Biology subjects

Go, D.

Publications and source records attributed to Go, D..

3 recordsLinked to original sources

bioRxiv2025

AtSDR4L and its paralog DIG2 repress somatic embryogenesis during post-embryonic development in Arabidopsis

Somatic embryogenesis, a developmental process advantageous as an alternative means for plant propagation due to the lack of maternal tissues and the ease of in vivo to in vitro knowledge transfer of embryogenesis, has been applied in studies on the regulatory mechanisms governing the developmental plasticity in plants. Core and accessory components of the polycomb repressive complexes (PRCs), the epigenetic regulatory machinery, are known to repress the transcription of genes that positively regulate the somatic embryogenesis in seedlings. Recent studies revealed that Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSDR4L), an interactor of a PRC accessory, represses the embryo developmental program for a successful switch from seed to seedling. However, little is known about the regulation of cell differentiation by AtSDR4L in seedlings. Here, we show that AtSDR4L, its paralog Dynamic Influencer of Gene expression 2 (DIG2), and PRC components share similar transcriptional regulatory dynamics, particularly on somatic embryogenesis-related genes. We further demonstrate that mutations in AtSDR4L and DIG2 lead to the formation of somatic embryo-like structures and a delay in cellular differentiation. Thus, transcriptional changes reflected by morphological defects associated with somatic embryogenesis in Atsdr4l dig2 mutants suggest that AtSDR4L and DIG2 prevent the dedifferentiation of cells for proper seedling growth through the transcriptional control of cell identity.

plant biology↗

bioRxiv2025

Transcription factors overcome the repressive impact of Polycomb-associated methylation in tumors

DNA methylation is a key epigenetic regulator often disrupted in cancer, yet how promoter methylation dynamics translate into transcriptional changes during cancer progression remains incompletely understood. Here, we employed targeted bisulfite sequencing and RNA-seq on paired tumor and non-tumor tissues from 80 Korean colorectal cancer (CRC) patients to map promoter methylation and gene expression dynamics. Promoters with high baseline methylation in non-tumor tissues tended to become hypomethylated in tumors, while those with low baseline methylation underwent partial hypermethylation. However, these changes did not consistently correlate with gene silencing or activation. Strikingly, promoters marked by Polycomb (PcG+) in non-tumor tissue were prone to hypermethylation yet often remained transcriptionally active in tumors, a paradox most prominent in transcription factor (TF) genes. In contrast, hypermethylation in PcG- promoters was more consistently associated with transcriptional repression. Our findings suggest that epigenetic plasticity at PcG+ TF gene promoters can override the typically repressive effects of DNA methylation, potentially enabling tumors to maintain or enhance the expression of key regulatory genes. This highlights the importance of PcG occupancy in shaping the functional consequences of methylation changes during colorectal tumorigenesis, warranting deeper investigation into how these epigenetic adaptations drive cancer progression.

bioinformatics↗

bioRxiv2024

AtSDR4L and paralog promote seed-to-seedling transition in multiple seed compartments

Development is a series of decision-making events. Success of seed plants at individual and population levels strongly depends on the timing of germination and the rapidness of seedling establishment. Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSDR4L) and its paralog Dynamic Influencer of Gene Expression 2 (DIG2) are transcriptional co-repressors that promote seed-to-seedling phase transition. Their regulatory roles in promoting germination at the temporal and tissue-specific scales remain elusive. We show that strong germination arrest of Atsdr4l dig2 is alleviated by ABA antagonists. Isolated mutant embryos develop faster than intact seeds, but still exhibit delayed growth. Atsdr4l dig2 seeds show extensive changes in gene expression in both the seed coat and the embryo, with a subset of the genes differentially expressed tissue-specifically. MIKC-type MADS-box genes are the top-enriched transcription factor family among up-regulated genes in both seed compartments of Atsdr4l dig2, and AGAMOUS-LIKE44 (AGL44) is a dirct target of both AtSDR4L and DIG2. Many hormonal genes and hypoxia-responsive genes are misregulated in the double mutant seeds, accompanied by an over-accumulation of abscisic acid, auxin, their derivatives, as well as the immediate precursor of ethylene. Together, these results provide new mechanistic insights into how AtSDR4L and DIG2 work in concert to coordinate multiple pathways and prepare seeds for germination.

plant biology↗