Biology subjects

Schmitz, R. J.

Publications and source records attributed to Schmitz, R. J..

57 records · Page 4Linked to original sources

bioRxiv2017

TET-mediated epimutagenesis of the Arabidopsis thaliana methylome

DNA methylation in the promoters of plant genes sometimes leads to transcriptional repression, and the wholesale removal of DNA methylation as seen in methyltransferase mutants results in drastic changes in gene expression and severe developmental defects. However, many cases of naturally-occurring DNA methylation variations have been reported, whereby the altered expression of differentially methylated genes is responsible for agronomically important traits. The ability to manipulate plant methylomes to generate populations of epigenetically distinct individuals could provide invaluable resources for breeding and research purposes. Here we describe \"epimutagenesis\", a novel method to rapidly generate variation of DNA methylation through random demethylation of the Arabidopsis thaliana genome. This method involves the expression of a human Ten-eleven translocation (TET) enzyme, and results in widespread hypomethylation that can be inherited to subsequent generations, mimicking mutants in the maintenance DNA methyltransferase met1. Application of TET-mediated epimutagenesis to agriculturally significant plants may result in differential expression of alleles normally silenced by DNA methylation, uncovering previously hidden phenotypic variations.

plant biology↗

bioRxiv2017

Changes Of Gene Expression But Not Cytosine Methylation Are Associated With Behavioural Plasticity Of Parental Care

Behaviour is often on the front line of plasticity in response to different environments. At the genetic level, behavioural changes are likely to be associated with changes of gene expression. Most studies to date have focused on gene expression differences associated with discrete behavioural states reflecting development or age-related changes, such as honey bee castes. However, more rapidly flexible behaviour is often observed in response to social context or simple individual variation. The differences in genetic influences for the different forms of plasticity are poorly understood. In this study we contrasted gene expression during male parental care of the burying beetle, Nicrophorus vespilloides, in a factorial design. Male N. vespilloides males typically do not provide care when females are present. However, male care is inducible by the removing female and has parental effects equivalent to female care. We used this experimental manipulation to isolate gene expression and cytosine methylation associated with differences of behavioural state, differences of social context, or differences of individual flexibility for expressing care. The greatest number of differentially expressed genes was associated with behavioural state, followed by differences of social contexts, and lastly differences of individual variation. DNA methylation has been hypothesized to regulate the transcriptional architecture that regulates behavioural transitions. We tested this hypothesis by quantifying differences of cytosine methylation that were associated with differences of behavioural state and individual flexibility. Changes of cytosine methylation were not associated with changes of gene expression. Our results suggest a hierarchical association between gene expression and the different sources of variation that influence behaviour, but that this process is not controlled by DNA methylation despite reflecting levels of plasticity in behaviour. Our results further suggest that the extent that a behaviour is transient plays an underappreciated role in determining the molecular mechanisms that underpin the behaviour.

genetics↗

bioRxiv2016

Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower.

The importance and applications of polyploidy have long been recognized, from shaping the evolutionary success of flowering plants to improving agricultural productivity. Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. How quickly one subgenome dominates within a newly formed polyploid, if immediate or after millions of years, and the genomic features that determine which genome dominates remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and that subgenome expression dominance significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within transposons in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and submissive subgenomes in the natural allopolyploid. Our analyses reveal that the subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following the hybridization. These findings not only provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events, but may also contribute to uncovering the mechanistic basis of heterosis and subgenomic dominance.

genomics↗