Alternative polyadenylation and non-stop mRNAs in Arabidopsis

Posttranscriptional controls are important for the regulation of gene expression. The steps of gene expression through which such regulation is accomplished include virtually all of the processes attendant with mRNA biosynthesis, transport, and turnover. One such process involves the formation of the polyadenylated 3’ end of the mature mRNA. Control through polyadenylation is usually accomplished by alternative polyadenylation; in this way, the structures of the resulting mRNAs may vary, encoding different proteins or being differentially transported or broken down. In a recently-published conducted to assess poly(A) site choice in Arabidopsis on a genome-wide basis, it was found that many Arabidopsis genes are subject to a form of alternative processing in which the RNAs are polyadenylated within the protein-coding region of the gene. These RNAs do not have translation termination codons and are expected to be unstable and/or poorly translated. Interestingly, this phenomenon (nonstop RNA-linked alternative polyadenylation) affected two classes of Arabidopsis genes disproportionately; these classes were those genes encoding defense-related receptors, and genes involved in responses to abiotic stress. These observations reveal a new mechanism for possible control of important plant genes. The proposed research is intended to study coding region-associated polyadenylation, with the goal of clarifying both mechanism and consequence of the process. The hypothesis that coding region-associated polyadenylation is accomplished via conventional modes of alternative polyadenylation will be tested using a battery of in vitro assays and genome-wide approaches. The hypothesis that non-stop mRNA decay is used for regulation will be tested by studying the stabilities of non-stop mRNAs and the association of non-stop mRNAs with polysomes. The hypothesis that polyadenylation within coding regions is involved in gene regulation will be studied by examining the effects of various stress tretaments on polyadenylation within coding regions. The involvement of polyadenylation within coding regions on gene function will be examined by studying the effects of removal of coding region poly(A) sites on the functioning of genes that possess such sites.