High-calorie food leads to nonalcoholic fatty liver disease (NAFLD) through dysregulation of genes involved in lipid metabolism, but the precise mechanism remains unclear. DNA methylation represents one of the mechanisms that contributes to dysregulation of gene expression via interaction with environmental factors. Berberine can alleviate fatty liver in db/db and ob/ob mice. Here, we investigated whether DNA methylation is involved in the pathogenesis of NAFLD induced by a high-fat diet (HFD) and whether berberine improves NAFLD through influencing the methylation status of promoters of key genes. HFD markedly decreased the mRNA levels encoding CPT-1α, MTTP, and LDLR in the liver. In parallel, DNA methylation levels in the MTTP promoter of rats with NAFLD were elevated in the liver. Interestingly, berberine reversed the downregulated expression of these genes and selectively inhibited HFD-induced increase in the methylation of MTTP. Consistently, berberine increased hepatic triglyceride (TG) export and ameliorated HFD-induced fatty liver. Furthermore, a close negative correlation was observed between the MTTP expression and its DNA methylation (at sites −113 and −20). These data indicate that DNA methylation of the MTTP promoter likely contributes to its downregulation during HFD-induced NAFLD and, further, that berberine can partially counteract the HFD-elicited dysregulation of MTTP by reversing the methylation state of its promoter, leading to reduced hepatic fat content.

CRISPR-Cas9 technology has been widely used for genome engineering. Its RNA-guided endonuclease Cas9 binds specifically to target DNA and then cleaves the two DNA strands with HNH and RuvC nuclease domains. However, structural information regarding the DNA cleavage-activating state of two nuclease domains remains sparse. Here, we report a 5.2 Å cryo-EM structure of Cas9 in complex with sgRNA and target DNA. This structure reveals a conformational state of Cas9 in which the HNH domain is closest to the DNA cleavage site. Compared with two known HNH states, our structure shows that the HNH active site moves toward the cleavage site by about 25 and 13 Å, respectively. In combination with EM-based molecular dynamics simulations, we show that residues of the nuclease domains in our structure could form cleavage-compatible conformations with the target DNA. Together, these results strongly suggest that our cryo-EM structure resembles a DNA cleavage-activating architecture of Cas9.

Background: Rapid economic growth in China in the past decades has been accompanied by dramatic changes in lifestyle and environmental exposures. The burdens of non-communicable diseases, such as cardiovascular diseases, diabetes and cancer, have also increased substantially. Methods/design: We initiated a large prospective cohort–the Taizhou Longitudinal Study–in Taizhou (a medium-size city in China) to explore the environmental and genetic risk factors for common non-communicable diseases. The sample size of the cohort will be at least 100,000 adults aged 30–80 years drawn from the general residents of the districts of Hailin, Gaogang, and Taixing (sample frame, 1.8 million) of Taizhou. A three-stage stratified sampling method will be applied. Baseline investigations include interviewer-administered questionnaire, anthropometric measurements, and collection of buccal mucosal cells and blood specimens. DNA will be extracted for genetic studies and serum samples will be used for biochemical examinations. A follow-up survey will be conducted every three years to obtain information on disease occurrence and information on selected lifestyle exposures. Study participants will be followed-up indefinitely by using a chronic disease register system for morbidity and cause-specific mortality. Information on non-fatal events will be obtained for certain major categories of disease (e.g., cancer, stroke, myocardial infarction) through established registry systems. Discussion: The Taizhou Longitudinal Study will provide a good basis for exploring the roles of many important environmental factors (especially those concomitant with the economic transformation in China) for common chronic diseases, solely or via interaction with genetic factors.

Austronesian is a linguistic family spread in most areas of the Southeast Asia, the Pacific Ocean, and the Indian Ocean. Based on their linguistic similarity, this linguistic family included Malayo-Polynesians and Taiwan aborigines. The linguistic similarity also led to the controversial hypothesis that Taiwan is the homeland of all the Malayo-Polynesians, a hypothesis that has been debated by ethnologists, linguists, archaeologists, and geneticists. It is well accepted that the Eastern Austronesians (Micronesians and Polynesians) derived from the Western Austronesians (Island Southeast Asians and Taiwanese), and that the Daic populations on the mainland are supposed to be the headstream of all the Austronesian populations. In this report, we studied 20 SNPs and 7 STRs in the non-recombining region of the 1,509 Y chromosomes from 30 China Daic populations, 23 Indonesian and Vietnam Malayo-Polynesian populations, and 11 Taiwan aboriginal populations. These three groups show many resemblances in paternal lineages. Admixture analyses demonstrated that the Daic populations are hardly influenced by Han Chinese genetically, and that they make up the largest proportion of Indonesians. Most of the population samples contain a high frequency of haplogroup O1a-M119, which is nearly absent in other ethnic families. The STR network of haplogroup O1a* illustrated that Indonesian lineages did not derive from Taiwan aborigines as linguistic studies suggest, but from Daic populations. We show that, in contrast to the Taiwan homeland hypothesis, the Island Southeast Asians do not have a Taiwan origin based on their paternal lineages. Furthermore, we show that both Taiwan aborigines and Indonesians likely derived from the Daic populations based on their paternal lineages. These two populations seem to have evolved independently of each other. Our results indicate that a super-phylum, which includes Taiwan aborigines, Daic, and Malayo-Polynesians, is genetically educible.

Aberrant activation of the translesion DNA synthesis (TLS) pathway has been suggested to play a role in tumorigenesis by promoting genetic mutations. We therefore examined glioma specimens for the expression of specialized DNA polymerases involved in TLS and assessed their prognostic significance. The expression levels of DNA polymerase κ (Pol κ), Pol ι, and Pol η were assessed in 40 primary glioma samples and 10 normal brain samples using quantitative real-time PCR and Western blot analysis. Their prognostic significance was evaluated using a population-based tissue microarray derived from a cohort of 104 glioma patients. Overexpression of Pol κ and Pol ι was observed in 57.5% (23–40) and 27.5% (11–40) of patients, respectively, whereas no significant expression of Pol η was seen in the specimens. Immunohistochemical studies revealed positive Pol κ and Pol ι staining in 72 (69.2%) and 33 (31.7%) of the 104 glioma specimens, respectively. Pol κ expression was associated with advanced stages of the disease. Both Pol κ– and Pol ι–positive staining were associated with shorter survival in glioma patients (P < .001 and P = .014, respectively). A multivariate survival analysis identified Pol κ as an independent prognostic factor for glioma patients (P < .001). These findings demonstrate, for the first time, that the expression of Pol κ and Pol ι is deregulated in gliomas, and upregulation of Pol κ is associated with poorer prognosis in glioma patients.