Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 29, 2012, Pages 11764-11769

  Harigaya, Yuriko ^a,b   Parker, Roy ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DCP2 PROTEIN; ENDONUCLEASE; MESSENGER RNA; UNCLASSIFIED DRUG;

ARTICLE; ENZYME SUBSTRATE; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA DEGRADATION; RNA SPLICING; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; BLOTTING, NORTHERN; ENDONUCLEASES; ENDORIBONUCLEASES; HALF-LIFE; KINETICS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PLASMIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA CAPS; RNA STABILITY; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EUKARYOTA; METAZOA; SACCHAROMYCES CEREVISIAE;

EID: 84863895769     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1119741109     Document Type: Article

References (29)

1. Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11:121-127. (Pubitemid 38146514)
2. Rissland OS, Norbury CJ (2009) Decapping is preceded by 3′ uridylation in a novel pathway of bulk mRNA turnover. Nat Struct Mol Biol 16:616-623.
3. Li WM, Barnes T, Lee CH (2010) Endoribonucleases - enzymes gaining spotlight in mRNA metabolism. FEBS J 277:627-641.
4. Tomecki R, Dziembowski A (2010) Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA 16:1692-1724.
5. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: Mechanisms and regulations. Genes Dev 20:759-771.
6. Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15:173-183. (Pubitemid 38950965)
7. Rymarquis LA, Souret FF, Green PJ (2011) Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories. RNA 17:501-511.
8. Karginov FV, et al. (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell 38:781-788.
9. Shin C, et al. (2010) Expanding the microRNA targeting code: Functional sites with centered pairing. Mol Cell 38:789-802.
10. Gatfield D, Izaurralde E (2004) Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429:575-578. (Pubitemid 38737663)
11. Doma MK, Parker R (2006) Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440:561-564.
12. Huntzinger E, Kashima I, Fauser M, Saulière J, Izaurralde E (2008) SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA 14:2609-2617.
13. Eberle AB, Lykke-Andersen S, Mühlemann O, Jensen TH (2009) SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat Struct Mol Biol 16:49-55.
14. Kimata Y, Kohno K (2011) Endoplasmic reticulum stress-sensing mechanisms in yeast and mammalian cells. Curr Opin Cell Biol 23:135-142.
15. German MA, et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26:941-946.
16. Muhlrad D, Decker CJ, Parker R (1994) Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5′ - >3′ digestion of the transcript. Genes Dev 8:855-866.
17. Hsu CL, Stevens A (1993) Yeast cells lacking 5′ - > 3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol Cell Biol 13:4826-4835. (Pubitemid 23220388)
18. Nagalakshmi U, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349. (Pubitemid 351929471)
19. Sidrauski C, Walter P (1997) The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 90:1031-1039. (Pubitemid 27408517)
20. Doma MK (2006) Identification and characterization of novel proteins and pathways for mRNA degradation and quality control in Saccharomyces cerevisiae. PhD thesis (Univ of Arizona, Tucson).
21. Hilleren PJ, Parker R (2003) Cytoplasmic degradation of splice-defective pre-mRNAs and intermediates. Mol Cell 12:1453-1465. (Pubitemid 38037014)
22. Mayas RM, Maita H, Semlow DR, Staley JP (2010) Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc Natl Acad Sci USA 107:10020-10025.
23. Spingola M, Grate L, Haussler D, Ares M, Jr. (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5:221-234. (Pubitemid 29079282)
24. Beelman CA, Parker R (1994) Differential effects of translational inhibition in cis and in trans on the decay of the unstable yeast MFA2 mRNA. J Biol Chem 269:9687-9692. (Pubitemid 24196570)
25. Xiang S, et al. (2009) Structure and function of the 5′ - > 3′ exoribonuclease Rat1 and its activating partner Rai1. Nature 458:784-788.
26. Jiao X, et al. (2010) Identification of a quality-control mechanism for mRNA 5′-end capping. Nature 467:608-611.
27. Liu H, Rodgers ND, Jiao X, Kiledjian M (2002) The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J 21:4699-4708. (Pubitemid 34984357)
28. van Dijk E, Le Hir H, Séraphin B (2003) DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway. Proc Natl Acad Sci USA 100:12081-12086.
29. Badis G, Saveanu C, Fromont-Racine M, Jacquier A (2004) Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell 15:5-15. (Pubitemid 38850215)