Recognizing importance of epigenetic and epigenomic regulations of medicinal plants
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Abstract:
Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. Epigenetics most often denotes changes in a chromosome that affect gene activity and expression, and also can be used to describe any heritable phenotypic change. Such effects on cellar and physiological phenotypic traits may result from external or exvironmental factors, or be part of normal developmental program. The standard definition of epigenetics requires these alterations to be heritable, either in the progeny of cells or of organisms. Epigenomics is the study based on the comprehensive analyses of the epigenome using high-throughput technologies. Many fundamental discoveries concerning epigenetics and the elucidation of mechanisms of epigenetic regulation have developed from studies performed in medicinal plants. Many techniques now allow genome-wide analyses of epigenetic regulation and help to understand how epigenetic regulatory mechanisms affect cellular and genome function with a particular focus on the epigenetics of medicinal plants. It is considered what has been historically understood by the “epigenetics” before turning to the advances in biochemistry, molecular biology, and genetics. It is given to know how advances in molecular techniques for more comprehensive understanding of epigenetic phenomena in medicinal plants. Some opportunities, challenges, and techniques for epigenetic research in both model and non-model medicinal plants, in particular for advancing understanding of the regulation of genome function by epigenetic mechanisms. In this issue of CHM journal, the article titled “Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants” (CHM, 2018, 10(3):xxx-xxx) is written by Professors Hao and Xiao. After reading it happily, the editor felt that there are three points worth mentioning to the readers: Firstly, recognizing the importance of epigenetic and epigenetic mechanisms of genuine medicinal materials; Secondly, the study of epigenetic processes opens up a new field of post-transcriptional gene regulation; Finally, the epigenome layer is critical in the age of multi-omics. Recognizing importance of epigenetic and epigenetic mechanisms of genuine medicinal materials Genuine medicinal material (geoherb) is produced in particular geographic regions. The special medicinal features of a plant are determined by its genome, while the proper ecological conditions have major effects on the formation of a geoherb, which is at least partially mediated by the epigenetics. By epigenetics/epigenomics, researchers uncover the complexities of the influence of the environment on the expression of genes that control medicinal plant growth, development, stress responses, and medicinal phytometabolite yield, and put the other "omics layers" in a meaningful biological context. The unique phenotypes of geoherb are closely related to the growth, development, and stress responses of medicinal plants. In addition to the commonly known genetic control, epigenetic machineries, active at the population level, play an essential role in the formation of geoherbs. This contribution gives a comprehensive overview of the epigenetic regulation of medicinal plants and the associated microbes, and the role of DNA methylation, small non-coding RNA, transposable elements, and histone modifications in the gene expression regulation of geoherbs and relevant microbiota. The epigenetic and epigenomic mechanisms should be highlighted in the study of specific phenotype and indigenousness of geoherbalism. Revealing the correlation between epigenetics and geoherbs could shed light on the quality assessment, authentication, molecular breeding, and sustainable utilization of medicinal plants and the associated microbes. Study of epigenetic processes opens up a new field of post-transcriptional gene regulation Various epigenetic processes affect the transcriptome of medicinal plant cells: (1) cytosine methylation influences gene expression by altering transcription and chromatin structure; (2) histone modifications have a profound impact on the structure of chromatin and can make DNA relatively accessible for transcription; (3) sRNAs, like miRNA and siRNAs, influence gene expression through targeted degradation of mRNA (PTGS) or induction of methylation at complementary DNA sequences (transcriptional gene silencing). Moreover, reversible mRNA methylation and other novel modifications, i.e., epitranscriptome, open a new realm of post-transcriptional gene regulation in plants. The regulation of mRNA metabolism is particularly crucial under stress conditions. With over 100 known RNA modifications, understanding the repertoire of RNA modifications in medicinal plant development and phytometabolite production is a huge enterprise. Epigenome layer is critical in age of multi-omics In epigenetic/epigenomic studies of medicinal plants, it becomes highly possible that large-scale epigenetic reprogramming to the establishment of transcriptionally permissive epigenetic landscapes that put the medicinal compound production onto a fast track. In the age of multi-omics, the numerous layers of biological systems to progressively understand cellular functions and interactions. From studying the genome and epigenome, one understands the complexities of the environmental interactions. Genome is based on study for the simplicity of understanding DNA sequences and the high level detection of genes. Progressive layers uncover further details: transcriptomics to understand mRNAs, proteomics to reveal protein expression and characterization, and metabolomics to study metabolites. Therefore, the epigenome layer is critical. Firstly, epigenomics aims to discover the complexities of the influence of the environment on the expression of genes and the other “omics layers” in a meaningful and pertinent biological context. Secondly, Epigenetic/epigenomic techniques could be alternative strategies for large scale in vitro or even in vivo production of high value phytochemicals, the deeper understanding of the molecular mechanisms underlying genotype-environment interactions is beneficial for long-term improvement of medicinal plant development. ?
Chang-xiao Liu. Recognizing importance of epigenetic and epigenomic regulations of medicinal plants[J]. Chinese Herbal Medicines (CHM),2018,10(3):237-238
