Non-targeted metabolomic analysis of variation of volatile fractions of ginseng from different habitats by HS-SPME-GC-MS coupled with chemometrics.

Cultivated ginseng (CG), transplanted ginseng (TG) and mountain cultivated ginseng (MCG) classified by the habitat type all belong to Panax ginseng and were reported to have similar types of secondary metabolites. Nonetheless, owing to the distinctly diverse habitats in which these ginseng types grow, their pharmacological effects differ. In the present study, an emerging analytical approach involving headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) was established to effectively distinguish among CG, TG and MCG. First, the volatile components were analysed and identified by using the NIST library combined with measured retention indices (Kovats', RI), and a total of 78 volatile components were finally characterized, which included terpenes, alcohols, esters, aldehydes and alkynols. Furthermore, multivariate statistical approaches, principal component analysis (PCA) and orthogonal partial least-squares discrimination analysis (OPLS-DA) were subsequently utilized to screen for compounds of significance. Under optimized HS-SPME-GC-MS conditions, 12, 16, and 16 differential markers were screened in the CG-TG, CG-MCG and TG-MCG groups, respectively. Our study suggested that HS-SPME-GC-MS analysis combined with metabolomic analytical methods and chemometric techniques can be applied as potent tools to identify chemical marker candidates to distinguish CG, TG and MCG.

A genome-wide analysis reveals the MeCP2-dependent regulation of genes in BGC-823 cells.

Methyl-CpG-binding protein 2 (MeCP2) epigenetically modulates gene expression through genome-wide binding to methylated CpG dinucleotides. This study aimed to evaluate the effect of MeCP2 on the global gene expression profile of human gastric adenocarcinoma to determine the potential molecular mechanism of MeCP2. To identify the gene targets of MeCP2 in gastric cancer cells, we combined the expression microarray and chromatin immunoprecipitation approaches of MeCP2, followed by sequencing (ChIP-seq) to define the MeCP2-binding sites across the whole genome. The methylation levels of the promoters in BGC-823 cells were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database (GSM1093053). A total of 5,684 ChIP-enriched peaks were identified by comparing IP and Input, using a p-value threshold of 10-5 in ChIP-seq. The bioinformatics analysis presented a predictive model of the genome-wide MeCP2-binding pattern, in which the MeCP2 binding site is closely related to the transcription start site region in the genome. The results of motif detection showed that the MeCP2-binding regions contained not only the core CpG motif but also the extended poly (A/T) motifs. Finally, an integrative analysis of the sequence features and DNA methylation states revealed that MeCP2's function as a multifunctional transcriptional regulator may not be directly related to the methylation status of the binding site. The first MeCP2 ChIP-seq and gene expression microarray analysis in BGC-823 cells revealed that MeCP2 plays multiple roles in the regulation of gene expression depending on the microenvironment, such as sequence characteristics and the methylation levels of binding sites.