Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm

Role of epigenetics in mangroves: recent progress and future perspectives

Epigenetic modifications in plants involve heritable changes in gene expression patterns that are not due to changes in gene sequences. Unlike genetic adaptations, which are long-term evolutionary changes, epigenetic modifications, such as DNA methylation, histone modifications, and noncoding RNAs, act as adaptive responses and allow plants to better cope with environmental stresses. As mangroves are uniquely located between the land and sea and remain continuously exposed to varying salinity, submergence, and hypoxia stresses, it is expected that certain epigenetic mechanisms might help them withstand the impacts of recurring stress fluctuations. Therefore, understanding the role of epigenetic regulation in mangrove stress adaptations to the intertidal environment is crucial. Despite only few studies to date having investigated epigenetic responses in mangroves, they nonetheless provide important insights into this process on which to base future research. Here, we present an update on recent progress in mangrove epigenetic research and offer perspectives on the potential roles of various epigenetic players in mangrove adaptations to the intertidal environment.

Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant

Nanopore sequencing enables comprehensive detection of 5-methylcytosine (5mC), particularly in repeat regions. However, CHH methylation detection in plants is limited by the scarcity of high-methylation positive samples, reducing generalization across species. Dorado, the only tool for plant 5mC detection on the R10.4 platform, lacks extensive species testing. Here, we develop DeepPlant, a deep learning model incorporating both Bi-LSTM and Transformer architectures, which significantly improves CHH detection accuracy and performs well for CpG and CHG motifs. We address the scarcity of methylation-positive CHH training samples through screening species with abundant high-methylation CHH sites using bisulfite-sequencing and generate datasets that cover diverse 9-mer motifs for training and testing DeepPlant. Evaluated across nine species, DeepPlant achieves high whole-genome methylation frequency correlations (0.705-0.838) with BS-seq data on CHH, improved by 23.4- 117.6% compared to Dorado. DeepPlant also demonstrates superior single-molecule accuracy and F1 score, offering strong generalization for plant epigenetics research.

Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm

In angiosperms, epigenetic profiles for genomic imprinting are established before fertilization. However, the causal relationships between epigenetic modifications and imprinted expression are not fully understood. In this study, we classified 'persistent' and 'stage-specific' imprinted genes on the basis of time-course transcriptome analysis in rice (Oryza sativa) endosperm and compared them to epigenetic modifications at a single time point. While the levels of epigenetic modifications are relatively low in stage-specific imprinted genes, they are considerably higher in persistent imprinted genes. Overall trends revealed that the maternal alleles of maternally expressed imprinted genes are activated by DNA demethylation, while the maternal alleles of paternally expressed imprinted genes with gene body methylation (gbM) are silenced by DNA demethylation and H3K27me3 deposition, and these regions are associated with an enriched motif related to Tc/Mar-Stowaway. Our findings provide insight into the stability of genomic imprinting and the potential variations associated with endosperm development, different cell types and parental genotypes.