M. Albrecht and T. Lengauer, Novel Sm-like proteins with long C-terminal tails and associated methyltransferases, FEBS Letters, vol.166, issue.1-3, pp.18-26, 2004.
DOI : 10.1016/j.febslet.2004.03.126

URL : http://hdl.handle.net/11858/00-001M-0000-000F-2990-F

D. C. Amberg, A. L. Goldstein, C. , and C. N. , Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA., Genes & Development, vol.6, issue.7, pp.1173-1189, 1992.
DOI : 10.1101/gad.6.7.1173

N. Amrani, S. Ghosh, D. A. Mangus, and A. Jacobson, Translation factors promote the formation of two states of the closed-loop mRNP, Nature, vol.17, issue.7199, pp.1276-1280, 2008.
DOI : 10.1038/nature06974

J. T. Anderson, S. M. Wilson, K. V. Datar, and M. S. Swanson, NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability., Molecular and Cellular Biology, vol.13, issue.5, pp.2730-2741, 1993.
DOI : 10.1128/MCB.13.5.2730

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC359649

Y. Araki, S. Takahashi, T. Kobayashi, H. Kajiho, S. Hoshino et al., Ski7p G protein interacts with the exosome and the Ski complex for 3'-to-5' mRNA decay in yeast, The EMBO Journal, vol.20, issue.17, pp.4684-4693, 2001.
DOI : 10.1093/emboj/20.17.4684

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences, vol.18, issue.45, pp.3889-3894, 2003.
DOI : 10.1038/sj.onc.1203131

J. T. Arigo, K. L. Carroll, J. M. Ames, and J. L. And-corden, Regulation of Yeast NRD1 Expression by Premature Transcription Termination, Molecular Cell, vol.21, issue.5, pp.641-651, 2006.
DOI : 10.1016/j.molcel.2006.02.005

C. M. Arraiano, F. Mauxion, S. C. Viegas, R. G. Matos, and B. Séraphin, Intracellular ribonucleases involved in transcript processing and decay: Precision tools for RNA, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1829, issue.6-7, pp.491-513, 2013.
DOI : 10.1016/j.bbagrm.2013.03.009

G. Badis, C. Saveanu, M. Fromont-racine, and A. Jacquier, Targeted mRNA Degradation by Deadenylation-Independent Decapping, Molecular Cell, vol.15, issue.1, pp.5-15, 2004.
DOI : 10.1016/j.molcel.2004.06.028

URL : https://hal.archives-ouvertes.fr/pasteur-01404698

B. W. Baer and R. D. Kornberg, Repeating structure of cytoplasmic poly(A)-ribonucleoprotein., Proceedings of the National Academy of Sciences, vol.77, issue.4, pp.1890-1892, 1980.
DOI : 10.1073/pnas.77.4.1890

B. W. Baer and R. D. Kornberg, The protein responsible for the repeating structure of cytoplasmic poly(A)-ribonucleoprotein, The Journal of Cell Biology, vol.96, issue.3, pp.717-721, 1983.
DOI : 10.1083/jcb.96.3.717

K. J. Bandyra, M. Bouvier, A. J. Carpousis, and B. F. Luisi, The social fabric of the RNA degradosome, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1829, issue.6-7, pp.514-522, 2013.
DOI : 10.1016/j.bbagrm.2013.02.011

URL : https://hal.archives-ouvertes.fr/hal-00944960

V. I. Bashkirov, H. Scherthan, J. A. Solinger, J. M. Buerstedde, and W. D. Heyer, A Mouse Cytoplasmic Exoribonuclease (mXRN1p) with Preference for G4 Tetraplex Substrates, The Journal of Cell Biology, vol.60, issue.4, pp.761-773, 1997.
DOI : 10.1016/0022-2836(75)90222-3

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2132493

J. Basquin, V. V. Roudko, M. Rode, C. Basquin, B. Séraphin et al., Architecture of the Nuclease Module of the Yeast Ccr4-Not Complex: the Not1-Caf1-Ccr4 Interaction, Molecular Cell, vol.48, issue.2, pp.207-218, 2012.
DOI : 10.1016/j.molcel.2012.08.014

C. A. Beelman, A. Stevens, G. Caponigro, T. E. Lagrandeur, L. Hatfield et al., An essential component of the decapping enzyme required for normal rates of mRNA turnover, Nature, vol.382, issue.6592, pp.642-646, 1996.
DOI : 10.1038/382642a0

R. Boeck, S. Tarun, . Jr, M. Rieger, J. A. Deardorff et al., The yeast Pan2 protein is required for poly(A)-binding protein-stimulated poly(A)-nuclease activity, J. Biol. Chem, vol.271, pp.432-438, 1996.

R. Boeck, B. Lapeyre, C. E. Brown, and A. B. Sachs, Mutant, Molecular and Cellular Biology, vol.18, issue.9, pp.5062-5072, 1998.
DOI : 10.1128/MCB.18.9.5062

M. S. Borja, K. Piotukh, C. Freund, and J. D. Gross, Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition, RNA, vol.17, issue.2, pp.278-290, 2011.
DOI : 10.1261/rna.2382011

C. Bousquet-antonelli, C. Presutti, and D. Tollervey, Identification of a Regulated Pathway for Nuclear Pre-mRNA Turnover, Cell, vol.102, issue.6, pp.765-775, 2000.
DOI : 10.1016/S0092-8674(00)00065-9

E. Bouveret, G. Rigaut, A. Shevchenko, M. Wilm, and B. Séraphin, A Sm-like protein complex that participates in mRNA degradation, The EMBO Journal, vol.19, issue.7, pp.1661-1671, 2000.
DOI : 10.1093/emboj/19.7.1661

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310234

A. Bregman, M. Avraham-kelbert, O. Barkai, L. Duek, A. Guterman et al., Promoter Elements Regulate Cytoplasmic mRNA Decay, Cell, vol.147, issue.7, pp.1473-1483, 2011.
DOI : 10.1016/j.cell.2011.12.005

URL : http://doi.org/10.1016/j.cell.2011.12.005

C. E. Brown and A. B. Sachs, Occurs by Message-Specific Deadenylation, Molecular and Cellular Biology, vol.18, issue.11, pp.6548-6559, 1998.
DOI : 10.1128/MCB.18.11.6548

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC109240

C. E. Brown, S. Z. Tarun, . Jr, R. Boeck, and A. B. Sachs, PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in Saccharomyces cerevisiae., Molecular and Cellular Biology, vol.16, issue.10, pp.5744-5753, 1996.
DOI : 10.1128/MCB.16.10.5744

K. Burger, B. Mühl, M. Kellner, M. Rohrmoser, A. Gruber-eber et al., 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response, RNA Biology, vol.54, issue.10, 2013.
DOI : 10.1083/jcb.200501141

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866244

J. S. Butler, M. , and P. , Rrp6, Rrp47 and Cofactors of the Nuclear Exosome, Adv. Exp. Med. Biol, vol.702, pp.91-104, 2011.
DOI : 10.1007/978-1-4419-7841-7_8

