Hsieh, W.-H. | bioRxiv Science

bioRxiv2025

Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening

We profiled developmental-series transcriptome, methylome, and metabolome profiling to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Fruit tissues exhibit globally higher DNA methylation than leaves, particularly in CHG and CHH contexts. Local methylation in all cytosine contexts progressively decreases in promoter regions during ripening, whereas CHG and CHH methylation increase in transposon-rich regions. Two primary methylation transitions--promoter hypomethylation and CHH hypermethylation--govern transcriptional shifts in genes involved in ripening processes. Methyl-binding transcription factors with activation potential likely promote CHH hypermethylation-linked transcriptional activation. Multi-omics integration revealed coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory genes within coherent networks. Elevated non-CG methylation in heterochromatin coincides with increased transcription of histone variants mediating chromatin compaction, suggesting chromatin remodelers fine-tune accessibility for methyltransferases. Our study highlights both genome-wide and locus-specific epigenetic reprogramming and demonstrates a coordinated interplay between DNA methylation and transcriptional regulation during black raspberry fruit ripening.

genomics↗

bioRxiv2023

Temporal Transcriptome Analysis Uncovers Regulatory Modules Programming Embryo Development from Embryonic Morphogenesis to Post-Germination

We profiled the soybean seed embryo transcriptome across embryonic development to post-germinative development to understand gene activities and regulatory networks promoting these processes. Transcriptomic landscapes feature highly prevalent transcripts which are categorized into early and late groups with major functions of reserve accumulation and energy generation, respectively, and both functions are dominant during late reserve accumulation as the transitioning stage. During the mid-reserve accumulation, regulatory events simultaneously dominate at the transcriptional and chromatin levels, followed by the emergence of distinct mRNA populations during late reserve accumulation throughout germination. We identified diverse functions conducted by sequentially activated genes across developmental stages. Gene coexpression network analysis reveals modules associated with developmental stages, some of which are enriched in genes with functions involved in specific developmental processes. We identified an early-desiccation-associated gene module, containing most transcription factors responsive to abiotic stress, within which one transcription factor is functionally validated to demonstrate increased drought tolerance in Arabidopsis overexpression lines. Finally, we found that a subset of genes is under purifying selection, surpasses the number of their Arabidopsis germination-specific homologs and most are active before germination from embryonic morphogenesis through dormancy, suggesting a potential role in governing physical dormancy in soybean compared to physiological dormancy in Arabidopsis. Our data represent a step toward identifying genes and regulatory networks in the soybean genome facilitating developmental programs across transition phases to bridge embryonic and germinative development.

plant biology↗