Biology subjects

Moore, J. D.

Publications and source records attributed to Moore, J. D..

6 recordsLinked to original sources

bioRxiv2022

Unified establishment and epigenetic inheritance of DNA methylation through cooperative MET1 activity

Methylation of CG dinucleotides (mCG), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity remains mysterious. Here we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z. Based on these observations, we develop a mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing as input. The model reveals that intragenic mCG undergoes large, millennia-long epigenetic fluctuations, and can therefore mediate evolution on this timescale. Our results demonstrate how genic methylation patterns are created, reconcile imperfect mCG maintenance with long-term stability, and establish a quantitative model that unifies the establishment and epigenetic inheritance of mCG. HighlightsO_LIMET1 mediates a unified process of mCG establishment and maintenance within genes C_LIO_LIROS1 and H2A.Z regulate the epigenetic dynamics of genic mCG C_LIO_LIA mathematical model predicts genic mCG patterns and their population variance C_LIO_LIGenic mCG undergoes large epigenetic fluctuations that can last thousands of years C_LI

genetics↗

bioRxiv2021

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for designing new approaches in crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

evolutionary biology↗

bioRxiv2021

Gene body methylation mediates epigenetic inheritance of plant traits

Genetic variation is regarded as a prerequisite for evolution. In principle, epigenetic information inherited independently of DNA sequence can also enable evolution, but whether this occurs in natural populations is unknown. Here we show that natural epigenetic DNA methylation polymorphism in Arabidopsis thaliana gene bodies regulates gene expression and influences the variation of complex traits: fitness under heat and drought, flowering time, and accumulation of diverse minerals. The phenotypic effects of DNA methylation and local DNA sequence polymorphism are comparable, but they operate through largely distinct gene sets. Our epigenetic association analyses directly identify the relevant gene more frequently than genetic associations, likely due to reduced linkage disequilibrium. We identify numerous associations between methylation epialleles and diverse environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Overall, our results demonstrate that epigenetic methylation variation fundamentally shapes phenotypic diversity in natural populations.

evolutionary biology↗

bioRxiv2020

Time series transcriptomics reveals a BBX32-directed control of dynamic acclimation to high light in mature Arabidopsis leaves

The photosynthetic capacity of mature leaves increases after several days exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. This is termed dynamic acclimation but how it is initiated and controlled is unknown. From fully expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6h time-series transcriptomics experiment. It was hypothesised that among such genes were those that contribute to the initiation of dynamic acclimation. By focussing on HL differentially expressed transcription (co-)factor (TF) genes and applying dynamic statistical modelling to the temporal transcriptomics data, a gene regulatory network (GRN) of 47 predominantly photoreceptor-regulated (co)-TF genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants over-expressing BBX32 were strongly impaired in dynamic acclimation and displayed perturbed expression of genes involved in its initiation. These observations led to demonstrating that as well as regulation of dynamic acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are also important regulators of this process. Additionally, the BBX32-centric GRN provides a view of the transcriptional control of dynamic acclimation distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

plant biology↗

bioRxiv2020

Recombination in enteroviruses is a ubiquitous event independent of sequence homology and RNA structure

Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation and compromises vaccine efficacy. Both the molecular mechanism and initial products of recombination are relatively poorly understood. We used an established poliovirus-based in vitro recombination assay to investigate the roles of sequence identity and RNA structure, both implicated or inferred from analysis of circulating recombinant viruses, in the process. In addition, we used next generation sequencing to investigate the early products of recombination after cellular co-infection with different poliovirus serotypes. In independent studies we find no evidence for a role for RNA identity or structure in determining recombination junctions location. Instead, genome function and fitness are of greater importance in determining the identity of recombinant progeny. These studies provide further insights into this important evolutionary mechanism and emphasise the critical nature of the selection process on a mixed virus population.

microbiology↗

bioRxiv2019

DNA methylation and histone H1 cooperatively repress transposable elements and aberrant intragenic transcripts

DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Loss of H1 also activates antisense transcripts within demethylated genes. Our results demonstrate that H1 and DNA methylation cooperatively maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes. HighlightsO_LIHistone H1 is enriched in methylated DNA independently of methylation C_LIO_LILoss of H1 activates genes, alters nucleosome organization and disperses heterochromatin C_LIO_LIDNA methylation and H1 jointly silence transposons C_LIO_LIDNA methylation and H1 cooperatively suppress intragenic antisense transcripts C_LI

genetics↗