K. P. Callahan and J. S. Butler, TRAMP Complex Enhances RNA Degradation by the Nuclear Exosome Component Rrp6, Journal of Biological Chemistry, vol.285, issue.6, pp.3540-3547, 2010.
DOI : 10.1074/jbc.M109.058396

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823493

J. H. Chang, X. Jiao, K. Chiba, C. Oh, C. E. Martin et al., Dxo1 is a new type of eukaryotic enzyme with both decapping and 5???-3??? exoribonuclease activity, Nature Structural & Molecular Biology, vol.19, issue.10, pp.1011-1017, 2012.
DOI : 10.1073/pnas.192445599

A. Chowdhury, J. Mukhopadhyay, and S. Tharun, The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs, RNA, vol.13, issue.7, pp.998-1016, 2007.
DOI : 10.1261/rna.502507

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894922

M. D. Cleary, C. D. Meiering, E. Jan, R. Guymon, and J. C. Boothroyd, Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay, Nature Biotechnology, vol.8, issue.2, pp.232-237, 2005.
DOI : 10.1101/gr.145100

M. A. Collart and O. O. Panasenko, The Ccr4???Not complex, Gene, vol.492, issue.1, pp.42-53, 2012.
DOI : 10.1016/j.gene.2011.09.033

J. Coller, P. , and R. , General Translational Repression by Activators of mRNA Decapping, Cell, vol.122, issue.6, pp.875-886, 2005.
DOI : 10.1016/j.cell.2005.07.012

J. M. Coller, M. Tucker, U. Sheth, M. A. Valencia-sanchez, P. et al., The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes, RNA, vol.7, issue.12, pp.1717-1727, 2001.
DOI : 10.1017/S135583820101994X

J. L. Costello, J. A. Stead, M. Feigenbutz, R. M. Jones, M. et al., The C-terminal Region of the Exosome-associated Protein Rrp47 Is Specifically Required for Box C/D Small Nucleolar RNA 3'-Maturation, Journal of Biological Chemistry, vol.286, issue.6, pp.4535-4543, 2011.
DOI : 10.1074/jbc.M110.162826

N. Cougot, S. Babajko, and B. Séraphin, Cytoplasmic foci are sites of mRNA decay in human cells, The Journal of Cell Biology, vol.115, issue.1, pp.31-40, 2004.
DOI : 10.1016/S0962-8924(01)01982-1

M. C. Daugeron, F. Mauxion, and B. Séraphin, The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation, Nucleic Acids Research, vol.29, issue.12, pp.2448-2455, 2001.
DOI : 10.1093/nar/29.12.2448

L. Decourty, C. Saveanu, K. Zemam, F. Hantraye, E. Frachon et al., Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles, Proceedings of the National Academy of Sciences, vol.26, issue.4, pp.5821-5826, 2008.
DOI : 10.1093/nar/26.4.942

URL : https://hal.archives-ouvertes.fr/pasteur-01404694

C. Deneke, R. Lipowsky, and A. Valleriani, Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA, PLoS ONE, vol.7, issue.2, p.55442, 2013.
DOI : 10.1371/journal.pone.0055442.s001

M. V. Deshmukh, B. N. Jones, D. Quang-dang, J. Flinders, S. N. Floor et al., mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2, Molecular Cell, vol.29, issue.3, pp.324-336, 2008.
DOI : 10.1016/j.molcel.2007.11.027

B. Dichtl, A. Stevens, and D. Tollervey, Lithium toxicity in yeast is due to the inhibition of RNA processing enzymes, The EMBO Journal, vol.16, issue.23, pp.7184-7195, 1997.
DOI : 10.1093/emboj/16.23.7184

E. Van-dijk, N. Cougot, S. Meyer, S. Babajko, E. Wahle et al., Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures, The EMBO Journal, vol.21, issue.24, pp.6915-6924, 2002.
DOI : 10.1093/emboj/cdf678

E. L. Van-dijk, C. L. Chen, Y. Aubenton-carafa, S. Gourvennec, M. Kwapisz et al., XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast, Nature, vol.7, issue.7354, pp.114-117, 2011.
DOI : 10.1038/nature10118

A. Dmochowska, P. Golik, and P. P. Stepien, The novel nuclear gene DSS-1 of Saccharomyces cerevisiae is necessary for mitochondrial biogenesis, Current Genetics, vol.8, issue.2, pp.108-112, 1995.
DOI : 10.1007/BF00315775

L. Dölken, Z. Ruzsics, B. Rädle, C. C. Friedel, R. Zimmer et al., High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol.14, issue.9, pp.1959-1972, 2008.
DOI : 10.1261/rna.1136108

S. Dong, C. Li, D. Zenklusen, R. H. Singer, A. Jacobson et al., YRA1 Autoregulation Requires Nuclear Export and Cytoplasmic Edc3p-Mediated Degradation of Its Pre-mRNA, Molecular Cell, vol.25, issue.4, pp.559-573, 2007.
DOI : 10.1016/j.molcel.2007.01.012

URL : http://doi.org/10.1016/j.molcel.2007.01.012

M. Dori-bachash, O. Shalem, Y. S. Manor, Y. Pilpel, and I. Tirosh, Widespread promoter-mediated coordination of transcription and mRNA degradation, Genome Biology, vol.13, issue.12, p.114, 2012.
DOI : 10.1073/pnas.092538799

I. A. Drinnenberg, G. R. Fink, and D. P. Bartel, Compatibility with Killer Explains the Rise of RNAi-Deficient Fungi, Science, vol.9, issue.1, p.1592, 2011.
DOI : 10.1128/AEM.69.1.649-653.2003

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056

URL : https://hal.archives-ouvertes.fr/hal-00104411

T. Dunckley, P. , and R. , The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif, The EMBO Journal, vol.18, issue.19, pp.5411-5422, 1999.
DOI : 10.1093/emboj/18.19.5411

T. Dunckley, M. Tucker, P. , and R. , Two related proteins, Edc1p and Edc2p, stimulate mRNA decapping in Saccharomyces cerevisiae, Genetics, vol.157, pp.27-37, 2001.

