UltraFast PhotoInduced double duplex DNA invasion into a 400-mer dsDNA target.

BACKGROUND: Natural DNA restriction enzymes bind duplex DNA with high affinity at multiple sites; however, for some of the artificial chemical-based restriction moieties, invasion of the double-strand for efficient cleavage is an obstacle. We have previously reported photo-induced double-duplex invasion (pDDI) using 3-cyanovinylcarbazole (K)-containing probes for both the target strands that photo-crosslink with pyrimidine bases in a sequence-specific manner on both the strands, stabilizing the opened double-strand for cleavage. The drawback of the pDDI was low efficiency due to inter-probe cross-linking, solved by the inclusion of 5-cyano-uridine at -1 position on the complimentary strand with respect to K in both probes. Although this led to reduced inter-probe cross-linking, the pDDI efficiency was still low. RESULTS: Here, we report that inter-probe cross-linking and intra-probe cross-linking of a single probe is also leading to reduced pDDI efficiency. We addressed this problem by designing DDI probes to inhibit both inter-probe and intra-probe cross-linking. CONCLUSION: Based on the new design of pDDI probe with 5-cyano uridine led to a drastic increase in the efficiency of pDDI in (400-mer) double-stranded DNA with only 1 s of photo-irradiation.

The Role of the Exonic lncRNA PRKDC-210 in Transcription Regulation.

In recent years, long noncoding RNAs (lncRNAs) have received increasing attention and have been reported to be associated with various genetic abnormalities. However, the functions of many lncRNAs, including those of long exonic noncoding RNAs (lencRNAs), have not yet been elucidated. Here, we used a novel tethering luciferase assay to analyze the transcriptional regulatory functions of five lencRNAs that are upregulated in cancer. We found that the lencRNA PRKDC-210 interacts with MED12, a component of the CDK8 complex, to regulate the transcription of several genes. The transcriptional activation ability of PRKDC-210 was abolished in siRNA-treated CDK8-depleted cells. We also confirmed the enrichment of PRKDC-210 on RNA polymerase II. RNA-seq analysis of cells in which PRKDC-210 or PRKDC mRNA was knocked down using antisense oligonucleotides revealed that PRKDC-210 can affect the expression levels of genes related to fatty acid metabolism. Finally, we used a ChIRP assay to examine PRKDC-210-enriched sites in the genome. Overall, our findings demonstrate that the lencRNA PRKDC-210 promotes transcription through the CDK8 complex pathway at the transcription initiation site. We propose that PRKDC-210 can affect the transcription of adjacent genes after its transcription and splicing.

Hepatocyte growth factor is a prognostic marker in patients with colorectal cancer: a meta-analysis.

Hepatocyte growth factor (HGF) is a crucial factor associated with development, progression and metastasis of colorectal cancer (CRC). However, its prognostic value remains unclear. Thus studies referring to the correlation between HGF and CRC patients' prognosis were included to explore the role of HGF in CRC. At last nine articles were included. The results showed that the over-expression of HGF was associated with a poor prognosis, presented through overall survival (OS, Hazard ratio (HR) = 2.50, 95% confidence interval (CI): 2.12-2.96) and disease-free survival (DFS, HR = 1.99, 95% CI: 1.59-2.50). Subgroup analysis indicated that no significant difference was found between the Asian countries (OS: HR = 2.37; DFS: HR = 2.02) and the non-Asian countries (OS: HR = 3.15; DFS: HR = 1.87), between the studies that used univariate analyses (OS: HR = 2.51; DFS: HR = 2.07) and those that used multivariate analyses (OS: HR = 2.65; DFS: HR = 1.78), and between metastatic CRC (OS: HR = 2.26; DFS: HR = 2.06) and stage I-IV CRC (OS: HR = 3.08; DFS: HR = 0.70). Our meta-analysis has shown that the over-expression of HGF is valuable in CRC prognosis evaluation. This conclusion should be further confirmed by large-sample cohort studies.