Biology subjects

Mackenzie, S.

Publications and source records attributed to Mackenzie, S..

3 recordsLinked to original sources

bioRxiv2018

Epigenomic plasticity of Arabidopsis msh1mutants under prolonged cold stress

Dynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known. MutS Homolog 1 (MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress-response and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes, msh1 mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures and bacterial pathogen P syringae. Our results suggest that chronic cold and low light stress (10 {degrees}C, 150 E) influences non-CG methylation to a greater degree in msh1 mutants compared to wild type Col-0. Furthermore, CHG changes are more closely pericentromeric, whereas CHH changes are generally more dispersed. This increased variation in non-CG methylation pattern does not significantly affect the msh1-derived enhanced growth behavior after mutants are crossed with isogenic wild type, reiterating the importance of CG methylation changes in msh1-derived enhanced vigor. These results indicate that msh1methylome is hyper-responsive to environmental stress in a manner distinct from the wild type response, but CG methylation changes are potentially responsible for growth vigor changes in the crossed progeny.

plant biology↗

bioRxiv2018

Enhancing resolution of natural methylome reprogramming behavior in plants

BackgroundNatural methylome reprogramming within chromatin involves changes in local energy landscapes that are subject to thermodynamic principles. Signal detection permits the discrimination of methylation signal from dynamic background noise that is induced by thermal fluctuation. Current genome-wide methylation analysis methods do not incorporate biophysical properties of DNA, and focus largely on DNA methylation density changes, which limits resolution of natural, more subtle methylome behavior in relation to gene activity.\n\nResultsWe present here a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection step, and the method was designed to discriminate methylation regulatory signal from background variation. Comparisons with commonly used programs and two publicly available methylome datasets, involving stages of seed development and drought stress effects, were implemented. Information divergence between methylation levels from different groups, measured in terms of Hellinger divergence, provides discrimination power between control and treatment samples. Differentially informative methylation positions (DIMPs) achieved higher sensitivity and accuracy than standard differentially methylated positions (DMPs) identified by other methods. Differentially methylated genes (DMG) that are based on DIMPs were significantly enriched in biologically meaningful networks.\n\nConclusionsMethyl-IT analysis enhanced resolution of natural methylome reprogramming behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods.

genomics↗

bioRxiv2017

An epigenetic breeding system in soybean for increased yield and stability

Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defense, phytohormone, and abiotic stress response pathways. This msh1-conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene-null memory effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study investigates amenability of the MSH1 system for inducing epigenetic variation in soybean that may be of value agronomically. We developed epi-line populations by crossing with msh1-acquired soybean memory lines. Derived soybean epi-lines showed increase in variance for multiple yield-related traits including pods per plant, seed weight, and maturity time in both greenhouse and field trials. Selected epi-F2:4 and epi-F2:5 lines showed an increase in seed yield over wild type. By epi-F2:6, we observed a return of MSH1-derived enhanced growth back to wild type levels. Epi-populations also showed evidence of reduced epitype-by-environment (e x E) interaction, indicating higher yield stability. Transcript profiling of the soybean epi-lines identified putative signatures of enhanced growth behavior across generations. Genes related to cell cycle, abscisic acid biosynthesis, and auxin-response, particularly SMALL AUXIN UP RNAs (SAURs), were differentially expressed in epi-F2:4 lines that showed increased yield when compared to epi-F2:6. These data support the potential of msh1-derived epigenetic variation in plant breeding for enhanced yield and yield stability.

plant biology↗