A. Dziembowski, E. Lorentzen, E. Conti, and B. Séraphin, A single subunit, Dis3, is essentially responsible for yeast exosome core activity, Nature Structural & Molecular Biology, vol.8, issue.1, pp.15-22, 2007.
DOI : 10.1093/nar/29.12.2448

URL : https://hal.archives-ouvertes.fr/hal-00167461

S. R. Engel, C. , and J. M. , The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database, Database, vol.2013, issue.0, 2013.
DOI : 10.1093/database/bat012

M. J. Ensinger, S. A. Martin, E. Paoletti, M. , and B. , Modification of the 5'-terminus of mRNA by soluble guanylyl and methyl transferases from vaccinia virus., Proceedings of the National Academy of Sciences, vol.72, issue.7, pp.2525-2529, 1975.
DOI : 10.1073/pnas.72.7.2525

A. Eulalio, I. Behm-ansmant, and E. Izaurralde, P bodies: at the crossroads of post-transcriptional pathways, Nature Reviews Molecular Cell Biology, vol.89, issue.1, pp.9-22, 2007.
DOI : 10.1038/nrm2080

A. Eulalio, I. Behm-ansmant, D. Schweizer, and E. Izaurralde, P-Body Formation Is a Consequence, Not the Cause, of RNA-Mediated Gene Silencing, Molecular and Cellular Biology, vol.27, issue.11, pp.3970-3981, 2007.
DOI : 10.1128/MCB.00128-07

T. C. Fleischer, C. M. Weaver, K. J. Mcafee, J. L. Jennings, and A. J. Link, Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes, Genes & Development, vol.20, issue.10, pp.1294-1307, 2006.
DOI : 10.1101/gad.1422006

B. C. Foat, S. S. Houshmandi, W. M. Olivas, and H. J. Bussemaker, Profiling condition-specific, genome-wide regulation of mRNA stability in yeast, Proceedings of the National Academy of Sciences, vol.10, issue.2, pp.17675-17680, 2005.
DOI : 10.1002/yea.320100203

S. A. Fromm, V. Truffault, J. Kamenz, J. E. Braun, N. A. Hoffmann et al., The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex, The EMBO Journal, vol.12, issue.2, pp.279-290, 2012.
DOI : 10.1038/emboj.2011.408

M. Fromont-racine, J. C. Rain, and P. Legrain, Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens, Nature Genetics, vol.88, issue.3, pp.277-282, 1997.
DOI : 10.1016/0378-1119(96)00230-2

M. Fromont-racine, A. E. Mayes, A. Brunet-simon, J. C. Rain, A. Colley et al., Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins, Yeast, vol.24, issue.2, pp.95-110, 2000.
DOI : 10.1002/1097-0061(20000630)17:2<95::AID-YEA16>3.0.CO;2-H

URL : http://doi.org/10.1002/1097-0061(20000630)17:2<95::aid-yea16>3.0.co;2-h

Y. Furuichi, A. Lafiandra, and A. J. Shatkin, 5???-Terminal structure and mRNA stability, Nature, vol.15, issue.5599, pp.235-239, 1977.
DOI : 10.1038/266235a0

W. Garland, M. Feigenbutz, M. Turner, M. , and P. , Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6, RNA, vol.19, issue.12, pp.1659-68, 2013.
DOI : 10.1261/rna.039388.113

A. P. Gerber, D. Herschlag, and P. O. Brown, Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast, PLoS Biology, vol.390, issue.3, p.79, 2004.
DOI : 10.1371/journal.pbio.0020079.st011

C. Goebels, A. Thonn, S. Gonzalez-hilarion, O. Rolland, F. Moyrand et al., Introns Regulate Gene Expression in Cryptococcus neoformans in a Pab2p Dependent Pathway, PLoS Genetics, vol.18, issue.8, 2013.
DOI : 10.1371/journal.pgen.1003686.s009

A. C. Goldstrohm, B. A. Hook, D. J. Seay, and M. Wickens, PUF proteins bind Pop2p to regulate messenger RNAs, Nature Structural & Molecular Biology, vol.98, issue.6, pp.533-539, 2006.
DOI : 10.1038/nsmb1100

A. C. Goldstrohm, D. J. Seay, B. A. Hook, and M. Wickens, PUF Protein-mediated Deadenylation Is Catalyzed by Ccr4p, Journal of Biological Chemistry, vol.282, issue.1, pp.109-114, 2007.
DOI : 10.1074/jbc.M609413200

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.139.4893

S. Granneman, G. Kudla, E. Petfalski, and D. Tollervey, Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs, Proceedings of the National Academy of Sciences, vol.9, issue.19, pp.9613-9618, 2009.
DOI : 10.1101/gad.9.19.2433

D. M. Green, K. A. Marfatia, E. B. Crafton, X. Zhang, X. Cheng et al., Nab2p Is Required for Poly(A) RNA Export in Saccharomyces cerevisiae and Is Regulated by Arginine Methylation via Hmt1p, Journal of Biological Chemistry, vol.277, issue.10, pp.7752-7760, 2002.
DOI : 10.1074/jbc.M110053200

J. Grigull, S. Mnaimneh, J. Pootoolal, M. D. Robinson, and T. R. Hughes, Genome-Wide Analysis of mRNA Stability Using Transcription Inhibitors and Microarrays Reveals Posttranscriptional Control of Ribosome Biogenesis Factors, Molecular and Cellular Biology, vol.24, issue.12, pp.5534-5547, 2004.
DOI : 10.1128/MCB.24.12.5534-5547.2004

M. Gu, K. R. Rajashankar, and C. D. Lima, Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA Capping Apparatus, Structure, vol.18, issue.2, pp.216-227, 1993.
DOI : 10.1016/j.str.2009.12.009

R. K. Gudipati, H. Neil, F. Feuerbach, C. Malabat, and A. Jacquier, gene is regulated by modulation between two modes of transcription termination, The EMBO Journal, vol.121, issue.10, pp.2427-2437, 2012.
DOI : 10.1038/emboj.2012.81

F. Halbach, P. Reichelt, M. Rode, and E. Conti, The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex, Cell, vol.154, issue.4, pp.814-826, 2013.
DOI : 10.1016/j.cell.2013.07.017

URL : http://doi.org/10.1016/j.cell.2013.07.017

R. E. Halbeisen, T. Scherrer, and A. P. Gerber, Affinity purification of ribosomes to access the translatome, Methods, vol.48, issue.3, pp.306-310, 2009.
DOI : 10.1016/j.ymeth.2009.04.003

Y. Harigaya, B. N. Jones, D. Muhlrad, J. D. Gross, P. et al., Identification and Analysis of the Interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae, Molecular and Cellular Biology, vol.30, issue.6, pp.1446-1456, 2010.
DOI : 10.1128/MCB.01305-09

W. He, P. , and R. , The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation, Genetics, vol.158, pp.1445-1455, 2001.

