The cytoplasmic mRNA degradation factor Pat1 is required for rRNA processing

References

• Pérez-Ortín JE, de Miguel-Jiménez L, Chávez S. Genome-wide studies of mRNA synthesis and degradation in eukaryotes. Biochim Biophys Acta 2012; 1819:604–15; PMID:22182827; http://dx.doi.org/10.1016/j.bbagrm.2011.12.002
   PubMed Web of Science ®Google Scholar
• Balagopal V, Fluch L, Nissan T. Ways and means of eukaryotic mRNA decay. Biochim Biophys Acta 2012; 1819:593–603; PMID:22266130; http://dx.doi.org/10.1016/j.bbagrm.2012.01.001
   PubMed Web of Science ®Google Scholar
• Parker R, Song H. The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 2004; 11:121–7; PMID:14749774; http://dx.doi.org/10.1038/nsmb724
   PubMed Web of Science ®Google Scholar
• Franks TM, Lykke-Andersen J. The Control of mRNA Decapping and P-Body Formation. Mol Cell 2008; 32:605–15; PMID:19061636; http://dx.doi.org/10.1016/j.molcel.2008.11.001
   PubMed Web of Science ®Google Scholar
• Nissan T, Rajyaguru P, She M, Song H, Parker R. Decapping Activators in Saccharomyces cerevisiae Act by Multiple Mechanisms. Molecular Cell 2010; 39:773–83; PMID:20832728; http://dx.doi.org/10.1016/j.molcel.2010.08.025
   PubMed Web of Science ®Google Scholar
• Marnef A, Standart N. Pat1 proteins: a life in translation, translation repression and mRNA decay. Biochem Soc Trans 2010; 38:1602; PMID:21118134; http://dx.doi.org/10.1042/BST0381602
   PubMed Web of Science ®Google Scholar
• Coller J, Parker R. General translational repression by activators of mRNA decapping. Cell 2005; 122:875–86; PMID:16179257; http://dx.doi.org/10.1016/j.cell.2005.07.012
   PubMed Web of Science ®Google Scholar
• Holmes LEA, Campbell SG, De Long SK, Sachs AB, Ashe MP. Loss of Translational Control in Yeast Compromised for the Major mRNA Decay Pathway. Mol Cell Biol 2004; 24:2998–3010; PMID:15024087; http://dx.doi.org/10.1128/MCB.24.7.2998-3010.2004
   PubMed Web of Science ®Google Scholar
• Pilkington GR, Parker R. Pat1 Contains Distinct Functional Domains That Promote P-Body Assembly and Activation of Decapping. Mol Cell Biol 2008; 28:1298–312; PMID:18086885; http://dx.doi.org/10.1128/MCB.00936-07
   PubMed Web of Science ®Google Scholar
• Tharun S, He W, Mayes AE, Lennertz P, Beggs JD, Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 2000; 404:515–8; PMID:10761922; http://dx.doi.org/10.1038/35006-676
   PubMed Web of Science ®Google Scholar
• Bouveret E, Rigaut G, Shevchenko A, Wilm M, Séraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J 2000; 19:1661–71; PMID:10747033; http://dx.doi.org/10.1093/emboj/19.7.1661
   PubMed Web of Science ®Google Scholar
• Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, Chávez S, Pérez-Ortín JE, Darzacq X, Choder M. Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis. Cell 2013; 153:1000–11; PMID:23706738; http://dx.doi.org/10.1016/j.cell.2013.05.012
   PubMed Web of Science ®Google Scholar
• Teixeira D, Parker R. Analysis of P-body assembly in Saccharomyces cerevisiae. Mol Biol Cell 2007; 18:2274–87; PMID:17429074; http://dx.doi.org/10.1091/mbc.E07-03-0199
   PubMed Web of Science ®Google Scholar
• Marnef A, Weil D, Standart N. RNA-related nuclear functions of human Pat1b, the P-body mRNA decay factor. Mol Biol Cell 2011; 23:213–24; PMID:22090346; http://dx.doi.org/10.1091/mbc.E11-05-0415
   PubMed Web of Science ®Google Scholar
• Wang X, Watt PM, Louis EJ, Borts RH, Hickson ID. Pat1: a topoisomerase II-associated protein required for faithful chromosome transmission in Saccharomyces cerevisiae. Nucleic Acids Res 1996; 24:4791–7; PMID:8972867; http://dx.doi.org/10.1093/nar/24.23.4791
   PubMed Web of Science ®Google Scholar
• Wang X, Watt PM, Borts RH, Louis EJ, Hickson ID. The topoisomerase II-associated protein, Pat1p, is required for maintenance of rDNA locus stability in Saccharomyces cerevisiae. Mol Gen Genet 1999; 261:831–40; PMID:10394921; http://dx.doi.org/10.1007/s004380050027
   PubMedGoogle Scholar
• Sun M, Schwalb B, Pirkl N, Maier KC, Schenk A, Failmezger H, Tresch A, Cramer P. Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels. Mol Cell 2013; 52:52–62; PMID:24119399; http://dx.doi.org/10.1016/j.molcel.2013.09.010
