINSOLVER has provided comprehensive information on the influences that shape this important Ag binding region of V(H) chains.

Algorithms↗

PubMed1999

The applications of FISH in tumor pathology.

The current FISH technology was greatly improved during the past 10 years. A large number of cosmids and yeast (YACs), bacterial (BACs), phage P1 derived (PACs) artificial chromosomes have been rapidly mapped and are useful as probes. In parallel, methods were established to specifically "paint" entire chromosomes or chromosome segments. Using these chromosome libraries as probes, complex rearrangements and marker chromosomes can be identified irrespective of their banding pattern. Ripetitive DNA probes specific for each chromosome centromere (alpha satellite sequences), are also available and may be used to identify specific aneuploidies. The use of sensitive digital imaging systems on the basis of "colour" rather than morphology increased the improvement of new FISH techniques. In particular, colour karyotyping results in the differential colour display of all human chromosomes. Another recent development of FISH technology is comparative genome hybridization (CGH), a genome-scanning technique that allows to identify and map chromosomal and subchromosomal gains and losses. FISH techniques may be used to investigate chromosome abnormalities not only on metaphasic chromosomes but also on interphasic nuclei. Any given tissue or cell source, such as sections of frozen tumors, imprinted cells, cultured cells, paraffin-embedded sections may be hybridized. The interphasic FISH may be extremely informative in tumor pathology even if the results are dependent on a good technical quality and adequate controls.

Cell Nucleus↗