R. E. Hector, K. R. Nykamp, S. Dheur, J. T. Anderson, P. J. Non et al., Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export, The EMBO Journal, vol.21, issue.7, pp.1800-1810, 2002.
DOI : 10.1093/emboj/21.7.1800

T. Hirayama, T. Matsuura, S. Ushiyama, M. Narusaka, Y. Kurihara et al., A poly(A)-specific ribonuclease directly regulates the poly(A) status of mitochondrial mRNA in Arabidopsis, Nature Communications, vol.85, 2013.
DOI : 10.1093/pcp/pcr080

B. Hoffmann, J. Nickel, F. Speer, and B. Schafer, The 3??? Ends of Mature Transcripts Are Generated by a Processosome Complex in Fission Yeast Mitochondria, Journal of Molecular Biology, vol.377, issue.4, pp.1024-1037, 2008.
DOI : 10.1016/j.jmb.2008.01.038

T. J. Hofmann, J. Min, and H. P. Zassenhaus, Formation of the 3??? end of yeast mitochondrial mRNAs occurs by site-specific cleavage two bases downstream of a conserved dodecamer sequence, Yeast, vol.7, issue.12, pp.1319-1330, 1993.
DOI : 10.1002/yea.320091205

D. J. Hogan, D. P. Riordan, A. P. Gerber, D. Herschlag, and P. O. Brown, Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System, PLoS Biology, vol.53, issue.10, p.255, 2008.
DOI : 10.1371/journal.pbio.0060255.sd014

P. Holub, J. Lalakova, H. Cerna, J. Pasulka, M. Sarazova et al., Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation, Nucleic Acids Research, vol.40, issue.12, pp.5679-5693, 2012.
DOI : 10.1093/nar/gks223

J. Houseley, J. Lacava, and D. Tollervey, RNA-quality control by the exosome, Nature Reviews Molecular Cell Biology, vol.126, issue.7, pp.529-539, 2006.
DOI : 10.1038/nrm1964

C. L. Hsu and A. Stevens, Yeast cells lacking 5'-->3' exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5' cap structure., Molecular and Cellular Biology, vol.13, issue.8, pp.4826-4835, 1993.
DOI : 10.1128/MCB.13.8.4826

W. Hu, T. J. Sweet, S. Chamnongpol, K. E. Baker, and J. Coller, Co-translational mRNA decay in Saccharomyces cerevisiae, Nature, vol.99, issue.7261, pp.225-229, 2009.
DOI : 10.1038/nature08265

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745705

N. Iglesias, E. Tutucci, C. Gwizdek, P. Vinciguerra, V. Dach et al., Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export, Genes & Development, vol.24, issue.17, 1927.
DOI : 10.1101/gad.583310

URL : https://hal.archives-ouvertes.fr/hal-00518145

D. Ingelfinger, D. J. Arndt-jovin, R. Lührmann, and T. Achsel, The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci, RNA N. Y. N, vol.8, pp.1489-1501, 2002.

N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, and J. S. Weissman, Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling, Science, vol.71, issue.1, pp.218-223, 2009.
DOI : 10.1016/0092-8674(92)90269-I

J. S. Jackson, . Jr, S. S. Houshmandi, F. Lopez-leban, and W. M. Olivas, Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast, RNA, vol.10, issue.10, pp.1625-1636, 2004.
DOI : 10.1261/rna.7270204

S. Jain, P. , and R. , The Discovery and Analysis of P Bodies, Adv. Exp. Med. Biol, vol.768, pp.23-43, 2013.
DOI : 10.1007/978-1-4614-5107-5_3

T. H. Jensen, A. Jacquier, and D. Libri, Dealing with Pervasive Transcription, Molecular Cell, vol.52, issue.4, pp.473-484, 2013.
DOI : 10.1016/j.molcel.2013.10.032

URL : http://doi.org/10.1016/j.molcel.2013.10.032

X. Jiao, S. Xiang, C. Oh, C. E. Martin, L. Tong et al., Identification of a quality-control mechanism for mRNA 5???-end capping, Nature, vol.17, issue.7315, pp.608-611, 2010.
DOI : 10.1038/nature09338

A. Jimenez, D. J. Tipper, and J. Davies, Mode of Action of Thiolutin, an Inhibitor of Macromolecular Synthesis in Saccharomyces cerevisiae, Antimicrobial Agents and Chemotherapy, vol.3, issue.6, pp.729-738, 1973.
DOI : 10.1128/AAC.3.6.729

A. W. Johnson, Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively., Molecular and Cellular Biology, vol.17, issue.10, pp.6122-6130, 1997.
DOI : 10.1128/MCB.17.10.6122

J. D. Keene, RNA regulons: coordination of post-transcriptional events, Nature Reviews Genetics, vol.103, issue.7, pp.533-543, 2007.
DOI : 10.1038/nrg2111

J. D. Keene and S. A. Tenenbaum, Eukaryotic mRNPs May Represent Posttranscriptional Operons, Molecular Cell, vol.9, issue.6, pp.1161-1167, 2002.
DOI : 10.1016/S1097-2765(02)00559-2

URL : http://doi.org/10.1016/s1097-2765(02)00559-2

K. Guisbert, K. Duncan, K. Li, H. , G. et al., Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles, RNA, vol.11, issue.4, pp.383-393, 2005.
DOI : 10.1261/rna.7234205

D. M. Klass, M. Scheibe, F. Butter, G. J. Hogan, M. Mann et al., Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae, Genome Research, vol.23, issue.6, pp.1028-1038, 2013.
DOI : 10.1101/gr.153031.112

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668357

M. Kshirsagar, P. , and R. , Identification of Edc3p as an Enhancer of mRNA Decapping in Saccharomyces cerevisiae, Genetics, vol.166, issue.2, pp.729-739, 2004.
DOI : 10.1534/genetics.166.2.729

J. Lacava, J. Houseley, C. Saveanu, E. Petfalski, E. Thompson et al., RNA Degradation by the Exosome Is Promoted by a Nuclear Polyadenylation Complex, Cell, vol.121, issue.5, pp.713-724, 2005.
DOI : 10.1016/j.cell.2005.04.029

URL : https://hal.archives-ouvertes.fr/pasteur-01404697

F. W. Larimer and A. Stevens, Disruption of the gene XRN1, coding for a 5??????3??? exoribonuclease, restricts yeast cell growth, Gene, vol.95, issue.1, pp.85-90, 1990.
DOI : 10.1016/0378-1119(90)90417-P

D. Lay, N. Schu, D. J. Gottesman, and S. , Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices, Journal of Biological Chemistry, vol.288, issue.12, pp.7996-8003, 2013.
DOI : 10.1074/jbc.R112.441386

A. Lebreton, R. Tomecki, A. Dziembowski, and B. Séraphin, Endonucleolytic RNA cleavage by a eukaryotic exosome, Nature, vol.20, issue.7224, pp.993-996, 2008.
DOI : 10.1038/nature07480

URL : https://hal.archives-ouvertes.fr/hal-01350769

P. Legrain and M. Rosbash, Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm, Cell, vol.57, issue.4, pp.573-583, 1989.
DOI : 10.1016/0092-8674(89)90127-X

C. Lemieux and F. Bachand, Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs, Nucleic Acids Research, vol.37, issue.10, pp.3418-3430, 2009.
DOI : 10.1093/nar/gkp207

M. Lidschreiber, K. Leike, and P. Cramer, Cap Completion and C-Terminal Repeat Domain Kinase Recruitment Underlie the Initiation-Elongation Transition of RNA Polymerase II, Molecular and Cellular Biology, vol.33, issue.19, pp.3805-3816, 2013.
DOI : 10.1128/MCB.00361-13

H. Liu and M. Kiledjian, Scavenger Decapping Activity Facilitates 5' to 3' mRNA Decay, Molecular and Cellular Biology, vol.25, issue.22, pp.9764-9772, 2005.
DOI : 10.1128/MCB.25.22.9764-9772.2005