   PubMed Web of Science ®Google Scholar
• Hurto RL, Hopper AK. P-body components, Dhh1 and Pat1, are involved in tRNA nuclear-cytoplasmic dynamics. RNA 2011; 17:912–24; PMID:21398402; http://dx.doi.org/10.1261/rna.2558511
   PubMed Web of Science ®Google Scholar
• Kramer EB, Hopper AK. Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2013; 110:21042–21047; PMID:24297920; http://dx.doi.org/10.1073/pnas.1316579110
   Google Scholar
• Mishra PK, Ottmann AR, Basrai MA. Structural integrity of centromeric chromatin and faithful chromosome segregation requires Pat1. Genetics 2013; 195:369–79; PMID:23893485; http://dx.doi.org/10.1534/genetics.113.155291
   PubMed Web of Science ®Google Scholar
• Sharif H, Conti E. Architecture of the lsm1-7-pat1 complex: a conserved assembly in eukaryotic mRNA turnover. Cell Rep 2013; 5:283–91; PMID:24139796; http://dx.doi.org/10.1016/j.celrep.2013.10.004
   PubMed Web of Science ®Google Scholar
• He W, Parker R. Functions of Lsm proteins in mRNA degradation and splicing. Curr Opin Cell Biol 2000; 12:346–50; PMID:10801455; http://dx.doi.org/10.1016/S0955-0674(00)00098-3
   PubMed Web of Science ®Google Scholar
• Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D. Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex. Mol Cell Biol 2004; 24:9646–57; PMID:15485930; http://dx.doi.org/10.1128/MCB.24.21.9646-9657.2004
   PubMed Web of Science ®Google Scholar
• Kufel J. Lsm Proteins Are Required for Normal Processing and Stability of Ribosomal RNAs. J Biol Chem 2003; 278:2147–56; PMID:12438310; http://dx.doi.org/10.1074/jbc.M208856200
   PubMed Web of Science ®Google Scholar
• Séraphin B. Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J 1995; 14:2089–98; PMID:7744014
   PubMed Web of Science ®Google Scholar
• Mayes AE. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. EMBO J 1999; 18:4321–31; PMID:10428970; http://dx.doi.org/10.1093/emboj/18.15.4321
   PubMed Web of Science ®Google Scholar
• Luhtala N, Parker R. LSM1 over-expression in Saccharomyces cerevisiae depletes U6 snRNA levels. Nucleic Acids Res 2009; 37:5529–36; PMID:19596813; http://dx.doi.org/10.1093/nar/gkp572
   PubMed Web of Science ®Google Scholar
• Bousquet-Antonelli C, Presutti C, Tollervey D. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 2000; 102:765–75; PMID:11030620; http://dx.doi.org/10.1016/S0092-8674(00)00065-9
   PubMed Web of Science ®Google Scholar
• Allmang C, Kufel J, Chanfreau G, Mitchell P, Petfalski E, Tollervey D. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 1999; 18:5399–410; PMID:10508172; http://dx.doi.org/10.1093/emboj/18.19.5399
   PubMed Web of Science ®Google Scholar
• Tollervey D, Kiss T. Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 1997; 9:337–42; PMID:9159079; http://dx.doi.org/10.1016/S0955-0674(97)80005-1
   PubMed Web of Science ®Google Scholar
• Kufel J. A complex pathway for 3' processing of the yeast U3 snoRNA. Nucleic Acids Res 2003; 31:6788–97; PMID:14627812; http://dx.doi.org/10.1093/nar/gkg904
   PubMed Web of Science ®Google Scholar
• Antic S, Wolfinger MT, Skucha A, Hosiner S, Dorner S. General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells. Mol Cell Biol 2015; 35:2309–20; PMID:25918245; http://dx.doi.org/10.1128/MCB.01346-14
   PubMed Web of Science ®Google Scholar
• Wyers F, Minet M, Dufour ME, Vo LT, Lacroute F. Deletion of the PAT1 gene affects translation initiation and suppresses a PAB1 gene deletion in yeast. Mol Cell Biol 2000; 20:3538–49; PMID:10779343; http://dx.doi.org/10.1128/MCB.20.10.3538-3549.2000
   PubMed Web of Science ®Google Scholar
• Wu D, Muhlrad D, Bowler MW, Jiang S, Liu Z, Parker R, Song H. Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation. Cell Res 2014; 24:233–46; PMID:24247251; http://dx.doi.org/10.1038/cr.2013.152
   PubMed Web of Science ®Google Scholar
• Woolford JL, Baserga SJ. Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae. Genetics 2013; 195:643–81; PMID:24190922; http://dx.doi.org/10.1534/genetics.113.153197
   PubMed Web of Science ®Google Scholar
