Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

3' UTRs play important roles in the gene regulation network via their influence on mRNA stability, translational efficiency, and subcellular localization. For a given gene, 3' UTRs of different lengths generated by alternative polyadenylation (APA) may result in functional differences in regulation. The mechanistic details of how length changes of 3' UTRs alter gene function remain unclear. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs were bound with more polysomes in six cell lines but not in NIH3T3 cells, suggesting that changing 3' UTRs to shorter isoforms may lead to a higher gene translational efficiency. By interfering with the expression of TNRC6A and analyzing AGO2-PAR-CLIP data, we revealed that the APA effect on translational efficiency was mainly regulated by miRNAs, and this regulation was cell cycle dependent. The discrepancy between NIH3T3 and other cell lines was due to contact inhibition of NIH3T3. Thus, the crosstalk between APA and miRNAs may be needed for the regulation of protein translational efficiency.

A pentadentate Schiff base bis(N-salicylidene)-3-oxapentane-1,5-diamine (H 2 L) and its lanthanide (III) complexes, [GdL(NO 3 )(DMF)(H 2 O)] (1) and [Dy 2 L 2 (NO 3 ) 2 ]·2H 2 O (2), have been synthesized and characterized by physical, chemical, and spectroscopic methods. Single crystal X-ray structure reveals that 1 is a discrete mononuclear species with nine-coordinate Gd(III) in a distorted monocapped square antiprism geometry. Complex 2 is a centrosymmetric binuclear neutral entity, in which Dy(III) is eight-coordinate in a distorted square antiprism. Electronic absorption titration spectra, ethidium bromide competitive experiments, and viscosity measurements indicate that both the ligand and complexes bind calf thymus DNA, presumably via groove binding. Investigations of antioxidant activities show that both complexes have some scavenging effects for hydroxyl and superoxide radicals.

Three novel structure Ag(i) complexes have been synthesized and characterized. The three ligands and Ag(i) complexes bind to DNA in an intercalation mode. The Ag(i) complexes have stronger ability of antioxidation for hydroxyl radical and superoxide radical.