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1280280

H. Liu, N. D. Rodgers, X. Jiao, and M. Kiledjian, The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases, The EMBO Journal, vol.21, issue.17, pp.4699-4708, 2002.
DOI : 10.1093/emboj/cdf448

Q. Liu, J. C. Greimann, and C. D. Lima, Reconstitution, Activities, and Structure of the Eukaryotic RNA Exosome, Cell, vol.127, issue.6, pp.1223-1237, 2006.
DOI : 10.1016/j.cell.2006.10.037

T. L. Lo, Y. Qu, N. Uwamahoro, T. Quenault, T. H. Beilharz et al., The mRNA Decay Pathway Regulates the Expression of the Flo11 Adhesin and Biofilm Formation in Saccharomyces cerevisiae, Genetics, vol.191, issue.4, pp.1387-1391, 2012.
DOI : 10.1534/genetics.112.141432

J. E. Lowell, D. Z. Rudner, and A. B. Sachs, 3'-UTR-dependent deadenylation by the yeast poly(A) nuclease., Genes & Development, vol.6, issue.11, pp.2088-2099, 1992.
DOI : 10.1101/gad.6.11.2088

G. Luo, M. Costanzo, C. Boone, and R. C. Dickson, Nutrients and the Pkh1/2 and Pkc1 Protein Kinases Control mRNA Decay and P-body Assembly in Yeast, Journal of Biological Chemistry, vol.286, issue.11, pp.8759-8770, 2011.
DOI : 10.1074/jbc.M110.196030

W. Luo, A. W. Johnson, and D. L. Bentley, The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model, Genes & Development, vol.20, issue.8, pp.954-965, 2006.
DOI : 10.1101/gad.1409106

D. L. Makino, M. Baumgärtner, and E. Conti, Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex, Nature, vol.448, issue.7439, pp.70-75, 2013.
DOI : 10.1016/j.jmb.2006.09.076

D. L. Makino, F. Halbach, and E. Conti, The RNA exosome and proteasome: common principles of degradation control, Nature Reviews Molecular Cell Biology, vol.267, issue.10, pp.654-660, 2013.
DOI : 10.1042/0264-6021:3460155

M. Malecki, S. C. Viegas, T. Carneiro, P. Golik, C. Dressaire et al., The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway, The EMBO Journal, vol.109, issue.13, pp.1842-1854, 2013.
DOI : 10.1073/pnas.1007060107

N. Malys, K. Carroll, J. Miyan, D. Tollervey, and J. E. Mccarthy, The 'scavenger' m7GpppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast, Nucleic Acids Research, vol.32, issue.12, pp.3590-3600, 2004.
DOI : 10.1093/nar/gkh687

D. A. Mangus, N. Amrani, and A. Jacobson, Poly(A)-Binding Protein, Regulates Polyadenylation, Molecular and Cellular Biology, vol.18, issue.12, pp.7383-7396, 1998.
DOI : 10.1128/MCB.18.12.7383

D. A. Mangus, M. M. Smith, J. M. Mcsweeney, and A. Jacobson, Identification of Factors Regulating Poly(A) Tail Synthesis and Maturation, Molecular and Cellular Biology, vol.24, issue.10, pp.4196-4206, 2004.
DOI : 10.1128/MCB.24.10.4196-4206.2004

D. A. Mangus, M. C. Evans, N. S. Agrin, M. Smith, P. Gongidi et al., Positive and Negative Regulation of Poly(A) Nuclease, Molecular and Cellular Biology, vol.24, issue.12, pp.5521-5533, 2004.
DOI : 10.1128/MCB.24.12.5521-5533.2004

M. J. Matunis, E. L. Matunis, and G. Dreyfuss, PUB1: a major yeast poly(A)+ RNA-binding protein., Molecular and Cellular Biology, vol.13, issue.10, pp.6114-6123, 1993.
DOI : 10.1128/MCB.13.10.6114

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC364671/pdf

G. Menschaert, W. Van-criekinge, T. Notelaers, A. Koch, J. Crappé et al., Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events, Molecular & Cellular Proteomics, vol.12, issue.7, pp.1780-1790, 2013.
DOI : 10.1074/mcp.M113.027540

C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Dümcke et al., Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast, Molecular Systems Biology, vol.472, issue.1, p.458, 2011.
DOI : 10.1186/1471-2105-11-194

L. Milligan, L. Decourty, C. Saveanu, J. Rappsilber, H. Ceulemans et al., A Yeast Exosome Cofactor, Mpp6, Functions in RNA Surveillance and in the Degradation of Noncoding RNA Transcripts, Molecular and Cellular Biology, vol.28, issue.17, pp.5446-5457, 2008.
DOI : 10.1128/MCB.00463-08

URL : https://hal.archives-ouvertes.fr/pasteur-01404695

J. Min, R. M. Heuertz, and H. P. Zassenhaus, Isolation and characterization of an NTP-dependent 3'-exoribonuclease from mitochondria of Saccharomyces cerevisiae, J Biol Chem, vol.268, pp.7350-7357, 1993.

P. Mitchell, E. Petfalski, A. Shevchenko, M. Mann, and D. Tollervey, The Exosome: A Conserved Eukaryotic RNA Processing Complex Containing Multiple 3??????5??? Exoribonucleases, Cell, vol.91, issue.4, pp.457-466, 1997.
DOI : 10.1016/S0092-8674(00)80432-8

S. F. Mitchell, S. Jain, M. She, P. , and R. , Global analysis of yeast mRNPs, Nature Structural & Molecular Biology, vol.27, issue.1, pp.127-133, 2013.
DOI : 10.1038/nsmb.2468

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537908

S. Moteki, P. , and D. , Functional Coupling of Capping and Transcription of mRNA, Molecular Cell, vol.10, issue.3, pp.599-609, 2002.
DOI : 10.1016/S1097-2765(02)00660-3

D. Muhlrad, C. J. Decker, P. , and R. , Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5'-->3' digestion of the transcript., Genes & Development, vol.8, issue.7, pp.855-866, 1994.
DOI : 10.1101/gad.8.7.855

S. E. Munchel, R. K. Shultzaberger, N. Takizawa, and K. Weis, Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay, Molecular Biology of the Cell, vol.22, issue.15, pp.2787-2795, 2011.
DOI : 10.1091/mbc.E11-01-0028

R. Narayanaswamy, M. Levy, M. Tsechansky, G. M. Stovall, J. D. O-'connell et al., Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation, Proceedings of the National Academy of Sciences, vol.3, issue.suppl_1, pp.10147-10152, 2009.
DOI : 10.1186/1471-2105-3-35

T. Nissan, P. Rajyaguru, M. She, H. Song, P. et al., Decapping Activators in Saccharomyces cerevisiae Act by Multiple Mechanisms, Molecular Cell, vol.39, issue.5, pp.773-783, 2010.
DOI : 10.1016/j.molcel.2010.08.025

URL : http://doi.org/10.1016/j.molcel.2010.08.025

M. Nonet, C. Scafe, J. Sexton, Y. , and R. , Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis., Molecular and Cellular Biology, vol.7, issue.5, pp.1602-1611, 1987.
DOI : 10.1128/MCB.7.5.1602

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC365259

O. Connell, J. D. Zhao, A. Ellington, A. D. Marcotte, and E. M. , Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies, Annual Review of Cell and Developmental Biology, vol.28, issue.1, pp.89-111, 2012.
DOI : 10.1146/annurev-cellbio-101011-155841

W. Olivas, P. , and R. , The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast, The EMBO Journal, vol.19, issue.23, pp.6602-6611, 2000.
DOI : 10.1093/emboj/19.23.6602

K. A. Osinga, E. De-vries, G. Van-der-horst, and H. F. Tabak, Processing of yeast mitochondrial messenger RNAs at a conserved dodecamer sequence, EMBO J, vol.3, pp.829-834, 1984.

