No abstract

DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swdmr/) for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation.

Retinoblastoma (RB) is a childhood intraocular tumor, affecting millions of patients worldwide. ) was demonstrated to be involved in the tumorigenesis of various human cancers; however, its role in RB remains undetermined. In this study, quantitative real-time PCR (qRT-PCR) and Western blot assays were used to determine the expression levels of miR-140-5p, cell migration-inducing protein (CEMIP), and cell adhesion molecule 3 (CADM3) in RB tissues and cell-lines. The proliferation ability was detected by cell-counting kit 8 (CCK-8), Edu staining, and colony formation assay. The cell cycle and migration and invasion abilities were measured by flow cytometry, wound-healing assay and Transwell assays, respectively. The correlation between miR-140-5p and CEMIP/CADM3 were then confirmed by immunofluorescence (IF) and dual-luciferase reporter assays. The results showed that miR-140-5p expression was significantly decreased; however, CEMIP and CADM3 expression was increased in RB tissues and cells. Overexpression of miR-140-5p inhibited proliferation, migration, and invasion of RB cells. We also found that miR-140-5p inhibited CEMIP and CADM3 expressions in RB cells. In addition, we demonstrated that miR-140-5p might negatively regulate the transcriptional activities of CEMIP and CADM3 by targeting their 3'-UTR. Therefore, we suggested that miR-140-5p could be a potential therapeutic target for the treatment of RB through CEMIP and CADM3.