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Genomic imbalance determines positive and negative modulation of gene expression in diploid maize.

ABSTRACT: Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

SUBMITTER: Shi X

PROVIDER: S-EPMC8226301 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

Project description:We examined the impact of both increased and decreased dosage of fifteen distal and one interstitial chromosomal regions via RNA-seq of maize mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated towards the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which expression of many genes under genome imbalance are modulated towards the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

2021-02-02 | GSE149186 | GEO

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

Project description:Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

| PRJNA627610 | ENA

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize.

Project description:The genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis of maize (Zea mays) aneuploids revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). However, little is known regarding the role of microRNAs (miRNAs) under genomic imbalance. Here, we report the impact of aneuploidy and polyploidy on the expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. By contrast, polyploids show less differential miRNA expression than aneuploids. Significant correlations between expression levels of miRNAs and their targets are identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance.

| S-EPMC9156689 | biostudies-literature

Genomic imbalance modulates transposable element expression in maize.

Project description:Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set. Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes (trans) with both the addition or subtraction of chromosome arms. Transposable elements (TEs) comprise a substantial fraction of the genome, and their reaction to genomic imbalance is therefore of interest. Here, we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs, but reductions in monosomy and increases in disomy and trisomy were also common. By contrast, the ploidy series showed little TE modulation. The modulation of TEs and genes in the same experimental group were compared, and TEs showed greater modulation than genes, especially in disomy. Class I and II TEs were differentially modulated in most aneuploidies, and some superfamilies in each TE class also showed differential modulation. Finally, the significantly upregulated TEs in three disomies (TB-7Lb, TB9Lc, and TB-10L19) did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs, indicating that modulations of TEs do not compound the effect on genes. These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs, similar to the response of core genes to genomic imbalance.

| S-EPMC10030319 | biostudies-literature

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

Project description:Genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis on RNA-sequencing data of varied dosage of various chromosomal regions in maize (Zea mays) revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). Dysregulation of microRNA (miRNA) dosage has been reported to have profound deleterious effects in many species. miRNAs are preferentially retained as duplicates following whole-genome duplication in grass species and are postulated to be dosage-sensitive. However, little is known regarding the role of miRNAs under genomic imbalance. We examined the impact of increased and/or decreased dosage of 1 interstitial and 19 distal chromosomal regions in concert with a whole-genome ploidy series of haploid, diploid, triploid, and tetraploid via small RNA-sequencing of diploid and haploid maize mature leaf tissue to investigate the impact of aneuploidy and polyploidy on expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. Significant correlations between expression levels of miRNAs and their targets were identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance. The findings provide novel insights into understanding of gene balance from the aspect of the function of miRNAs.

2022-05-12 | GSE189317 | GEO

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

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

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

Project description:Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

| PRJNA782967 | ENA

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

Project description:Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

| PRJNA556850 | ENA

Gamma-tocotrienol modulation of senescence-associated gene expression prevents cellular aging in human diploid fibroblasts.

Project description:ObjectiveHuman diploid fibroblasts undergo a limited number of cellular divisions in culture and progressively reach a state of irreversible growth arrest, a process termed cellular aging. The beneficial effects of vitamin E in aging have been established, but studies to determine the mechanisms of these effects are ongoing. This study determined the molecular mechanism of γ-tocotrienol, a vitamin E homolog, in the prevention of cellular aging in human diploid fibroblasts using the expression of senescence-associated genes.MethodsPrimary cultures of young, pre-senescent, and senescent fibroblast cells were incubated with γ-tocotrienol for 24 h. The expression levels of ELN, COL1A1, MMP1, CCND1, RB1, and IL6 genes were determined using the quantitative real-time polymerase chain reaction. Cell cycle profiles were determined using a FACSCalibur Flow Cytometer.ResultsThe cell cycle was arrested in the G(0)/G(1) phase, and the percentage of cells in S phase decreased with senescence. CCND1, RB1, MMP1, and IL6 were upregulated in senescent fibroblasts. A similar upregulation was not observed in young cells. Incubation with γ-tocotrienol decreased CCND1 and RB1 expression in senescent fibroblasts, decreased cell populations in the G(0)/G(1) phase and increased cell populations in the G(2)/M phase. γ-Tocotrienol treatment also upregulated ELN and COL1A1 and downregulated MMP1 and IL6 expression in young and senescent fibroblasts.Conclusionγ-Tocotrienol prevented cellular aging in human diploid fibroblasts, which was indicated by the modulation of the cell cycle profile and senescence-associated gene expression.

| S-EPMC3275122 | biostudies-literature

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize.

Project description:The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified 17 distal segmental haploid disomies that cover ∼80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.

| S-EPMC8226288 | biostudies-literature

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