Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa
Journal
Proceedings of the National Academy of Sciences of the United States of America
Journal Volume
115
Journal Issue
48
Start Page
E11321
End Page
E11330
ISSN
0027-8424
Date Issued
2018-11-14
Author(s)
Hou, Jie
Shi, Xiaowen
Chen, Chen
Islam, Md. Soliman
Johnson, Adam F.
Kanno, Tatsuo
Huettel, Bruno
Yen, Ming-Ren
et al.
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
Subjects
Aneuploidy
Dosage compensation
Gene balance hypothesis
Polyploidy
Trisomy
Publisher
National Academy of Sciences
Type
journal article