MicroRNA dosage alterations – what is the consequence?

MicroRNAs play critical regulatory roles in various biological processes in plants, including growth, development, cell fate, stress responses, etc. However, little is known about the impact of dysregulated plant microRNA dosage. Our data provide insights into the understanding of this problem.
MicroRNA dosage alterations – what is the consequence?
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In living organisms, the genome consists of long molecules of DNA called chromosomes. Changes in the number of chromosomes may cause serious problems with growth, development, and function of an organism. There are two basic types of abnormality of chromosome numbers. One is changing the number of individual chromosomes or chromosomal segments (aneuploidy). One famous example, in this case, would be Down Syndrome, one of the most common human aneuploid conditions due to changes in the number of chromosome 21. The other is altering the number of whole sets of chromosomes (polyploidy).

The concept of genomic imbalance.

About a century ago, scientists found out that aneuploidy typically causes more phenotypic defects in plants than polyploidy. Later, this phenomenon became known as genomic imbalance or dosage effect and a gene balance hypothesis was proposed to explain this observation. In an aneuploid condition, the quantitative relationship/ratio of components of protein complexes would be disrupted, thus causing negative fitness consequences. By contrast, this relationship is not affected in polyploidy. Indeed, such effects have been found in large-scale biology studies in many organisms such as Drosophila, Arabidopsis, human, etc.

Photo of maize with increased or decreased dosage of chromosome segments (number of chromosomes:10+1; 20-1; 20+1; 20+2) versus haploid that loses a set of chromosomes (number of chromosomes: 10) relative to the diploid control (number of chromosomes: 20).

Among diploid genetic model organisms, which contain two complete sets of chromosomes, each from one parent, maize is the most tolerant to aneuploidy as evidenced by the fact that it is possible to recover plants with both increased and decreased dosage for all chromosomes. Also, it is possible to produce haploids consisting of only one set of chromosomes with increased chromosomal dosage, together with a range of maize plants composed of various sets of chromosomes. This allows us to address questions about genomic balance that are not readily investigated in other species, considering that most aneuploidies are lethal in mammals. In previous studies published in 2021, we demonstrated that a greater number of genes was differentially expressed in the aneuploids than in the polyploids using mRNA sequencing, which matches their phenotypic observation. In addition, our results suggest that aneuploidy induces changes in gene expression globally, not only on the varied chromosome but also on the chromosomes whose dosage is not altered, which further supports the gene balance hypothesis.

microRNAs (miRNAs) are a class of 20- to 24-nt endogenous small non-coding RNAs that control gene expression through translational inhibition and mRNA target cleavage. They play critical regulatory roles in various biological processes in plants, including growth, development, cell fate, stress responses, etc. A great deal of interest has been placed on the dosage effect of miRNAs in mammals due to their importance in human diseases. However, little is known about the impact of dysregulated miRNA dosage in plants. It is also unclear how aneuploidy or polyploidy affects miRNA expression on a global scale or on a per miRNA basis.

Microscope image of a maize plant with an extra copy of the short arm of chromosome 3 (3S) by fluorescence in situ hybridization.

To address these questions, we assayed the miRNA expression level in a collection of 20 maize lines containing various dosages of chromosomal segments covering 82% of the maize genome, in concert with a ploidy series containing one through four sets of chromosomes. Maize plants were grown in the greenhouse and their chromosomal dosage was verified by fluorescence in situ hybridization. Later, small RNA sequencing was performed on the collected maize mature leaf tissue. Similar to that of protein-coding gene modulation reported in our previous studies, aneuploidy causes significant changes in miRNA expression both on the varied chromosome and the remainder of the genome, and the extent of modulation in aneuploids is much more than that which occurs in polyploids. In addition, miRNAs with varied dosage in aneuploids present a predominant gene-dosage effect, i.e., the amount of gene product is generally a directly proportional reflection of the varied chromosomal dosage although some were unchanged. An inverse correlation between the chromosomal dosage and the amount of miRNA located elsewhere in the genome was observed while examining the modulation of miRNA expression from the unvaried portion of the genome, although other types of responses also occur. Further, to test if miRNAs function as regulators in the changes in global gene expression induced by aneuploidy, we examined correlations between expression levels of miRNAs and their putative targets. We observed significant correlations between expression levels of a number of miRNAs and their putative targets, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance. Varied chromosomal dosage results in modulation of dosage-sensitive miRNAs, and thus causes changes in the expression of their targets, which could operate in cascades affecting more genes. This observation fits with the gene balance hypothesis.

Results in this study imply the potential application of changing the dosage of specific miRNAs as regulators of gene expression under genomic imbalance. In other words, modulation of miRNA expression could reduce the genomic imbalance through neutralizing changes in the expression of key dosage-dependent modifiers occurring with aneuploidy. Considering our data consist of DNA and RNA levels of miRNAs at various dosages, this study also provides a valuable resource for the identification of potential targets of specific miRNAs by investigating the correlation of expression levels between them. Transgenic expression of these miRNAs in maize would facilitate research on the function and molecular mechanism of specific miRNAs.

Read the full article at:

Shi, X., Yang, H., Chen, C. , Hou, J.,  Ji, T.,  Cheng, J., Birchler, J. Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize. Nat Commun 13, 3014 (2022). https://doi.org/10.1038/s41467-022-30704-x