(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://genome.bucm.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.
Search by using
a ID (currently Ensembl or UCSC ID only), gene name, symbols
or description variable in publications and databases.
(Ensembl id only for Danio rerio),
(UCSC id only for Mus musculus and Homo sapiens).
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.