Epigenomes

Mikania micrantha, a highly invasive weed, faces constraints on its northward range expansion in South China due to low winter temperatures. Although DNA methylation is increasingly recognized as a mediator of plant stress adaptation, it remains unknown whether epigenetic regulation couples cold-stress tolerance with the production of allelopathic secondary metabolites in invasive plants. Here, we comprehensively characterized genome-wide DNA methylation dynamics and their transcriptional consequences in germinating embryos under three temperature regimes (14 °C, 25 °C, and 30 °C) by integrating whole-genome bisulfite sequencing and RNA-Seq. Exposure to 14 °C significantly delayed germination without arresting the process. Global methylation levels were highest at CG sites (80.21–84.63%), followed by CHG (63.67–66.77%) and CHH (6.63–7.51%) contexts. Integrative analysis identified 1103 differentially methylated region-associated genes, of which 434 were also differentially expressed. Notably, KEGG enrichment of the 434 overlapping genes revealed significant overrepresentation of the sesquiterpenoid and triterpenoid biosynthesis pathways, with key mevalonate (MVA) pathway genes showing altered expression in association with DMRs at 14 °C. Because this is an integrative methylome–transcriptome association study without metabolite quantification or functional validation, these results are consistent with the hypothesis that cold-induced epigenetic reprogramming is associated with transcriptional changes in terpenoid biosynthesis, which may contribute to antioxidant and membrane-protective functions under chilling stress; the possible accumulation of allelopathic sesquiterpene lactones and any role in maintaining competitive advantage during cold seasons remain working hypotheses that require experimental validation. The results of this study offer new epigenetic perspectives and supporting data for the management and prevention of M. micrantha invasion.

Plants are important sources for obtaining diverse secondary metabolites which have pharmaceutical importance. Out of multiple factors that modulate their accumulation in vitro and in vivo, epigenetic factors play critical roles, adding an extra layer of regulation. This review focuses on (a) dynamic changes that occur in DNA methylation, histone acetylation, and the role of small RNAs in transcriptional and post-transcriptional modulation that alter secondary metabolism in plants under abiotic stress and (b) the role of epigenetics in secondary metabolite accumulation in the plant cell cultures. Such epigenetic factors are manipulated by applying inhibitors of DNA methylation like 5-azacytidine or histone deacetylation such as trichostatin A in intact plants as well as in cultured plant cells and hairy roots for enhanced production. This article synthesizes current findings on epigenetic engineering for improved synthesis of anticancer compounds and nutraceuticals and lists out limitations and challenges that the pharmaceutical industry is facing for their large scale production and commercialization. Main conclusion: Through epigenetic changes such as DNA methylation, histone acetylation, and non-coding RNAs, plants dynamically fine-tune specific gene expressions to adjust to environmental stresses and mediate secondary metabolite accumulation as a chemical combat mechanism.

Background/Objectives: The aim of this scoping review was to investigate the current role and possible clinical applications of long non-coding RNAs (lncRNAs) in breast cancer diagnosis and treatment. Methods: A thorough search of the PubMed/MEDLINE and Scopus/EMBASE databases was carried out in accordance with the PRISMA-ScR guidelines. The inclusion criteria were as follows: Studies with lncRNA analyses of specimens from breast cancer patients and clinically relevant studies. The exclusion criteria were as follows: in silico and in vitro studies involving animal models; reviews; case series; case reports; comments; editorials; and papers not written in English. The study protocol was registered in the Open Science Framework. Results: After the identification of 1139 records, 312 publications were retrieved and 228 articles were selected for data extraction. Data analysis and the synthesis of evidence showed that lncRNA studies were conducted in breast tumor specimens in 212 studies and in blood samples from breast cancer patients in 20 studies. The most commonly used method was quantitative RT-PCR (in 216 studies), while many studies were complemented by in vitro (n = 177) and animal experiments (n = 75). There were 39 studies that included at least 100 specimens from breast cancer patients. Conclusions: At present, lncRNA analysis is not used in routine clinical practice. Clinically relevant findings coupled by results from in vitro and animal experiments suggest that various lncRNAs after appropriate validation may be used as biomarkers for breast cancer diagnosis and treatment, most notably HSAT164, CCAT2, HOTAIR, and MALAT1. To this end, larger studies involving clinical specimens from clinically relevant subgroups of breast cancer patients will be needed.