R. Parker, RNA Degradation in Saccharomyces cerevisae, Genetics, vol.191, issue.3, pp.671-702, 2012.
DOI : 10.1534/genetics.111.137265

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389967

E. L. Pearson, M. , and C. L. , by the Termination Factor Rat1, Journal of Biological Chemistry, vol.288, issue.27, pp.19750-19759, 2013.
DOI : 10.1074/jbc.M112.434985

V. Pelechano and J. E. Pérez-ortín, The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast, Yeast, vol.99, issue.2, pp.85-92, 2008.
DOI : 10.1002/yea.1548

V. Pelechano, S. Chávez, and J. E. Pérez-ortín, A Complete Set of Nascent Transcription Rates for Yeast Genes, PLoS ONE, vol.20, issue.11, 2010.
DOI : 10.1371/journal.pone.0015442.s011

J. E. Perez-ortin, L. De-miguel-jimenez, and S. Chavez, Genome-wide studies of mRNA synthesis and degradation in eukaryotes, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1819, issue.6, pp.604-615, 2012.
DOI : 10.1016/j.bbagrm.2011.12.002

O. Porrua, F. Hobor, J. Boulay, K. Kubicek, Y. D-'aubenton-carafa et al., SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination, The EMBO Journal, vol.457, issue.19, pp.3935-3948, 2012.
DOI : 10.1038/emboj.2012.237

C. Qiu, A. Kershner, Y. Wang, C. P. Holley, D. Wilinski et al., Divergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding Pocket, Journal of Biological Chemistry, vol.287, issue.9, pp.6949-6957, 2012.
DOI : 10.1074/jbc.M111.326264

T. Quenault, T. Lithgow, and A. Traven, PUF proteins: repression, activation and mRNA localization, Trends in Cell Biology, vol.21, issue.2, pp.104-112, 2011.
DOI : 10.1016/j.tcb.2010.09.013

V. Ramachandran, K. H. Shah, and P. K. Herman, The cAMP-Dependent Protein Kinase Signaling Pathway Is a Key Regulator of P Body Foci Formation, Molecular Cell, vol.43, issue.6, pp.973-981, 2011.
DOI : 10.1016/j.molcel.2011.06.032

R. L. Read, R. G. Martinho, S. Wang, A. M. Carr, and C. J. Norbury, Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest, Proceedings of the National Academy of Sciences, vol.21, issue.9, pp.12079-12084, 2002.
DOI : 10.1093/emboj/21.9.2139

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129401

O. S. Rissland and C. J. Norbury, Decapping is preceded by 3??? uridylation in a novel pathway of bulk mRNA turnover, Nature Structural & Molecular Biology, vol.16, issue.6, pp.616-623, 2009.
DOI : 10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y

A. T. Rogowska, O. Puchta, A. M. Czarnecka, A. Kaniak, P. P. Stepien et al., Balance between Transcription and RNA Degradation Is Vital for Saccharomyces cerevisiae Mitochondria: Reduced Transcription Rescues the Phenotype of Deficient RNA Degradation, Molecular Biology of the Cell, vol.17, issue.3, pp.1184-1193, 2006.
DOI : 10.1091/mbc.E05-08-0796

K. M. Roth, M. K. Wolf, M. Rossi, and J. S. Butler, The Nuclear Exosome Contributes to Autogenous Control of NAB2 mRNA Levels, Molecular and Cellular Biology, vol.25, issue.5, pp.1577-1585, 2005.
DOI : 10.1128/MCB.25.5.1577-1585.2005

K. M. Roth, J. Byam, F. Fang, and J. S. Butler, Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex, RNA, vol.15, issue.6, pp.1045-1058, 2009.
DOI : 10.1261/rna.709609

A. B. Sachs, D. , and R. W. , The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation, Cell, vol.58, issue.5, pp.857-867, 1989.
DOI : 10.1016/0092-8674(89)90938-0

A. B. Sachs and J. A. Deardorff, Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast, Cell, vol.70, issue.6, pp.961-973, 1992.
DOI : 10.1016/0092-8674(92)90246-9

A. B. Sachs, M. W. Bond, and R. D. Kornberg, A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: Domain structure and expression, Cell, vol.45, issue.6, pp.827-835, 1986.
DOI : 10.1016/0092-8674(86)90557-X

A. B. Sachs, R. W. Davis, and R. D. Kornberg, A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability., Molecular and Cellular Biology, vol.7, issue.9, pp.3268-3276, 1987.
DOI : 10.1128/MCB.7.9.3268

Y. Saint-georges, M. Garcia, T. Delaveau, L. Jourdren, L. Crom et al., Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization, PLoS ONE, vol.98, issue.6, 2008.
DOI : 10.1371/journal.pone.0002293.s012

URL : https://hal.archives-ouvertes.fr/hal-00333137

J. Salgado-garrido, E. Bragado-nilsson, S. Kandels-lewis, and B. Séraphin, Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin, The EMBO Journal, vol.18, issue.12, pp.3451-3462, 1999.
DOI : 10.1093/emboj/18.12.3451

S. Paolo, S. Vanacova, S. Schenk, L. Scherrer, T. Blank et al., Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism, PLoS Genetics, vol.14, issue.7, 2009.
DOI : 10.1371/journal.pgen.1000555.s014

C. M. Santiveri, Y. Mirassou, P. Rico-lastres, S. Martínez-lumbreras, and J. M. Pérez-cañadillas, Pub1p C-Terminal RRM Domain Interacts with Tif4631p through a Conserved Region Neighbouring the Pab1p Binding Site, PLoS ONE, vol.51, issue.9, p.24481, 2011.
DOI : 10.1371/journal.pone.0024481.s004

S. Sayani and G. F. Chanfreau, Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae, RNA, vol.18, issue.8, pp.1563-1572, 2012.
DOI : 10.1261/rna.033779.112

D. Schaeffer, B. Tsanova, A. Barbas, F. P. Reis, E. G. Dastidar et al., The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities, Nature Structural & Molecular Biology, vol.20, issue.1, pp.56-62, 2009.
DOI : 10.1038/nsmb.1528

K. Schmidt, Z. Xu, D. H. Mathews, and J. S. Butler, Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance, RNA, vol.18, issue.10, pp.1934-1945, 2012.
DOI : 10.1261/rna.033431.112

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446715

C. Schneider, J. T. Anderson, and D. Tollervey, The Exosome Subunit Rrp44 Plays a Direct Role in RNA Substrate Recognition, Molecular Cell, vol.27, issue.2, pp.324-331, 2007.
DOI : 10.1016/j.molcel.2007.06.006

C. Schneider, E. Leung, J. Brown, and D. Tollervey, The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome, Nucleic Acids Research, vol.37, issue.4, pp.1127-1140, 2009.
DOI : 10.1093/nar/gkn1020

D. Schulz, B. Schwalb, A. Kiesel, C. Baejen, P. Torkler et al., Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis, Cell, vol.155, issue.5, pp.1075-1087, 2013.
DOI : 10.1016/j.cell.2013.10.024

D. Schwartz, C. J. Decker, P. , and R. , The enhancer of decapping proteins, Edc1p and Edc2p, bind RNA and stimulate the activity of the decapping enzyme, RNA, vol.9, issue.2, pp.239-251, 2003.
DOI : 10.1261/rna.2171203

K. H. Shah, B. Zhang, V. Ramachandran, and P. K. Herman, Processing Body and Stress Granule Assembly Occur by Independent and Differentially Regulated Pathways in Saccharomyces cerevisiae, Genetics, vol.193, issue.1, pp.109-123, 2013.
DOI : 10.1534/genetics.112.146993

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527240

O. Shalem, O. Dahan, M. Levo, M. R. Martinez, I. Furman et al., Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation, Molecular Systems Biology, vol.17, p.223, 2008.
DOI : 10.1101/gr.997703

H. Sharif and E. Conti, Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic mRNA Turnover, Cell Reports, vol.5, issue.2, pp.283-291, 2013.
DOI : 10.1016/j.celrep.2013.10.004

H. Sharif, S. Ozgur, K. Sharma, C. Basquin, H. Urlaub et al., Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions, Nucleic Acids Research, vol.41, issue.17, pp.8377-8390, 2013.
DOI : 10.1093/nar/gkt600

A. J. Shatkin and J. L. Manley, The ends of the affair: capping and polyadenylation, Nature Structural Biology, vol.7, issue.10, pp.838-842, 2000.
DOI : 10.1038/79583

D. Sheiness, L. Puckett, D. , and J. E. , Possible relationship of poly(A) shortening to mRNA turnover., Proceedings of the National Academy of Sciences, vol.72, issue.3, pp.1077-1081, 1975.
DOI : 10.1073/pnas.72.3.1077

U. Sheth, P. , and R. , Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies, Science, vol.300, issue.5620, pp.805-808, 2003.
DOI : 10.1126/science.1082320

F. Sinturel, D. Bréchemier-baey, M. Kiledjian, C. Condon, and L. Bénard, Activation of 5'-3' exoribonuclease Xrn1 by cofactor Dcs1 is essential for mitochondrial function in yeast, Proceedings of the National Academy of Sciences, vol.18, issue.5, pp.8264-8269, 2012.
DOI : 10.2741/2835

C. E. Sripati, Y. Groner, W. , and J. R. , Methylated, blocked 5' termini of yeast mRNA, J. Biol. Chem, vol.251, pp.2898-2904, 1976.

J. A. Stead, J. L. Costello, M. J. Livingstone, M. , and P. , The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein, Nucleic Acids Research, vol.35, issue.16, pp.5556-5567, 2007.
DOI : 10.1093/nar/gkm614

M. Steiger, A. Carr-schmid, D. C. Schwartz, M. Kiledjian, P. et al., Analysis of recombinant yeast decapping enzyme, RNA, vol.9, issue.2, pp.231-238, 2003.
DOI : 10.1261/rna.2151403

P. P. Stepien, S. P. Margossian, D. Landsman, and R. A. Butow, The yeast nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP-dependent RNA helicase., Proceedings of the National Academy of Sciences, vol.89, issue.15, pp.6813-6817, 1992.
DOI : 10.1073/pnas.89.15.6813

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC49594

A. Stevens, An exoribonuclease from saccharomyces cerevisiae: Effect of modifications of 5??? end groups on the hydrolysis of substrates to 5??? mononucleotides, Biochemical and Biophysical Research Communications, vol.81, issue.2, pp.656-661, 1978.
DOI : 10.1016/0006-291X(78)91586-3

A. Stevens, An mRNA decapping enzyme from ribosomes of Saccharomyces cerevisiae, Biochemical and Biophysical Research Communications, vol.96, issue.3, pp.1150-1155, 1980.
DOI : 10.1016/0006-291X(80)90072-8

A. Stevens, mRNA-decapping enzyme from Saccharomyces cerevisiae: purification and unique specificity for long RNA chains., Molecular and Cellular Biology, vol.8, issue.5, 1988.
DOI : 10.1128/MCB.8.5.2005

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC363379/pdf

M. Sun, B. Schwalb, D. Schulz, N. Pirkl, S. Etzold et al., Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation, Genome Research, vol.22, issue.7, pp.1350-1359, 2012.
DOI : 10.1101/gr.130161.111

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396375

M. Sun, B. Schwalb, N. Pirkl, K. C. Maier, A. Schenk et al., Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels, Molecular Cell, vol.52, issue.1, pp.52-62, 2013.
DOI : 10.1016/j.molcel.2013.09.010

T. Sweet, C. Kovalak, and J. Coller, The DEAD-Box Protein Dhh1 Promotes Decapping by Slowing Ribosome Movement, PLoS Biology, vol.194, issue.6, p.1001342, 2012.
DOI : 10.1371/journal.pbio.1001342.s009

URL : http://doi.org/10.1371/journal.pbio.1001342

T. J. Sweet, B. Boyer, W. Hu, K. E. Baker, and J. Coller, Microtubule disruption stimulates P-body formation, RNA, vol.13, issue.4, pp.493-502, 2007.
DOI : 10.1261/rna.355807

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1831866

K. D. Swisher, P. , and R. , Localization to, and effects of Pbp1, Pbp4, Lsm12, Dhh1, and Pab1 on stress granules in Saccharomyces cerevisiae, 2010.

