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PubMed2004

Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements.

We have investigated the fluidity of the Salmonella chromosome architecture using the phage lambda site-specific recombination system as a probe. We determined how chromosome position affects the extent of integrase-mediated recombination between pairs of inversely oriented att sites at various loci. We also investigated the accessibility of each chromosomal att site to an extrachromosomal partner carried on a low-copy plasmid. Recombination events were assayed by semi-quantitative polymerase chain reaction of the attP product. The extent of recombination between the chromosome and the plasmid was generally higher than intrachromosomal recombination except for two loci, araA::attL and galT::attL, which gave no detectable recombination with any other locus. Based on 20 intervals, we found that chromosomal locations are not equally accessible to each other. Although multiple factors probably affect accessibility, the most important is the specific combination of the end-points used. Neither the size of the intervals nor the accessibility of individual end-points to extrachromosomal sequences is as important. These results suggest that the chromosome is not completely fluid but rather organized in some way, with barriers that limit the movement of DNA within the cell. The nature of the barriers involved in chromosomal organization remains to be determined.

Attachment Sites, Microbiological↗
PubMed2005

Increased frequency of multiradial chromosome structures in mouse embryonic fibroblasts lacking functional Werner syndrome protein and poly(ADP-ribose) polymerase-1.

To determine whether the mouse Werner syndrome homologue (Wrn) and the poly (ADP-ribose) polymerase-1 (PARP-1) enzymes act in concert to prevent specific chromosomal rearrangements, mice with a mutation in the helicase domain of the Wrn gene (Wrn(Deltahel/Deltahel) mice) were crossed to PARP-1 null mice. Spectral karyotyping of the mouse metaphases was used in correlation with conventional G-banded karyotype analysis to precisely define the chromosomal aberrations in cells. Although there was no recurrent clonal chromosome aberration, PARP-1 null/Wrn(Deltahel/Deltahel) fibroblasts were distinguished by an increased frequency of chromatid breaks. Interestingly, multiradial structures were the only type of DNA rearrangement that was significantly higher in such PARP-1 null/Wrn(Deltahel/Deltahel) cells. These results indicate that Wrn and PARP-1 enzymes may be part of a protein complex involved in the processing of DNA breaks that can ultimately lead to multiradial structures when both enzymes are nonfunctional. Finally, regions of chromosomes known to be fragile sites in the mouse genome are not more prone to DNA rearrangements in the absence of both PARP-1 and functional Wrn proteins. Moreover, the low number of recurrent rearranged chromosome at any given site suggest a random mutagenesis process in PARP-1 null/Wrn(Deltahel/Deltahel) fibroblasts.

Animals↗
PubMed1999

Selective termination for structural, chromosomal, and mendelian anomalies: international experience.

OBJECTIVE: Our purpose was to evaluate the outcomes of selective termination for fetal anomalies at 8 centers with the largest known experiences worldwide. STUDY DESIGN: Outcomes in 402 cases of selective termination in pregnancies with dizygotic twins from 8 centers in 4 countries were analyzed by year, gestational age at procedure, and indication. Reductions of fetuses were as follows: 2 to 1, n = 345; 3 to 2, 39; >/=4 to 2 or 3, n = 18. Potassium chloride was used in all procedures. RESULTS: Selective termination resulted in delivery of a viable infant or infants in >90% of cases. Loss up to 24 weeks occurred in 7.1% of cases in which the final result was a singleton fetus and in 13.0% of cases in which the final result was twins. Loss was 6.6% as a result of structural abnormalities, 7.0% for chromosomal abnormalities, and 10% for mendelian abnormalities (difference not statistically significant). Loss rates for procedures were as follows: 9-12 weeks, 5.4%; 13-18 weeks, 8.7%; 19-24 weeks, 6.8%; and >/=25 weeks, 9.1% (difference not statistically significant). Mean gestational age at delivery was 35.7 weeks. No differences were seen in outcomes by maternal age. The rate of very early premature deliveries has fallen in recent years. There were no known cases of disseminated intravascular coagulation or serious maternal complications. CONCLUSION: (1) Selective termination, in the most experienced hands, can be technically performed in all 3 trimesters with good outcomes in >90% of cases. (2) The previously observed increase in second- versus first-trimester losses has diminished. (3) Third-trimester procedures, where legal, can be performed with a good outcome for the surviving fetus.

Chromosome Aberrations↗
PubMed2004

Combined spectral karyotyping, multicolor banding, and microarray comparative genomic hybridization analysis provides a detailed characterization of complex structural chromosomal rearrangements associated with gene amplification in the osteosarcoma cell line MG-63.

The advancement of fluorescence in situ hybridization-based assays has permitted more refined delineation of chromosomal loci involved in complex chromosomal rearrangements (CCRs) and gene amplification. In this detailed molecular cytogenetic analysis, spectral karyotyping (SKY), multicolor banding (mBAND) analysis, and microarray comparative genomic hybridization (CGH) were used to refine the analysis of chromosomes with amplifications and small intrachromosomal rearrangements such as inverted duplications and interstitial deletions present in the osteosarcoma cell line MG-63. SKY analysis has limited resolving power to delineate cryptic chromosomal rearrangements, so mBAND assays were performed for a subset of chromosomes (i.e., 6, 8, 17, and 20). Of the 10 clonal CCRs analyzed in detail with mBAND, 5 were found to have rearrangements between 8q24 and either 6p23 approximately pter or 6p21, with multiple copies of this translocation inserted at various sites in the different chromosomes. In two CCRs, 6p21 and 8q24 generated an alternating pattern of mBAND probe hybridization, indicating the presence of a large coamplified repeat unit within homogeneously staining regions. Microarray CGH analysis demonstrated focal high-level amplification of 8q23 approximately q24, 6p22 approximately pter, and 6p21, in agreement with the pattern of chromosome subband gains identified with mBAND. Thus, sequential SKY, mBAND, and microarray CGH provided a comprehensive description of some of the intricate chromosomal aberrations present in the complex MG-63 karyotype and permitted reconstruction of the fine structure of the genomic rearrangements, thus providing some important mechanistic clues concerning the details of the amplification process in tumors.

