Gross rearrangement breakpoint database (GRaBD?)

2004 ◽  
Vol 23 (3) ◽  
pp. 219-221 ◽  
Author(s):  
Shaun S. Abeysinghe ◽  
Peter D. Stenson ◽  
Michael Krawczak ◽  
David N. Cooper
Keyword(s):  
Rearrangement Breakpoint

Rearrangement and expression of erythropoietin genes in transformed mouse cells

1987 ◽  
Vol 7 (1) ◽  
pp. 365-370
Author(s):  
J McDonald ◽  
N Beru ◽  
E Goldwasser
Keyword(s):  
Cell Line ◽  
Murine Leukemia Virus ◽  
Normal Mouse ◽  
Leukemia Virus ◽  
Normal Gene ◽  
Erythroleukemia Cell ◽  
Mouse Cells ◽  
Viral Sequences ◽  
Murine Leukemia ◽  
Rearrangement Breakpoint

The erythroleukemia cell line IW32, derived by transformation with the Friend murine leukemia virus, has been shown previously to produce erythropoietin (EPO) constitutively. Here we demonstrate that, in addition to the normal mouse EPO locus, this cell line has another EPO locus which has undergone rearrangement and amplification. Both loci were cloned, and the rearrangement breakpoint of the second EPO locus was located within a 1.1-kilobase region upstream of an otherwise apparently normal EPO gene. There are no viral sequences present in the immediate vicinity of the rearranged EPO gene. DNase I digestion studies suggest that the rearranged gene is in a region where the chromatin is more sensitive to DNase hydrolysis than is the site of the normal gene. We conclude, tentatively, that the rearranged EPO locus is probably the transcriptionally active one and that either proviral sequences are acting at a distance to activate the EPO gene or the rearrangement itself has served to activate the gene.

scholarly journals Rearrangement and expression of erythropoietin genes in transformed mouse cells.

1987 ◽  
Vol 7 (1) ◽  
pp. 365-370 ◽  
Author(s):  
J McDonald ◽  
N Beru ◽  
E Goldwasser
Keyword(s):  
Cell Line ◽  
Murine Leukemia Virus ◽  
Normal Mouse ◽  
Leukemia Virus ◽  
Normal Gene ◽  
Erythroleukemia Cell ◽  
Mouse Cells ◽  
Viral Sequences ◽  
Murine Leukemia ◽  
Rearrangement Breakpoint

The erythroleukemia cell line IW32, derived by transformation with the Friend murine leukemia virus, has been shown previously to produce erythropoietin (EPO) constitutively. Here we demonstrate that, in addition to the normal mouse EPO locus, this cell line has another EPO locus which has undergone rearrangement and amplification. Both loci were cloned, and the rearrangement breakpoint of the second EPO locus was located within a 1.1-kilobase region upstream of an otherwise apparently normal EPO gene. There are no viral sequences present in the immediate vicinity of the rearranged EPO gene. DNase I digestion studies suggest that the rearranged gene is in a region where the chromatin is more sensitive to DNase hydrolysis than is the site of the normal gene. We conclude, tentatively, that the rearranged EPO locus is probably the transcriptionally active one and that either proviral sequences are acting at a distance to activate the EPO gene or the rearrangement itself has served to activate the gene.

The adenosine2 gene of Drosophila melanogaster encodes a formylglycineamide ribotide amidotransferase

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 924-934 ◽  
Author(s):  
S. Y. K. Tiong ◽  
D. Nash
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Genomic Dna ◽  
Gene Rearrangement ◽  
Single Gene ◽  
Genetic Material ◽  
Biosynthetic Enzyme ◽  
E Coli ◽  
Enzymatic Function ◽  
Rearrangement Breakpoint

Drosophila melanogaster genomic DNA spanning an adenosine2 gene rearrangement breakpoint (in cytological map region 26B1-2) was cloned and a composite ade2 base sequence was derived from this DNA and from a corresponding cDNA. Based on genetic evidence, the ade2 gene is thought to encode the purine biosynthetic enzyme formylglycineamide ribotide amidotransferase (FGARAT). The cDNA hybridizes to a 4.8-kb message that encodes a 1354 amino acid polypeptide with extensive similarity to Escherichia coli FGARAT. The D. melanogaster FGARAT amino acid sequence is considerably more like that of the E. coli enzyme than is the FGARAT of B. subtilis, which has two polypeptides with, collectively, 969 amino acids. It is suggested that the taxonomically anomalous similarity between the eukaryotic FGARAT and that from E. coli may indicate horizontal exchange of genetic material. On the basis of substantially greater conservation of sequences snared by all three species compared with those present only in E. coli and D. melanogaster, we suggest that no radical alteration of enzymatic function accompanied the transition between the single-gene and the two-gene state.Key words: Drosophila melanogaster, purine biosynthesis genes, formylglycineamide ribotide amidotransferase, formylglycineamidine ribotide synthase, adenosine2 locus, horizontal gene transfer.

scholarly journals A MEIOTIC UV-SENSITIVE MUTANT THAT CAUSES DELETION OF DUPLICATIONS IN NEUROSPORA

Genetics ◽  
1978 ◽  
Vol 89 (2) ◽  
pp. 245-269
Author(s):  
Dorothy Newmeyer ◽  
Donna R Galeazzi
Keyword(s):  
Neurospora Crassa ◽  
Single Gene ◽  
Complete Loss ◽  
Duplicate Segment ◽  
Sensitive Mutant ◽  
Rearrangement Breakpoint ◽  
Ascospore Formation

