SUMMARY We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follow the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the monomethylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus.

Upconversion emission dynamics have long been believed to be determined by the activator and its interaction with neighboring sensitizers. Herein this assumption is, however, shown to be invalid for nanostructures. We demonstrate that excitation energy migration greatly affects upconversion emission dynamics. “Dopant ions’ spatial separation” nanostructures are designed as model systems and the intimate link between the random nature of energy migration and upconversion emission time behavior is unraveled by theoretical modelling and confirmed spectroscopically. Based on this new fundamental insight, we have successfully realized fine control of upconversion emission time behavior (either rise or decay process) by tuning the energy migration paths in various specifically designed nanostructures. This result is significant for applications of this type of materials in super resolution spectroscopy, high‐density data storage, anti‐counterfeiting, and biological imaging.

Mapping genome-wide 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their biological functions. We present a cost-efficient mapping method that combines 5hmC-specific restriction enzyme PvuRts1I with a 5hmC chemical labeling enrichment method. The sensitive method enables detection of low-abundance 5hmC sites, providing a more complete 5hmC landscape than available bisulfite-based methods. This method generated a genome-wide 5fC map at single-base resolution. Parallel analyses revealed that 5hmC and 5fC in non-CpG context exhibit lower abundance, more dynamically, than those in CpG context. In the genic region, distribution of 5hmCpG and 5fCpG differed from 5hmCH and 5fCH (H = A, T, C). 5hmC and 5fC were distributed distinctly at regulatory protein-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at active and poised enhancers. This sensitive bisulfite conversion-free method can be applied to biological samples with limited starting material or low-abundance cytosine modifications.

Background and Aims HBV‐pgRNA (pregenomic RNA) has been proposed for predicting the response of nucleos(t)ide analogue (NA) treatment, guiding discontinuation of NA therapy and monitoring the emergence of viral mutations. However, the contributions of HBV‐pgRNA to HCC remain open for study. Approach and Results Double‐center cohorts of serum samples with undetectable serum HBV‐DNA (below the lower limit of detection) were obtained from long‐term NA‐treated (≥48 weeks) HBV‐related HCC patients. The correlation between serum pgRNA concentration and the prognosis of HCC were analyzed. The role pgRNA played in HCC development was assessed both in vitro and in vivo. Our findings revealed that for patients who underwent long‐term NA therapy with undetectable serum HBV‐DNA, patients with high serum pgRNA expression had a poorer overall survival rate and higher cumulative recurrence rate after hepatectomy. Experiments demonstrated that pgRNA promotes proliferation, stemness, and tumorigenicity of HCC cells. Mechanistically, we found that pgRNA could up‐regulate the expression of insulin‐like growth factor 2 mRNA‐binding protein 3 (IGF2BP3), a well‐proven oncoprotein, at the posttranscriptional level. Furthermore, interferon (IFN)‐α‐2a could degrade the stability of pgRNA through increasing its N6‐methyladenosine (m6A) RNA modification. Collectively, our findings uncover that serum pgRNA could serve as a potential biomarker for predicting the prognosis and recurrence of HCC in patients who received long‐term NA therapy with undetectable serum HBV‐DNA; and the pgRNA‐IGF2BP3 axis plays an important role in the development of HBV‐related HCC. Moreover, IFN‐α‐2a could reduce the stability of pgRNA by increasing its m6A RNA modification level, thereby suppressing the development of HBV‐related HCC. Conclusions In conclusion, our studies reveal a significance and mechanism of HBV‐pgRNA in increasing stemness features and offer a potential prognostic marker and a therapeutic target for HBV‐related HCC.