Array CGH data of A. oryzae strains bearing translocated chromosomal duplication and triplication
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus oryzae RIB40 Aspergillus oryzae
PROVIDER: GSE120604 | GEO | 2018/10/23
REPOSITORIES: GEO
Similar Datasets
Project description:Array CGH data of A. oryzae strains bearing translocated chromosomal duplication and triplication
| PRJNA493741 | ENA
Project description:We here describe the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had 5’ΔpyrG upstream of the region targeted for tandem chromosomal duplication and 3’ΔpyrG downstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under non-selective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.
2014-06-30 | GSE57246 | GEO
Project description:We here describe the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had 5M-bM-^@M-^YM-NM-^TpyrG upstream of the region targeted for tandem chromosomal duplication and 3M-bM-^@M-^YM-NM-^TpyrG downstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under non-selective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method. A. oryzae strain bearing a 210-kb targeted tandem chromosomal duplication, A. oryzae strain bearing a 700-kb targeted tandem chromosomal duplication, and A. oryzae RIB40 (wild type strain), were cultivated in Polypeptone-dextrin medium. After 3 days cultivation, genomic DNAs from the samples were extracted, and array CGH analysis was carried out to confirm the chromosomal duplications in the strains.
2014-06-30 | E-GEOD-57246 | biostudies-arrayexpress
Project description:Array CGH was performed to identify the breakpoints in 3 cases with deletions of 16p11.2p12.2 and 1 case with a duplication/triplication of 16p11.2p12.2.
2007-09-01 | E-TABM-286 | biostudies-arrayexpress
Project description:Sirtuin is considered to play a significant role in the growth phase-dependent gene expression. In this study, we characterized sirtuin in the white koji fungus, Aspergillus kawachii, to examine their role on regulation of amylolytic enzymes and citric acid productions during the solid-state culture (koji). Characterization of rice-koji made using five putative sirtuin gene disruptants indicated that they are involved in amylolytic activity and acidity of rice koji; especially the sirD disruptant showed lower levels of α-amylase activity and citric acid production per mycelial weight in the koji compared the control strain. In addition, the sirD disruptant also showed a change in mycelial pigmentation, higher sensitivity to cell wall biogenesis inhibitor such as calcofluor white and Congo red, and reduced conidia formation, indicating that SirD is required for secondary metabolism, cell wall integrity, and conidial development. The cap analysis gene expression (CAGE) indicated that the transcriptional changes related to the characteristic phenotype of the sirD disruptant (e.g., a reduced transcript level of acid-stable α-amylase gene and a citric acid exporter) in rice koji. These results indicated that SirD has a significant role on the global transcriptional regulation including productions of α-amylase and citric acid in A. kawachii during the solid-state fermentation process.
2019-06-15 | GSE132729 | GEO
Project description:Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex DUP-TRP/INV-DUP rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals M-bM-^@M-^S 16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homologyM-bM-^@M-^Tor homeologyM-bM-^@M-^Tdriven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication, and potentially higher order amplification of a genomic interval, can occur in a manner consistent with rolling circle amplification as predicted by the microhomology mediated break induced replication (MMBIR) model. To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the Xq22 chromosomal region to query the genomic DNA of 7 males with Pelizaeus-Merzbacher disease, and 5 unaffected or carrier/unaffected family members. A 4x44k Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website targeting the region of the genome encompassing the dosage-sensitive PLP1 gene.
2014-11-25 | E-GEOD-63594 | biostudies-arrayexpress
Project description:Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex DUP-TRP/INV-DUP rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals – 16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology—or homeology—driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication, and potentially higher order amplification of a genomic interval, can occur in a manner consistent with rolling circle amplification as predicted by the microhomology mediated break induced replication (MMBIR) model.
2014-11-25 | GSE63594 | GEO
Project description:A koji mold Aspergillus kawachii is used for making a Japanese distilled spirit, shochu. During making shochu, A. kawachii is grown in a solid-state culture comprised of steamed grains such as rice or barley, termed koji, to convert the starch to glucose and also to produce citric acid. During this process, cultivation temperature of A. kawachii is generally controlled by raising to 40M-BM-0C and then lowering to 30M-BM-0C. The cultivation at 40M-BM-0C and the following at lower temperature of 30M-BM-0C has important roles in the elevated activity of amylase and starting an accumulation of a large amount of citric acid, respectively. In this study, we investigated the effect of temperature on the gene expression of A. kawachii when barley was used as ingredient for making koji. The results of DNA microarray and gene ontology analysis showed that the expression of genes involved in the metabolic processes of glycerol, trehalose, and pentose phosphate that branch from glycolysis was down-regulated by shifting the cultivation temperature from 40M-BM-0C from 30M-BM-0C. In addition, reduction in the expression of the genes related with heat shock responses and increasing in the expression of the genes related with amino acid transport after the temperature lowering were found to be significant change. These results suggested that the cultivation at 40M-BM-0C is stressful event for the A. kawachii and the heat adaption lead to the depression of citric acid accumulation through activation of the branching pathways from glycolysis. The gene expression profile obtained in this study will help to understand the gene regulation during koji-making process to optimize A. kawachii as industrial microorganism. Gene expression of Aspergillus kawachii in barley koji was measured at 25, 26.5, and 44 hours at two different temperature control. Three independent experiments were performed at each time (25, 26.5, or 44 hours) using different barley koji for each expreriment.
2014-06-14 | E-GEOD-58454 | biostudies-arrayexpress
Project description:Down syndrome (DS) confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (ALL), yet the mechanisms underlying this association are undefined. We show that triplication of only 31 genes orthologous to the putative DS Critical Region (DSCR) on chr.21q22 is sufficient to promote B cell-autonomous self-renewal, in vivo maturation defects and leukemogenesis in concert with BCR-ABL. DSCR triplication results in histone H3 lysine 27 (H3K27) hypomethylation at gene promoters and a transcriptional signature characterized by de-repression of genes targeted by polycomb repressor complex 2 (PRC2), which methylates H3K27. The same signature is highly enriched among human DS-associated ALLs. Pharmacologic inhibition of PRC2 function is sufficient to confer self-renewal in wild-type B cells while inhibition of H3K27me3 demethylases completely blocks self-renewal induced by DSCR triplication. Finally, overexpression of the DSCR factor HMGN1, a nucleosome remodeling protein that suppresses H3K27me3, is necessary for self-renewal in B cells with DSCR triplication.
2014-04-20 | GSE48553 | GEO
Project description:Down syndrome (DS) confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (ALL), yet the mechanisms underlying this association are undefined. We show that triplication of only 31 genes orthologous to the putative DS Critical Region (DSCR) on chr.21q22 is sufficient to promote B cell-autonomous self-renewal, in vivo maturation defects and leukemogenesis in concert with BCR-ABL. DSCR triplication results in histone H3 lysine 27 (H3K27) hypomethylation at gene promoters and a transcriptional signature characterized by de-repression of genes targeted by polycomb repressor complex 2 (PRC2), which methylates H3K27. The same signature is highly enriched among human DS-associated ALLs. Pharmacologic inhibition of PRC2 function is sufficient to confer self-renewal in wild-type B cells while inhibition of H3K27me3 demethylases completely blocks self-renewal induced by DSCR triplication. Finally, overexpression of the DSCR factor HMGN1, a nucleosome remodeling protein that suppresses H3K27me3, is necessary for self-renewal in B cells with DSCR triplication. Gene expression analysis of 6 samples, 3 wild-type and 3 Ts1Rhr proB cells at passage 1
2014-04-20 | E-GEOD-48553 | biostudies-arrayexpress