ABSTRACT The meiotic-3 (mei-3) mutant of Neurospora crassa has several effects: (1) When homozygous, it almost completely blocks meiosis and ascospore formation, (2) it is sensitive to UV, (3) its growth is inhibited by histidine and, (4) it increases the instability of nontandem duplications. This was shown for duplications produced by five different rearrangements and was demonstrated by two different criteria. The effects on meiosis and duplication instability are expressed strongly at 25°; the effects on sensitivity to UV and to histidine are expressed strongly at 38.5° but only slightly at 25°. Nevertheless, all four effects were shown to be due to a single gene. mei-3 is not allelic with previously reported UV-sensitive mutants.—Two other results were obtained that are not necessarily due to mei-3: (1) A cross involving mei-3 produced a new unlinked meiotic mutant, mei-4, which is not sensitive to UV or histidine, and (2) a burst of several new mutants occurred in a different mei-3 stock, including a partial revertant of mei-3.—mei-3 has previously been shown to cause frequent complete loss of a terminal duplicate segment, beginning exactly at the original rearrangement breakpoint. Possible mechanisms are discussed by which a UV-sensitive mutant could cause such precise deletions.

scholarly journals Reference-free prediction of rearrangement breakpoint reads

2014 ◽  
Vol 30 (18) ◽  
pp. 2559-2567 ◽  
Author(s):  
Edward Wijaya ◽  
Kana Shimizu ◽  
Kiyoshi Asai ◽  
Michiaki Hamada
Keyword(s):  
Rearrangement Breakpoint

A Quantitative Measure of the Mitotic Pairing of Alleles in Drosophila melanogaster and the Influence of Structural Heterozygosity

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 385-400 ◽  
Author(s):  
Mary M Golic ◽  
Kent G Golic
Keyword(s):  
Cell Cycle ◽  
Quantitative Measure ◽  
Site Specific ◽  
Homologous Chromosomes ◽  
Structural Heterozygosity ◽  
Dividing Cells ◽  
Cycle Lengths ◽  
Existing Data ◽  
Rearrangement Breakpoint ◽  
Normal Pairing

Abstract In Drosophila there exist several examples of gene expression that can be modified by an interaction between alleles; this effect is known as transvection. The inference that alleles interact comes from the observations that homologous chromosomes pair in mitotically dividing cells, and that chromosome rearrangements can alter the phenotype produced by a pair of alleles. It is thought that heterozygous rearrangements impede the ability of alleles to pair and interact. However, because the existing data are inconsistent, this issue is not fully settled. By measuring the frequency of site-specific recombination between homologous chromosomes, we show that structural heterozygosity inhibits the pairing of alleles that lie distal to a rearrangement breakpoint. We suggest that some of the apparent conflicts may owe to variations in cell-cycle lengths in the tissues where the relevant allelic interactions occur. Cells with a longer cell cycle have more time to establish the normal pairing relationships that have been disturbed by rearrangements. In support, we show that Minute mutations, which slow the rate of cell division, partially restore a transvection effect that is disrupted by inversion heterozygosity.

Chromosome Rearrangement Breakpoint Clustering: The Role of Clonal Selection

2005 ◽  
Vol 39 (3) ◽  
pp. 313-320 ◽  
Author(s):  
O. N. Umanskaya ◽  
A. A. Bystritskiy ◽  
S. V. Razin
Keyword(s):  
Clonal Selection ◽  
Chromosome Rearrangement ◽  
Rearrangement Breakpoint

scholarly journals A Reexamination of Spreading of Position-Effect Variegation in the white-roughest Region of Drosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 259-272 ◽  
Author(s):  
Paul B Talbert ◽  
Steven Henikoff
Keyword(s):  
Chromosomal Rearrangements ◽  
Position Effect ◽  
White Gene ◽  
Position Effect Variegation ◽  
Continuous Linear ◽  
Effect Variegation ◽  
Drosophila Heterochromatin ◽  
In Trans ◽  
Linear Propagation ◽  
Rearrangement Breakpoint

Abstract In Drosophila, heterochromatin causes mosaic silencing of euchromatic genes brought next to it by chromosomal rearrangements. Silencing has been observed to “spread”: genes closer to the heterochromatic rearrangement breakpoint are silenced more frequently than genes farther away. We have examined silencing of the white and roughest genes in the variegating rearrangements In(1)wm4, In(1)wmMc, and In(1)wm51b. Eleven stocks bearing these chromosomes differ widely in the strength of silencing of white and roughest. Stock-specific differences in the relative frequencies of inactivation of white and roughest were found that map to the white-roughest region or the adjacent heterochromatin. Most stock-specific differences did not correlate with gross differences in the heterochromatic content of the rearranged chromosomes; however, two stocks, In(1)wm51b and In(1)wmMc, were found to have anomalous additional heterochromatin that may act in trans to suppress variegating alleles. In comparing different stocks, the frequency of silencing of the roughest gene, which is more distant from heterochromatin, does not correlate with the frequency of silencing of the more proximal white gene on the same chromosome, in contradiction to the expectation of models of continuous linear propagation of silencing. We frequently observed rough eye tissue that is pigmented, as though an active white gene is skipped.

scholarly journals Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification

2017 ◽  
Vol 38 (12) ◽  
pp. 1711-1722 ◽  
Author(s):  
Morten Hillmer ◽  
Anna Summerer ◽  
Victor-Felix Mautner ◽  
Josef Högel ◽  
David N. Cooper ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Haplotype Diversity ◽  
Recombination Hotspots ◽  
Nonallelic Homologous Recombination ◽  
Rearrangement Breakpoint
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