Dataset Information

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression.

ABSTRACT: In flowering plants, gene body methylation (gbM) is associated with a subset of constitutively expressed genes. It has been proposed that gbM modulates gene expression. Here, we show that there are no consistent and direct differences to expression following the loss of gbM. By comparing expression of gbM genes in Arabidopsis thaliana accessions to orthologous genes in two Eutrema salsugineum genotypes, we identified both positive and negative expression differences associated with gbM loss. However, expression is largely unaffected by gbM loss in E. salsugineum Expression differences between species were within the variation of expression observed within A. thaliana accessions that displayed variation in gbM. Furthermore, experimentally induced loss of gbM did not consistently lead to differences in expression compared to wild type. To date, there is no convincing data to support a direct causal link between the presence/absence of gbM and the modulation of expression in flowering plants.

SUBMITTER: Bewick AJ

PROVIDER: S-EPMC6686912 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression.

Bewick Adam J AJ Zhang Yinwen Y Wendte Jered M JM Wendte Jered M JM Zhang Xiaoyu X Schmitz Robert J RJ

G3 (Bethesda, Md.) 20190808 8

In flowering plants, gene body methylation (gbM) is associated with a subset of constitutively expressed genes. It has been proposed that gbM modulates gene expression. Here, we show that there are no consistent and direct differences to expression following the loss of gbM. By comparing expression of gbM genes in <i>Arabidopsis thaliana</i> accessions to orthologous genes in two <i>Eutrema salsugineum</i> genotypes, we identified both positive and negative expression differences associated with ...[more]

PMID: 31147389

Similar Datasets

Project description:BACKGROUND: Characterization of robustness and plasticity of phenotypes is a basic issue in evolutionary and developmental biology. The robustness and plasticity are concerned with changeability of a biological system against external perturbations. The perturbations are either genetic, i.e., due to mutations in genes in the population, or epigenetic, i.e., due to noise during development or environmental variations. Thus, the variances of phenotypes due to genetic and epigenetic perturbations provide quantitative measures for such changeability during evolution and development, respectively. RESULTS: Using numerical models simulating the evolutionary changes in the gene regulation network required to achieve a particular expression pattern, we first confirmed that gene expression dynamics robust to mutation evolved in the presence of a sufficient level of transcriptional noise. Under such conditions, the two types of variances in the gene expression levels, i.e. those due to mutations to the gene regulation network and those due to noise in gene expression dynamics were found to be proportional over a number of genes. The fraction of such genes with a common proportionality coefficient increased with an increase in the robustness of the evolved network. This proportionality was generally confirmed, also under the presence of environmental fluctuations and sexual recombination in diploids, and was explained from an evolutionary robustness hypothesis, in which an evolved robust system suppresses the so-called error catastrophe--the destabilization of the single-peaked distribution in gene expression levels. Experimental evidences for the proportionality of the variances over genes are also discussed. CONCLUSIONS: The proportionality between the genetic and epigenetic variances of phenotypes implies the correlation between the robustness (or plasticity) against genetic changes and against noise in development, and also suggests that phenotypic traits that are more variable epigenetically have a higher evolutionary potential.

Dataset Information

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression.

Publications

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets