Deciphering 3'ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing

Molecular Cell

Volumn 43, Issue 6, 2011, Pages 1033-1039

  Meyer, Markus ^a,d   Plass, Mireya ^b   Pérez Valle, Jorge ^d   Eyras, Eduardo ^b,c   Vilardell, Josep ^a,c  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^d INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; FUNGAL GENOME; GENETIC SELECTION; HEAT SHOCK; INTRON; NONHUMAN; PROTEIN FOLDING; RNA STRUCTURE; RNA THERMOSENSOR; SPLICEOSOME; THERMORECEPTOR; YEAST;

3' UNTRANSLATED REGIONS; ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; GENOME, FUNGAL; NUCLEIC ACID CONFORMATION; RNA PRECURSORS; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, RNA; SPLICEOSOMES;

EUKARYOTA;

EID: 80053008165     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2011.07.030     Document Type: Article

References (29)

1. Cellini A., Felder E., Rossi J.J. Yeast pre-messenger RNA splicing efficiency depends on critical spacing requirements between the branch point and 3' splice site. EMBO J. 1986, 5:1023-1030.
2. Chen S., Anderson K., Moore M.J. Evidence for a linear search in bimolecular 3' splice site AG selection. Proc. Natl. Acad. Sci. USA 2000, 97:593-598.
3. Chua K., Reed R. An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol. Cell. Biol. 2001, 21:1509-1514.
4. Clark T.A., Sugnet C.W., Ares M. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 2002, 296:907-910.
5. Collins C.A., Guthrie C. Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome. Genes Dev. 1999, 13:1970-1982.
6. Cooper T.A., Wan L., Dreyfuss G. RNA and disease. Cell 2009, 136:777-793.
7. Crotti L.B., Horowitz D.S. Exon sequences at the splice junctions affect splicing fidelity and alternative splicing. Proc. Natl. Acad. Sci. USA 2009, 106:18954-18959.
8. Deshler J.O., Rossi J.J. Unexpected point mutations activate cryptic 3' splice sites by perturbing a natural secondary structure within a yeast intron. Genes Dev. 1991, 5:1252-1263.
9. Fabrizio P., Dannenberg J., Dube P., Kastner B., Stark H., Urlaub H., Lührmann R. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol. Cell 2009, 36:593-608.
10. Frank D., Patterson B., Guthrie C. Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol. Cell. Biol. 1992, 12:5197-5205.
11. Goguel V., Rosbash M. Splice site choice and splicing efficiency are positively influenced by pre-mRNA intramolecular base pairing in yeast. Cell 1993, 72:893-901.
12. Hofacker I.L. RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics 2009, Chapter 12:Unit12.12.
13. Kaempfer R. RNA sensors: novel regulators of gene expression. EMBO Rep. 2003, 4:1043-1047.
14. Konarska M.M., Vilardell J., Query C.C. Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol. Cell 2006, 21:543-553.
15. Lesser C.F., Guthrie C. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 1993, 133:851-863.
16. Liu Z.R., Laggerbauer B., Lührmann R., Smith C.W. Crosslinking of the U5 snRNP-specific 116-kDa protein to RNA hairpins that block step 2 of splicing. RNA 1997, 3:1207-1219.
17. Luukkonen B.G., Séraphin B. The role of branchpoint-3' splice site spacing and interaction between intron terminal nucleotides in 3' splice site selection in Saccharomyces cerevisiae. EMBO J. 1997, 16:779-792.
18. Neupert J., Bock R. Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria. Nat. Protoc. 2009, 4:1262-1273.
19. Patterson B., Guthrie C. A U-rich tract enhances usage of an alternative 3' splice site in yeast. Cell 1991, 64:181-187.
20. Rogic S., Montpetit B., Hoos H.H., Mackworth A.K., Ouellette B.F., Hieter P. Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae. BMC Genomics 2008, 9:355-373.
21. Siatecka M., Reyes J.L., Konarska M.M. Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes Dev. 1999, 13:1983-1993.
22. Smith C.W., Chu T.T., Nadal-Ginard B. Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns. Mol. Cell. Biol. 1993, 13:4939-4952.
23. Smith D.J., Query C.C., Konarska M.M. "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Mol. Cell 2008, 30:657-666.
24. Spingola M., Grate L., Haussler D., Ares M. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 1999, 5:221-234.
25. Umen J.G., Guthrie C. The second catalytic step of pre-mRNA splicing. RNA 1995, 1:869-885.
26. Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol. 2010, 7:67-76.
27. Wahl M.C., Will C.L., Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009, 136:701-718.
28. Will C.L., Lührmann R. Splicing of a rare class of introns by the U12-dependent spliceosome. Biol. Chem. 2005, 386:713-724.
29. Yassour M., Kaplan T., Fraser H.B., Levin J.Z., Pfiffner J., Adiconis X., Schroth G., Luo S., Khrebtukova I., Gnirke A., et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl. Acad. Sci. USA 2009, 106:3264-3269.