• Li Z, Lee I, Moradi E, Hung N-J, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics. PLoS Biol 2009; 7:e1000213; PMID:19806183; http://dx.doi.org/10.1371/journal.pbio.1000213
   PubMed Web of Science ®Google Scholar
• KoS M, Koš M, Tollervey D. Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally. Molecular Cell 2010; 37:809–20; PMID:20347423; http://dx.doi.org/10.1016/j.molcel.2010.02.024
   PubMed Web of Science ®Google Scholar
• Venema J, Tollervey D. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 1999; 33:261–311; PMID:10690410; http://dx.doi.org/10.1146/annurev.genet.33.1.261
   PubMed Web of Science ®Google Scholar
• Kressler D, Linder P, la Cruz de J. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 1999; 19:7897–912; PMID:10567516; http://dx.doi.org/10.1128/MCB.19.12.7897
   PubMed Web of Science ®Google Scholar
• Allmang C, Mitchell P, Petfalski E, Tollervey D. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res 2000; 28:1684–91; PMID:10734186; http://dx.doi.org/10.1093/nar/28.8.1684
   PubMed Web of Science ®Google Scholar
• Kuai L, Fang F, Butler JS, Sherman F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2004; 101:8581–6; PMID:15173578; http://dx.doi.org/10.1073/pnas.0402888101
   PubMed Web of Science ®Google Scholar
• Wery M, Ruidant S, Schillewaert S, Lepore N, Lafontaine DL. The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA 2009; 15:406–19; PMID:19141608; http://dx.doi.org/10.1261/rna.1402709
   PubMed Web of Science ®Google Scholar
• Cole SE, LaRiviere FJ, Merrikh CN, Moore MJ. A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol Cell 2009; 34:440–50; PMID:19481524; http://dx.doi.org/10.1016/j.molcel.2009.04.017
   PubMed Web of Science ®Google Scholar
• He W, Parker R. The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3′ termini from partial degradation. Genetics 2001; 158:1445–55; PMID:11514438
   PubMed Web of Science ®Google Scholar
• Tansey WP. 6-azauracil sensitivity assay for yeast. CSH Protoc 2006; 2006; PMID:22484669
   PubMedGoogle Scholar
• Laribee RN, Hosni-Ahmed A, Workman JJ, Chen H. Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis; PLoS Genetics; 11(3); e1005113; PMID:25815716; http://dx.doi.org/10.1371/journal.pgen.1005113
   Google Scholar
• Hage el A, French SL, Beyer AL, Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev 2010; 24:1546–58; PMID:20634320; http://dx.doi.org/10.1101/gad.573310
   PubMed Web of Science ®Google Scholar
• Chowdhury A, Kalurupalle S, Tharun S. Pat1 contributes to the RNA binding activity of the Lsm1-7-Pat1 complex. RNA 2014; 20:1465–75; PMID:25035297; http://dx.doi.org/10.1261/rna.045252.114
   PubMed Web of Science ®Google Scholar
• Grzechnik P, Kufel J. Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell 2008; 32:247–58; PMID:18951092; http://dx.doi.org/10.1016/j.molcel.2008.10.003
   PubMed Web of Science ®Google Scholar
• Schmid M, Poulsen M, Olszewski P, Pelechano V, Saguez C, Gupta I, Steinmetz L, Moore C, Jensen T, Poulsen M, et al. Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins. Molecular Cell 2012; 47:267–80; PMID:22683267; http://dx.doi.org/10.1016/j.molcel.2012.05.005
   PubMed Web of Science ®Google Scholar
• Tudek A, Porrua O, Kabzinski T, Lidschreiber M, Kubicek K, Fortova A, Lacroute F, Vanacova S, Cramer P, Stefl R, et al. Molecular basis for coordinating transcription termination with noncoding RNA degradation. Mol Cell 2014; 55:467–81; PMID:25066235; http://dx.doi.org/10.1016/j.molcel.2014.05.031
   PubMed Web of Science ®Google Scholar
• Houseley J, Kotovic K, Hage El A, Tollervey D. Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 2007; 26:4996–5006; PMID:18007593; http://dx.doi.org/10.1038/sj.emboj.7601921
   PubMed Web of Science ®Google Scholar
• Sadoff BU, Heath-Pagliuso S, Castaño IB, Zhu Y, Kieff FS, Christman MF. Isolation of mutants of Saccharomyces cerevisiae requiring DNA topoisomerase I. Genetics 1995; 141:465–79; PMID:8647385
   PubMed Web of Science ®Google Scholar
• Castaño IB, Brzoska PM, Sadoff BU, Chen H, Christman MF. Mitotic chromosome condensation in the rDNA requires TRF4 and DNA topoisomerase I in Saccharomyces cerevisiae.
