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Analysis of genomic poly(A) sites
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Alternative polyadenylation (APA) plays fundamental roles in gene expression regulation from prokaryotes to eukaryotes, that enables a single gene to encode multiple mRNA variants with different encoded proteins and/or 3’-untranslated regions (3’-UTRs), and may affects mRNA localization, stability and translational efficiency. Increasing amounts of genes have been shown to undergo such important 3’-processing depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, so that the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed regulation of gene expression for a given biology.


APASdb website, addressed at http://mosas.sysu.edu.cn/utr, supports a web-accessible database of APA sites which was termed APASdb and designed to visualize the precise map and usage quantification of different APA isoforms on a genome-wide scale for all genes. The advances and biological information are outlined below.
(1). Based on the datasets generated with the new Sequencing Alternative PolyAdenylation Sites (SAPAS) method capable of high-throughput sequencing and quantifying the 3'-ends of polyadenylated transcripts, APASdb not only contains much more novel poly(A) sites, but also has near perfect coverage for APA sites of genes in three model organisms, human (Homo sapiens), mouse (Mus musculus) and zebrafish (Danio rerio).
(2). APASdb visualizes the precise map and usage quantification of different APA sites on a genome-wide scale for all genes in various biological conditions or diseases, This makes it possible to identify the condition-specific poly(A) sites and discover the loss and gain of miRNA binding-sites in the dynamic 3’-UTRs, as well as helps study APA-site switching involved in vertebrate embryogenesis, mammalian thymopoiesis and human diseases more readily.
(3). It was frequently observed that, multiple cleavage sites downstream a poly(A) signal were only a few nucleotides apart, a interesting phenomenon usually called heterogeneity. APASdb details all the heterogeneous cleavage sites clustered to a poly(A) site downstream each poly(A) signal in a genome-wide fashion, and compares the variation of heterogeneous cleavage sites clustered under many biological processes and diseases. This may promote studying the mechanism of polyadenylation, in particular, the selection of heterogeneous cleavage sites at a given time for a given 3’-end formation.
(4). As a user-friendly web database, APASdb supports URL-based retrieval, browsing and display of several types of information, including exon-intron structure, poly(A) signal type and positions, poly(A) sites location and usage reads, and 3’-UTR regions.


Searching:
Search by using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases. Examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).

Citation:
Leiming You, et al. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. Nucleic Acids Res. 2015, 43: D59-D67.

APASdb current version: 1.0  change log.

 

 
May 27, 2016. last modified
 
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