Plants are sessile organisms that are continuously exposed to different biotic and abiotic pressures. DNA mutations provide plants with new tools to build resistance or tolerance to environmental stress, but genetic mutation rates are usually low compared with the rate of environmental change. Therefore, additional sources of phenotypic plasticity are expected to play an important role in response to fluctuating stress conditions. Epigenetic mechanisms regulate gene expression without changing the genome sequence, with the potential to provide faster and reversible adaptation in fluctuating environments.
Epigenetic marks are covalent and reversible modifications to DNA and histone proteins, which alter the chromatin structure and, in specific cases, can be inherited to the next generation. DNA methylation is a well-studied epigenetic mark in animals and plants and can occur in different cytosine sequence contexts, such as CG, CHG, and CHH (where H is any base other than G). In plants, de novo DNA methylation is usually mediated by the RNA-directed DNA methylation (RdDM) pathway, guided by small RNAs (sRNAs). To analyze epigenetic modifications, high-throughput techniques like RiboMeth-Seq or BS-Seq have been developed and are constantly improved. Several relevant studies have assessed several aspects of DNA methylation, from its molecular basis and interaction with other pathways to its roles in adaptation and evolution. Histone modifications are another group of epigenetic mechanisms, which involve modification of histone proteins, deposition of histone variants, as well as the control of the entire nucleosome (and linker) positioning.
Epigenetic mechanisms play an active role in the plant response to biotic stressors such as bacteria, viruses, fungi, parasites, insects, and weeds by controlling the expression of several resistance genes. Furthermore, after the first stress exposure, plants can be primed and subsequently activate defense genes more efficiently against the next stress encounter. DNA methylation and histone modifications are involved in this immune memory state of plants, which, in certain cases, can be transmitted for short periods to the next generations of plants. As a second layer of epigenetic regulation, non-coding RNAs (ncRNAs) like lncRNAs, siRNA, and miRNAs were shown to be direct and indirect modulators. Therefore, identification of ncRNAs and differential expression of such RNAs play a major role in epigenetics research.
Epigenetic mechanisms, and the possibility of providing alternative phenotypes with the same genetic sequence, has represented a paradigm shift in genetics and had subsequent impacts on many disciplines. Therefore, much attention has been directed to understanding epigenetic mechanisms, their biological roles, and their natural variation. With the recent advances in genome sequencing, bioinformatics tools, and associated techniques such as ChIPseq, FAIRE-seq, Chromosome Conformation Capture or small RNA analysis, acquired knowledge about epigenetic responses in model plants could be transferred to crops and used to increase phenotypic variation for breeding purposes.
Therefore, in this Research Topic, we encourage the submission of studies assessing the role of epigenetics in modulating biotic interactions as well as the potential biotechnological use of these mechanisms in plants.
Plants are sessile organisms that are continuously exposed to different biotic and abiotic pressures. DNA mutations provide plants with new tools to build resistance or tolerance to environmental stress, but genetic mutation rates are usually low compared with the rate of environmental change. Therefore, additional sources of phenotypic plasticity are expected to play an important role in response to fluctuating stress conditions. Epigenetic mechanisms regulate gene expression without changing the genome sequence, with the potential to provide faster and reversible adaptation in fluctuating environments.
Epigenetic marks are covalent and reversible modifications to DNA and histone proteins, which alter the chromatin structure and, in specific cases, can be inherited to the next generation. DNA methylation is a well-studied epigenetic mark in animals and plants and can occur in different cytosine sequence contexts, such as CG, CHG, and CHH (where H is any base other than G). In plants, de novo DNA methylation is usually mediated by the RNA-directed DNA methylation (RdDM) pathway, guided by small RNAs (sRNAs). To analyze epigenetic modifications, high-throughput techniques like RiboMeth-Seq or BS-Seq have been developed and are constantly improved. Several relevant studies have assessed several aspects of DNA methylation, from its molecular basis and interaction with other pathways to its roles in adaptation and evolution. Histone modifications are another group of epigenetic mechanisms, which involve modification of histone proteins, deposition of histone variants, as well as the control of the entire nucleosome (and linker) positioning.
Epigenetic mechanisms play an active role in the plant response to biotic stressors such as bacteria, viruses, fungi, parasites, insects, and weeds by controlling the expression of several resistance genes. Furthermore, after the first stress exposure, plants can be primed and subsequently activate defense genes more efficiently against the next stress encounter. DNA methylation and histone modifications are involved in this immune memory state of plants, which, in certain cases, can be transmitted for short periods to the next generations of plants. As a second layer of epigenetic regulation, non-coding RNAs (ncRNAs) like lncRNAs, siRNA, and miRNAs were shown to be direct and indirect modulators. Therefore, identification of ncRNAs and differential expression of such RNAs play a major role in epigenetics research.
Epigenetic mechanisms, and the possibility of providing alternative phenotypes with the same genetic sequence, has represented a paradigm shift in genetics and had subsequent impacts on many disciplines. Therefore, much attention has been directed to understanding epigenetic mechanisms, their biological roles, and their natural variation. With the recent advances in genome sequencing, bioinformatics tools, and associated techniques such as ChIPseq, FAIRE-seq, Chromosome Conformation Capture or small RNA analysis, acquired knowledge about epigenetic responses in model plants could be transferred to crops and used to increase phenotypic variation for breeding purposes.
Therefore, in this Research Topic, we encourage the submission of studies assessing the role of epigenetics in modulating biotic interactions as well as the potential biotechnological use of these mechanisms in plants.
