Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae.

INTRODUCTION 233 METHODS FOR STUDYING mRNA TURNOVER IN S. CEREVISIAE 234 Approach to Steady-State Labeling 234 Inhibition of Transcription by Using Drugs 234 Inhibition of Transcription by Using a Conditional Allele of RNA Polymerase II 234 Inhibition of Transcription by Using Regulated Promoters 235 Transcriptional Pulse-Chase: a Method for Examining Pathways of Decay 235 Identification of Intermediates in mRNA Decay 235 DETERMINANTS OF mRNA STABILITY IN S. CEREVISIAE 236 Specific Sequences Influence mRNA Half-Lives 236 Nonspecific Features of mRNAs Generally Do Not Influence mRNA Half-Lives 237 There is no correlation between mRNA length and stability 237 Ribosome protection cannot account for mRNA half-lives 237 Rare codons are not general determinants of mRNA stability 238 A COMMON PATHWAY OF mRNA DECAY 238 Deadenylation Precedes the Decay of Some Yeast mRNAs 238 Decapping and 5*-to-3* Exonucleolytic Digestion Follow Deadenylation of Some Yeast mRNAs 239 Deadenylation-Dependent Decapping Is a Common Pathway of mRNA Decay 239 Control of mRNA Half-Lives through the Deadenylation-Dependent Decapping Pathway 240 Control of mRNA deadenylation 240 (i) Poly(A)-binding protein influences deadenylation 240 (ii) Poly(A)-binding protein-dependent nuclease activity from S. cerevisiae 240 (iii) Other proteins possibly involved in deadenylation 240 (iv) Models of poly(A) shortening 240 (v) Terminal deadenylation is not a rate-determining step for 5*-to-3* decay 241 Control of mRNA decapping 241 (i) The Pab1p-poly(A) tail complex inhibits mRNA decapping 241 (ii) Control of decapping after deadenylation 242 (iii) Decapping activities from S. cerevisiae 242 (iv) Translation and mRNA decapping 242 ADDITIONAL PATHWAYS OF mRNA DECAY IN S. CEREVISIAE 243 3*-to-5* mRNA Decay 243 Endonucleolytic Cleavage of mRNAs 243 mRNA Surveillance: Rapid Deadenylation-Independent Decapping 243 Early nonsense codons trigger mRNA decapping 243 Recognition of early nonsense codons 244 (i) Specific sequences are required 3* of early nonsense codons 244 (ii) Specific upstream elements partially block nonsense codon-mediated decay 245 trans-Acting factors in nonsense codon-mediated mRNA decay 245 Where in the cell does recognition of an early nonsense codon occur? 246 REGULATED mRNA TURNOVER IN S. CEREVISIAE 246 CONCLUSIONS 246 REFERENCES 246