Polyadenylation is a process in which a precursor mRNA is cleavaged at its 3' end and a poly(A) tail is consequently added to define the new 3' end of a mature mRNA transcript. As a critical post-transcriptional process, polyadenylation affects stability and transportability of mRNAs, as well as the recognition of mRNAs by cytoplasm export machinery and translational apparatus. Moreover, it has been shown to be correlated with the regulation of transcription and translation as well as affecting transcription termination in eukaryotes. The alternative processing of pre-mRNAs has been realized as a significant factor in plant gene expression. If different polyadenylation sites exist and are utilized, i.e., alternative polyadenylation, transcript isoforms with distinct 3'-ends can be derived from the same genes. If a poly(A) site locates in the middle (e.g., an intron or exon) of a pre-mRNA, rather than near the end, the alternatively polyadenylated mRNA will be shorter than the one from the regular polyadenylation, and perhaps it will encode proteins that are partially or not functional, or gain new functions. Both cis-elements and trans-factors have proved to be involved in the regulation of regular and alternative polyadenylation, but the underlying molecular and evolutionary mechanisms are not fully elucidated yet. Obviously, a comprehensive database of all regular and alternative poly(A) sites based on transcribed portions of various genomes is a critical prerequisite for us to unravel this important biological process. Toward this goal, we are building the RicePolyA database that currently contains more than 80,000 distinct polyadenylation sites for genic regions of the most recent Rice Genome Annotation (Rice Annotation Project, Build 4.0). Using the state-of-the-art web programming techniques, our web interfaces provide biologists with robust data search, filtration and visualization functionalities that will facilitate the study of regular and alternative polyadenylation in plants. |
