Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean.

Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.

Histopathological differences between prostate cancer foci that are detected and missed using multiparametric magnetic resonance imaging in Korean patients.

OBJECTIVES: We investigated whether multiparametric magnetic resonance imaging is appropriate to localize prostate cancer foci in Koreans. METHODS: A total of 141 prostate cancer foci in 115 prostate specimens from patients who had undergone radical prostatectomy with preoperative 3 Tesla multiparametric magnetic resonance imaging including T2-weighted imaging, diffusion weighted imaging and magnetic resonance spectroscopy. Differences in the histopathological findings between detected and undetected prostate cancer foci on multiparametric magnetic resonance imaging were investigated. RESULTS: The mean tumor size was 1.9 cm, and 31.9%, 48.9%, and 19.9% of the patients had Gleason scores of 6, 7, or ≥8, respectively. The detection rates of prostate cancer foci were 54.6%, 57.4%, 55.3%, and 45.4% on multiparametric magnetic resonance imaging, T2-weighted imaging, diffusion weighted imaging, and magnetic resonance spectroscopy, respectively. On multivariate analysis, tumor size ≥1.5 cm (odds ratio 3.1; 95% confidence interval 1.31­7.49), Gleason score >7 (4 + 3; odds ratio 2.9; 95% confidence interval 1.05­8.05), and a malignant epithelium/stroma ratio of ≥60% (odds ratio 2.9; 95% confidence interval 1.14­7.20) were significant independent predictors of prostate cancer foci detection on multiparametric magnetic resonance imaging and diffusion weighted imaging. In a multivariate linear model analysis, the apparent diffusion coefficient value was inversely associated with maximum tumor diameter (ß = −0.242, P < 0.05), Gleason score (ß = −0.234, P < 0.05)and high malignant epithelium/stroma ratio (ß = −0.229, P < 0.05). CONCLUSIONS: Distinct histological differences between prostate cancer foci that were detected and missed by multiparametric magnetic resonance imaging can be identified. Despite limitations, multiparametric magnetic resonance imaging seems useful for determining prostate cancer in Korean patients, particularly with Gleason score >7 and tumor diameter>1.5 cm.

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean.

BACKGROUND: Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized. RESULTS: Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways. CONCLUSIONS: The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.