Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

Gallusci, Philippe; Dai, Zhanwu; Génard, Michel; Gauffretau, Arnaud; Leblanc‐Fournier, Nathalie; Richard‐Molard, Céline; Vile, Denis; Brunel‐Muguet, Sophie

doi:10.1016/j.tplants.2017.04.009

Cited by 172 publications

(145 citation statements)

References 116 publications

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“…Epigenetic mechanisms are also major players during plant development, and have a role in shaping phenotypic plasticity (Gallusci et al , 2017). The latest advances in understanding the epigenetic dynamics associated with reproductive development in angiosperms are reviewed by Gehring (2019).…”

Section: Epigenetics and Plant Developmentmentioning

confidence: 99%

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

et al. 2020

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Section: Epigenetics and Plant Developmentmentioning

confidence: 99%

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

et al. 2020

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Section: Phenotypic Variation and The Epigenomementioning

confidence: 99%

“…Lastly, work has been started in modeling epigenetic trajectories for understanding of the evolutionary forces driving epigenome evolution at different time‐scales and conditions (Gallusci et al ., ; Huang and Ecker, ). Modeling efforts are either statistics‐based or processed‐based, and have been shown to furnish a mechanistic understanding of how the pieces fit together to form a well‐matched whole and quantify their impact on plant performances (Gallusci et al ., ). Some modeling work on classic epigenetic‐mediated examples includes description of the Polycomb‐based switching mechanism during the vernalization process involving Arabidopsis FLC (Richards et al ., ), and using DNA methylation as the predictor of variance in plant height (Hu et al ., ).…”

Section: Phenotypic Variation and The Epigenomementioning

confidence: 99%

Evolutionary and ecological functional genomics, from lab to the wild

2018

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Summary Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

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“…, Gallusci et al. , Lamke and Baurle ). These considerations also underscore the potential value of decoding Nannochloropsis epigenome.…”

mentioning

confidence: 98%

“…In plants, epigenetic enzymes participate in intricate gene regulatory networks orchestrating biological processes and developmental transitions. Moreover, selective transcriptional activation and silencing of genes can be regulated by epigenetic signals (Komar et al 2016, Nemhauser and Torii 2016, Vidalis et al 2016, Gallusci et al 2017, Lamke and Baurle 2017. These considerations also underscore the potential value of decoding Nannochloropsis epigenome.…”

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confidence: 99%

Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp.

Wei

2018

Journal of Phycology

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Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor-binding sites at the epigenetic level. Using ChIP-qPCR, genes related to photosynthetic carbon fixation in this microalga were systematically assessed. Furthermore, a ChIP-Seq protocol was established and optimized, which generated a genome-wide profile of histone modification events, using histone mark H3K9Ac as an example. These results are the first step for appreciation of the chromatin landscape in industrial oleaginous microalgae and for epigenetics-based microalgal feedstock development.

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Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

Cited by 172 publications

References 116 publications

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

Evolutionary and ecological functional genomics, from lab to the wild

Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp.

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