   Google Scholar
• Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 2006; 124:1069–81; PMID:16487579; http://dx.doi.org/10.1016/j.cell.2005.12.036
   PubMed Web of Science ®Google Scholar
• Petfalski E, Dandekar T, Henry Y, Tollervey D. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol Cell Biol 1998; 18:1181–9; PMID:9488433; http://dx.doi.org/10.1128/MCB.18.3.1181
   PubMed Web of Science ®Google Scholar
• Lindahl L, Bommankanti A, Li X, Hayden L, Jones A, Khan M, Oni T, Zengel JM. RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway. RNA 2009; 15:1407–16; PMID:19465684; http://dx.doi.org/10.1261/rna.1302909
   PubMed Web of Science ®Google Scholar
• Arribere J, Doudna J, Gilbert W. Reconsidering Movement of Eukaryotic mRNAs between Polysomes and P Bodies. Mol Cell 2011; 44:745–58; PMID:22152478; http://dx.doi.org/10.1016/j.molcel.2011.09.019
   PubMed Web of Science ®Google Scholar
• Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 2002; 99:5860–5; PMID:11972065; http://dx.doi.org/10.1073/pnas.092538799
   PubMed Web of Science ®Google Scholar
• Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR. Genome-Wide Analysis of mRNA Stability Using Transcription Inhibitors and Microarrays Reveals Posttranscriptional Control of Ribosome Biogenesis Factors. Mol Cell Biol 2004; 24:5534–47; PMID:15169913; http://dx.doi.org/10.1128/MCB.24.12.5534-5547.2004
   PubMed Web of Science ®Google Scholar
• Shalgi R, Lapidot M, Shamir R, Pilpel Y. A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol 2005; 6:R86; PMID:16207357; http://dx.doi.org/10.1186/gb-2005-6-10-r86
   PubMedGoogle Scholar
• Chowdhury A, Tharun S. lsm1 mutations impairing the ability of the Lsm1p-7p-Pat1p complex to preferentially bind to oligoadenylated RNA affect mRNA decay in vivo. RNA 2008; 14:2149–58; PMID:18719247; http://dx.doi.org/10.1261/rna.1094208
   PubMed Web of Science ®Google Scholar
• Kressler D, Hurt E, Baßler J. Driving ribosome assembly. Biochim Biophys Acta 2010; 1803:673–83; PMID:19879902; http://dx.doi.org/10.1016/j.bbamcr.2009.10.009
   PubMed Web of Science ®Google Scholar
• Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, et al. Mapping Pathways and Phenotypes by Systematic Gene Overexpression. Molecular Cell 2006; 21:319–30; PMID:16455487; http://dx.doi.org/10.1016/j.molcel.2005.12.011
   PubMed Web of Science ®Google Scholar
• Jorgensen P. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 2004; 18:2491–505; PMID:15466158; http://dx.doi.org/10.1101/gad.1228804
   PubMed Web of Science ®Google Scholar
• Muhlrad D, Parker R. Premature translational termination triggers mRNA decapping. Nature 1994; 370:578–81; PMID:8052314; http://dx.doi.org/10.1038/370578a0
   PubMed Web of Science ®Google Scholar
• Nissan T, Parker R. Analyzing P-bodies in Saccharomyces cerevisiae. Meth Enzymol 2008; 448:507–20; PMID:19111192; http://dx.doi.org/10.1016/S0076-6879(08)02625-6
   PubMed Web of Science ®Google Scholar
• Coller JM, Tucker M, Sheth U, Valencia-Sanchez MA, Parker R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA 2001; 7:1717–27; PMID:11780629; http://dx.doi.org/10.1017/S135583820101994X
   PubMed Web of Science ®Google Scholar
• Sambrook J, Russell DW. Sambrook: Molecular cloning. A laboratory manual. Third - Google Scholar. Cold pring Harbor Laboratory Press; 2001.
   Google Scholar
• Tollervey D. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J 1987; 6:4169–75; PMID:3327689
   PubMed Web of Science ®Google Scholar
• Zhou Y, Chen C, Johansson MJO. The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression. Nucleic Acids Research 2013; 41:5669–78; PMID:23605039; http://dx.doi.org/10.1093/nar/gkt269
   PubMed Web of Science ®Google Scholar