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Expression differences between inversions and their progenitors in Drosophila melanogaster

ABSTRACT: Inversions have a breakpoint within a "neighbourhood" of testis expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion. Keywords: Genome variation profiling by array

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE15565 | GEO | 2010/12/06

SECONDARY ACCESSION(S): PRJNA115733

REPOSITORIES: GEO

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Expression differences between inversions and their progenitors in Drosophila melanogaster

Project description:Inversions have a breakpoint within a "neighbourhood" of testis expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion. 12 different inversion stocks, 3 or 4 biological replicates for each, including dye swaps.

2010-06-25 | E-GEOD-16616 | biostudies-arrayexpress

Expression differences between inversions and their progenitors in Drosophila melanogaster

Project description:Inversions have a breakpoint within a "neighbourhood" of testis expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion. Keywords: Genome variation profiling by array 12 different inversion stocks, 3 or 4 biological replicates for each, including dye swaps.

2010-12-06 | E-GEOD-15565 | biostudies-arrayexpress

Expression differences between inversions and their progenitors in Drosophila melanogaster embryos

Project description:Inversions have a breakpoint within a "neighbourhood" of embryonically expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion.

2010-05-05 | GSE21607 | GEO

Expression differences between inversions and their progenitors in Drosophila melanogaster embryos

2010-05-05 | E-GEOD-21607 | biostudies-arrayexpress

Chromoanagenesis event underlies a de novo pericentric and multiple paracentric inversions in a single chromosome causing Coffin-Siris Syndrome

Project description:Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin-Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90 Mb pericentric and 47 Mb paracentric inversion on a single chromosome. Subsequent analysis using short-read whole genome sequencing, and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leading to CSS1. In all, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the 4th and 5th exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient’s clinical phenotype or resolving unsolved Mendelian disease cases.

2021-07-22 | GSE180423 | GEO

Transcription profiling by array of four strains of budding yeast with inversions engineered between TY1 elements against matching controls

Project description:Gene expression changes due to genome region inversions was studied. Four strains of Saccharomyces cerevisiae strains with inversions engineered between TY1 elements were compared to matching controls.

2014-11-05 | E-MTAB-2613 | biostudies-arrayexpress

Correction of a Factor VIII genomic inversion with designer recombinases

Project description:Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct a 140 kb int1h inversion frequently found in patients diagnosed with Hemophilia A. With the use of directed molecular evolution, we developed a linked heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from int1h patient derived iPSCs, resulted in prominent correction of the inversion and restored Factor VIII mRNA expression. Our data suggest that the development of designer-recombinases represent an efficient and specific mean towards treatment of large gene inversions causing monogenic diseases.

2021-12-31 | GSE159492 | GEO

Genes expression in case of PEV caused by chromosomal rearrangement

Project description:Heterochromatic position effect variegation (PEV) is the epigenetic disruption of genes expression near the new-formed eu-heterochromatic border. We characterized the inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the opposite normal chromosome in combination with the inversion. Euchromatic breakpoint of In(2)A4 inversion was localized at 105 bp region (chr2L:21182214-21182318) of the second exon of the Mcm10 gene, the heterochromatic breakpoint is located at the block of dodecasatellite in 2L pericentromeric heterochromatin. In order to check the effects of heterochromatin on neighbor euchromatic genes and estimate the distance of inactivation spreading, we performed RNA-seq analysis of genes expression in larvae and adults females of genotypes A12/A12 (control) and In(2)A4/In(2)A4. Cis-influence of heterochromatin in the inversion causes not only repression, but also activation of genes, and the effects of heterochromatin are different at different developmental stages. Cis-actions affect only a few genes located near the heterochromatin Comparison of genes expression in wild type and demonstrating PEV larvae and adults in two repeats each

2015-10-25 | E-GEOD-71842 | biostudies-arrayexpress

Genes expression in case of PEV caused by chromosomal rearrangement

2015-10-25 | GSE71842 | GEO

Recurrent 15q13 microdeletions

Project description:We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine patients, including six probands; two with de novo deletions, two who inherited the deletion from an affected parent, and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi/Angelman region extending 3.95 Mb distally to BP5. A smaller 1.5 Mb deletion has proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5 Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is likely responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is ~0.3% (6/2082 tested), a prevalence comparable to that of the Williams, Angelman, and Prader-Willi syndromes. Keywords: microdeletion, genomic disorder, mental retardation, epilepsy

2008-02-17 | GSE10189 | GEO

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