Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

• Published in: Cell 2014-02, Vol.156 (4), p.812-824
• Main Authors: Geisberg, Joseph V., Moqtaderi, Zarmik, Fan, Xiaochun, Ozsolak, Fatih, Struhl, Kevin
• Format: Article
• Language: English
• Subjects: Base Sequence; Genome, Fungal; Genome-Wide Association Study; Half-Life; Nucleotide Motifs; RNA Stability; RNA, Fungal - chemistry; RNA, Fungal - metabolism; RNA, Messenger - chemistry; RNA, Messenger - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Sequence Alignment
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2013.12.026

We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A)-binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilizing and stabilizing elements are linked to the propensity of the poly(A) tail to engage in double-stranded structures. Isoforms engineered to fold into 3′ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at 3′ ends are a major determinant of mRNA stability. [Display omitted] •New method for measuring mRNA half-lives of mRNA isoforms in yeast•Genome-wide identification of mRNA stabilization and destabilization elements•Identification of polyU stretches as mRNA stabilization elements•A new role for the poly(A) tail and secondary structure in mRNA stability A new method for profiling mRNA stability genome wide reveals structural elements accounting for the wide-range of mRNA isoform stability in yeast. 3′ end stem-loop structures appear particularly effective for mRNA stabilization.