Global modulation of gene expression and transcriptome size in aneuploid combinations of maize
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ABSTRACT:
PROVIDER: PRJNA1200771 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31783900_1.fastq.gz | Fastqsanger.gz | |||
| SRR31783900_2.fastq.gz | Fastqsanger.gz | |||
| SRR31783901_1.fastq.gz | Fastqsanger.gz | |||
| SRR31783901_2.fastq.gz | Fastqsanger.gz | |||
| SRR31783902_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic imbalance refers to the more severe phenotypic consequences of changing a single chromosome compared to changing the whole genome set. Previous genome imbalance studies in maize have identified gene expression modulation in aneuploids of single chromosome arms. Here, the modulation of gene expression in more complex aneuploids, e.g. monosomy of one chromosome arm and trisomy of another. To determine the extent that combination aneuploids were additive, multiplicative, or rebalanced in terms of their effect on gene expression. A series of genetic crosses was performed to produce one, two, and three copies of one arm with independent one, two, and three copies of the other arm in each of the three genotypes for the opposite arm. In total, 31 combinations were analyzed. By examining RNA modulation, we discovered that cis genes on varied chromosome arms are generally more dosage-compensated in aneuploid combinations than in single aneuploidy even though some showed a clear dosage effect. For genes on the unvaried chromosomes (trans), there is greater modulation in most of the aneuploidy combinations. Finally, 22 of the 31 combinations were found to have an altered transcriptome size, suggesting that extensive stoichiometric changes of genomic regions upsets global mRNA transcription. Overall, these results have important implications for understanding the role of genomic stoichiometry for mechanisms of gene expression, the evolution of dosage-sensitive duplicated genes, the evolution of sex chromosomes, the rapid growth adaptation of aneuploid cancer cells, and the diploid of quantitative traits.
2025-04-27 | GSE284999 | GEO
Project description:ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions. Keywords: Genotype comparison of wild-type and segmental aneuploid
2008-01-24 | GSE10243 | GEO
Project description:Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance
| PRJNA556850 | ENA
Project description:In Cyptococcus neoformas, 4 aneuploid strains were spread on YPD plates. We saw colony size variations. We randomly sequenced some large colonies derived from each of the 4 aneuploid strains.
2022-10-24 | E-MTAB-12287 | biostudies-arrayexpress
Project description:Several aneuploid Candida glabrata strains, each bearing a unique karyotype, were spread on YPD plates. They all exhibited colony size vairations. Randmly 10 large colonies from each strain were sequenced.
2023-06-07 | E-MTAB-12484 | biostudies-arrayexpress
Project description:During sexual dimorphism, the loss of one entire X chromosome in Drosophila males is achieved largely via a broad genome-wide aneuploid effect. Exploring how MSL proteins and two large non coding RNAs (roX1 and roX2) modulate trans-acting aneuploid effect for equality to females, we employ a system biology approach (microarray) to investigate the global aneuploid effect of maleless(mle) mutation by disrupting MSL binding. A large number of the genes (144) that encode a broad spectrum of cellular transport proteins and transcription factors are located in the autosomes of Drosophila melanogaster. We find these autosomal targets are sensitive to the aneuploid effect and are poorly conserved in primitive Drosophila species and Anopheles gambiae autosomes. It is expected that during evolutionary process, they shifted gradually from their X chromosomal position in primitive Drosophila to autosomes in melanogaster, suggesting that MSL favors inverse counteraction of these autosomal targets along with X-linked genes. These findings suggest a remarkable and previously unsuspected level of complexity among aneuploid-sensitive genes, that creates a functional shift of the aneuploid effect from X to autosomes during evolution, which is resolved by the binding of MSL complex on the X chromosome..
2016-03-31 | GSE78227 | GEO
Project description:Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of maize chromosome arm 1L was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insight into how the magnitude of genomic imbalance as well as hypoploidy affect global gene expression. While previously available methods required a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. Most studies of global aneuploid effects have concentrated on trisomics because other types of aneuploids are difficult to produce in most model genetic organisms. The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms. Thus, a detailed examination of expression changes both on the varied chromosome arm and elsewhere in the genome is possible, in both hypoploids and hyperploids, compared with euploid controls. Previous studies observed the inverse trans effect, in which genes not varied in DNA dosage are expressed in a negative relationship to the varied chromosomal region. This response was also the major type of change found globally in this study. It was also found that the effects of aneuploidy are progressive, with more severe aneuploids producing effects of greater magnitude.
2020-02-17 | GSE134936 | GEO
Project description:In Candida albicans, aneuploids are unstable. When grown on YPD-agar plates, aneuploids exhibit colony size variations. In this study, 6 aneuploid strains were spread on YPD-agar plates. The large colonies from each strain were sequenced. The small colonies were sequenced in another project.
2023-05-05 | E-MTAB-12409 | biostudies-arrayexpress
Project description:DNA aneuploid sublines in sporadic colorectal cancers (CRCs) are quite frequent (about 85%) and likely the consequence of chromosomal instability and DNA copy number aberrations (CNAs). In order to gain insight into the mechanisms of the diploid-aneuploid transition in CRCs, we compared the CNA status in both diploid and aneuploid sublines. We used fresh/frozen material from 17 aneuploid CRCs, which was separated into 17 DNA diploid and 17 aneuploid sublines using enrichment of the epithelial component by multiparameter flow cytometry and sorting. CNA status of both sublines was obtained by array comparative genomic hybridization. The DNA diploid sublines from the aneuploid CRCs showed already CNAs, in particular, gains at 20p and 20q. The same aberrations were detected at increased frequencies in the corresponding DNA aneuploid sublines. Moreover, the very frequent gains/losses of chromosomes 4, 7, 8, 13, 15, and 18 in the DNA aneuploid sublines were absent or rare in the DNA diploid sublines from the same sporadic aneuploid CRCs. The comparison of the DNA diploid and aneuploid sublines from aneuploid CRCs suggests that 20p and 20q gains may play a role in the diploid-aneuploid transition. The 20q chromosomal arm appears of particular interest since it harbors several genes implicated in chromosomal instability.
2014-10-20 | GSE47148 | GEO
Project description:Effect of various herbicide combinations on maize rhizobacterial community.
| PRJEB4333 | ENA