S. A. Synowsky and A. J. Heck, The yeast Ski complex is a hetero-tetramer, Protein Science, vol.17, issue.1, pp.119-125, 2008.
DOI : 10.1110/ps.073155908

S. A. Synowsky, M. Van-wijk, R. Raijmakers, and A. J. Heck, Comparative Multiplexed Mass Spectrometric Analyses of Endogenously Expressed Yeast Nuclear and Cytoplasmic Exosomes, Journal of Molecular Biology, vol.385, issue.4, pp.1300-1313, 2009.
DOI : 10.1016/j.jmb.2008.11.011

S. A. Tenenbaum, C. C. Carson, P. J. Lager, K. , and J. D. , Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays, Proceedings of the National Academy of Sciences, vol.96, issue.19, pp.14085-14090, 2000.
DOI : 10.1073/pnas.96.19.10632

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC18875

S. Tharun, P. , and R. , Targeting an mRNA for Decapping, Molecular Cell, vol.8, issue.5, pp.1075-1083, 2001.
DOI : 10.1016/S1097-2765(01)00395-1

URL : http://doi.org/10.1016/s1097-2765(01)00395-1

S. Tharun, W. He, A. E. Mayes, P. Lennertz, J. D. Beggs et al., Yeast Sm-like proteins function in mRNA decapping and decay, Nature, vol.404, issue.6777, pp.515-518, 2000.
DOI : 10.1038/35006676

A. Toh-e, P. Guerry, and R. B. Wickner, Chromosomal superkiller mutants of Saccharomyces cerevisiae, J. Bacteriol, vol.136, pp.1002-1007, 1978.

J. Trapman, J. Retèl, and R. J. Planta, Ribosomal precursor particles from yeast, Experimental Cell Research, vol.90, issue.1, pp.95-104, 1975.
DOI : 10.1016/0014-4827(75)90361-4

T. Trcek, D. R. Larson, A. Moldón, C. C. Query, and R. H. Singer, Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast, Cell, vol.147, issue.7, pp.1484-1497, 2011.
DOI : 10.1016/j.cell.2011.11.051

URL : http://doi.org/10.1016/j.cell.2011.11.051

A. C. Tuck and D. Tollervey, A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs, Cell, vol.154, issue.5, pp.996-1009, 2013.
DOI : 10.1016/j.cell.2013.07.047

E. M. Turk, V. Das, R. D. Seibert, and E. D. Andrulis, The Mitochondrial RNA Landscape of Saccharomyces cerevisiae, PLoS ONE, vol.17, issue.10, p.78105, 2013.
DOI : 10.1371/journal.pone.0078105.s001

S. A. Udem, K. Kaufman, W. , and J. R. , Small ribosomal ribonucleic acid species of Saccharomyces cerevisiae, J. Bacteriol, vol.105, pp.101-106, 1971.

J. Ule, K. B. Jensen, M. Ruggiu, A. Mele, A. Ule et al., CLIP Identifies Nova-Regulated RNA Networks in the Brain, Science, vol.302, issue.5648, pp.1212-1215, 2003.
DOI : 10.1126/science.1090095

S. Vanácová, J. Wolf, G. Martin, D. Blank, S. Dettwiler et al., A New Yeast Poly(A) Polymerase Complex Involved in RNA Quality Control, PLoS Biology, vol.409, issue.6, p.189, 2005.
DOI : 10.1371/journal.pbio.0030189.st001

Z. Wang and M. Kiledjian, Functional Link between the Mammalian Exosome and mRNA Decapping, Cell, vol.107, issue.6, pp.751-762, 2001.
DOI : 10.1016/S0092-8674(01)00592-X

URL : http://doi.org/10.1016/s0092-8674(01)00592-x

L. Wang, M. S. Lewis, J. , and A. W. , Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p, RNA, vol.11, issue.8, pp.1291-1302, 2005.
DOI : 10.1261/rna.2060405

S. W. Wang, T. Toda, R. Maccallum, A. L. Harris, and C. Norbury, Cid1, a Fission Yeast Protein Required for S-M Checkpoint Control when DNA Polymerase delta or varepsilon Is Inactivated, Molecular and Cellular Biology, vol.20, issue.9, pp.3234-3244, 2000.
DOI : 10.1128/MCB.20.9.3234-3244.2000

E. V. Wasmuth and C. D. Lima, Exo- and Endoribonucleolytic Activities of Yeast Cytoplasmic and Nuclear RNA Exosomes Are Dependent on the Noncatalytic Core and Central Channel, Molecular Cell, vol.48, issue.1, pp.133-144, 2012.
DOI : 10.1016/j.molcel.2012.07.012

T. Wegierski, A. Dmochowska, A. Jab?onowska, A. Dziembowski, E. Bartnik et al., Yeast nuclear PET127 gene can suppress deletions of the SUV3 or DSS1 genes: an indication of a functional interaction between 3' and 5' ends of mitochondrial mRNAs, Acta Biochim. Pol, vol.45, pp.935-940, 1998.

M. Wery, S. Ruidant, S. Schillewaert, N. Lepore, and D. L. Lafontaine, The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance, RNA, vol.15, issue.3, pp.406-419, 2009.
DOI : 10.1261/rna.1402709

M. Wickens, D. S. Bernstein, J. Kimble, P. , and R. , A PUF family portrait: 3???UTR regulation as a way of life, Trends in Genetics, vol.18, issue.3, pp.150-157, 2002.
DOI : 10.1016/S0168-9525(01)02616-6

W. R. Widner and R. B. Wickner, Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA., Molecular and Cellular Biology, vol.13, issue.7, pp.4331-4341, 1993.
DOI : 10.1128/MCB.13.7.4331

G. Wiesenberger and T. D. Fox, Pet127p, a membrane-associated protein involved in stability and processing of Saccharomyces cerevisiae mitochondrial RNAs., Molecular and Cellular Biology, vol.17, issue.5, pp.2816-2824, 1997.
DOI : 10.1128/MCB.17.5.2816

W. Wlotzka, G. Kudla, S. Granneman, and D. Tollervey, The nuclear RNA polymerase II surveillance system targets polymerase III transcripts, The EMBO Journal, vol.457, issue.9, pp.1790-1803, 2011.
DOI : 10.1038/emboj.2011.97

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102002

F. Wyers, M. Rougemaille, G. Badis, J. Rousselle, M. Dufour et al., Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase, Cell, vol.121, issue.5, pp.725-737, 2005.
DOI : 10.1016/j.cell.2005.04.030

S. Xiang, A. Cooper-morgan, X. Jiao, M. Kiledjian, J. L. Manley et al., Structure and function of the 5??????3??? exoribonuclease Rat1 and its activating partner Rai1, Nature, vol.9, issue.7239, pp.784-788, 2009.
DOI : 10.1038/nature07731

Y. Xue, X. Bai, I. Lee, G. Kallstrom, J. Ho et al., Saccharomyces cerevisiae RAI1 (YGL246c) Is Homologous to Human DOM3Z and Encodes a Protein That Binds the Nuclear Exoribonuclease Rat1p, Molecular and Cellular Biology, vol.20, issue.11, pp.4006-4015, 2000.
DOI : 10.1128/MCB.20.11.4006-4015.2000

S. Yamasaki, A. , and P. , Reprogramming mRNA translation during stress, Current Opinion in Cell Biology, vol.20, issue.2, pp.222-226, 2008.
DOI : 10.1016/j.ceb.2008.01.013

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841789

S. Zaman, S. I. Lippman, L. Schneper, N. Slonim, and J. R. Broach, Glucose regulates transcription in yeast through a network of signaling pathways, Mol. Syst. Biol, vol.5, p.245, 2009.