Bone Neoplasms↗
PubMed1993

Gene structure, chromosomal localization, and protein sequence of mouse CD53 (Cd53): evidence that the transmembrane 4 superfamily arose by gene duplication.

CD53 is a pan-leukocyte surface glycoprotein which spans the plasma membrane four times and is a member of the transmembrane 4 superfamily (TM4SF). The protein sequence and gene structure of mouse CD53 (Cd53) were determined by isolation of both genomic and cDNA clones. CD53 is highly conserved in evolution, as mouse Cd53 was 91% identical to rat CD53 and 82% identical to human CD53. The mouse Cd53 gene spanned approximately 9.0 kb of DNA and encoded the 219 amino acid residues of CD53 over seven exons. The Cd53 gene produced a 1.8 kb transcript which was dramatically upregulated after cell activation. The mouse Cd53 gene was mapped to chromosome 3, whereas the locus of another TM4SF member, CD37 (Cd37), was mapped to mouse chromosome 7. Three lines of evidence suggest that the TM4SF arose divergently from an ancestral gene. First, the gene structure of CD53 was strikingly similar to two other members of the TM4SF, CD63 and TAPA-1; second, Cd37 mapped to the same chromosome as Tapa-1; and, third, Cd37 mapped to a segment of chromosome 7 that contains a number of genes that are structurally or functionally related to genes closely linked to Cd53 on chromosome 3.

Amino Acid Sequence↗
PubMedDate not supplied

[Chromosomal structure of Pseudomonas testosteroni. II. Activity of the endogenous RNA-polymerase (author's transl)].

After careful lysis the nucleoid of Pseudomonas testosteroni can be isolated in three different forms with compact and unfolded DNA structures. The released nucleoids contain endogenous DNA-dependent RNA-polymerase activity using the chromosomal DNA as a template. RNA synthesis is proportional to duration of RNA-polymerase reaction and amount of DNA-protein-complexes. The sensitivity towards ionic strength and rifampicin indicates that a part of RNA-polymerase activity is tightly bound to the chromosomal DNA.

Chromosomes↗
PubMed1998

Chromosome structure and human immunodeficiency virus type 1 cDNA integration: centromeric alphoid repeats are a disfavored target.

Integration of retroviral cDNA into host chromosomal DNA is an essential and distinctive step in viral replication. Despite considerable study, the host determinants of sites for integration have not been fully clarified. To investigate integration site selection in vivo, we used two approaches. (i) We have analyzed the host sequences flanking 61 human immunodeficiency virus type 1 (HIV-1) integration sites made by experimental infection and compared them to a library of 104 control sequences. (ii) We have also analyzed HIV-1 integration frequencies near several human repeated-sequence DNA families, using a repeat-specific PCR-based assay. At odds with previous reports from smaller-scale studies, we found no strong biases either for or against integration near repetitive sequences such as Alu or LINE-1 elements. We also did not find a clear bias for integration in transcription units as proposed previously, although transcription units were found somewhat more frequently near integration sites than near controls. However, we did find that centromeric alphoid repeats were selectively absent at integration sites. The repeat-specific PCR-based assay also indicated that alphoid repeats were disfavored for integration in vivo but not as naked DNA in vitro. Evidently the distinctive DNA organization at centromeres disfavors cDNA integration. We also found a weak consensus sequence for host DNA at integration sites, and assays of integration in vitro indicated that this sequence is favored as naked DNA, revealing in addition an influence of target primary sequence.

Binding Sites↗
PubMed1978

[Chromosomal structure or porcine lymphocytes effected by food additives].

Different concentrations of food additives were introduced in cultures of pig lymphocytes. No special chromosomal damage were induced by anticoccidians. On the contrary some antibiotics caused chromosomic anomalies. Chloramphenicol and furazolidone assayed in vitro and in vivo had also an antimitotic effect. The purpose of this work was to know the cytotoxic effect of some substances: a preliminary and cheap test could be a cytogenetic examination in vitro.

Animals↗
PubMed1991

Structure, chromosome mapping, and expression of the mouse Lyl-1 gene.

The mouse Lyl-1 gene was cloned and shown to consist of four exons with extensive nucleotide and structural homology to the human LYL1 gene. The Lyl-1 gene was localized to the central region of mouse chromosome 8 which defines a new region of synteny with human chromosome 19p. The predicted mouse Lyl-1 protein is 78% identical to human LYL1. The region of highest similarity occurs in the basic DNA binding and helix-loop-helix dimerization motifs which are nearly identical in mouse and man differing by only one conservative amino acid substitution. Expression of the Lyl-1 gene was found to be low in murine spleen and undetectable in other tissues by Northern blot analysis. In lymphoid cell lines, Lyl-1 was expressed in most B lineage cells but downregulated during terminal differentiation and was not expressed in most T lineage cells. In a human T ALL cell line carrying a translocation that juxtaposed LYL1 with the beta TCR gene, the translocated LYL1 gene was transcriptionally active whereas the nontranslocated gene was transcriptionally silent. We conclude that LYL1 has the properties of a lineage- and differentiation-specific HLH protein that contributes to T-cell neoplasia through its deregulated expression following chromosomal translocation.

Amino Acid Sequence↗