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