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RESEARCH

Luhtala, N. and R. Parker. (2009) LSM1 over-expression in Saccharomyces cerevisiae depletes U6 snRNA levels. Nucleic Acids Research (in press)

REVIEW

Thompson, D.M. and R. Parker (2009) Stressing out over tRNA cleavage. Cell 138:215-219

REVIEW

Swisher, K.D. and R. Parker (2009) Related Mechanisms for mRNA and rRNA Quality Control.  Molecular Cell 34:401-402

RESEARCH

Passos, D.O., Doma, M.K, Shoemaker, C.J., Muhlrad, D., Green, J., Weissman, J., Hollien, J. and R. Parker.  (2009) Analysis of Dom34 and its function in No-Go Decay. Molecular Biology of the Cell (in press)

REVIEW

Balagopal, V. and R. Parker (2009) Polysomes, P bodies and Stress granules: States and Fates of Eukaryotic mRNAs. Current Opinion in Cell Biology 21:403-408

RESEARCH Chekulaeva, M., Filipowicz, W. and R. Parker.  (2009) Multiple independent domains of dGW182 function in miRNA-mediated repression in Drosophila. RNA 5:794-803
RESEARCH Thompson, D. and R. Parker (2009) The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. Journal of Cell Biology 185:43-50
RESEARCH Balagopal, V. and R. Parker. (2009) Stm1 modulates mRNA decay and Dhh1 function in Saccharomyces cerevisiae. Genetics 181:93-103
REVIEW Rajyaguru, P. and R. Parker (2009) Cgh-1 and the Control of Maternal mRNAs. Trends in Cell Biology 19:24-28
REVIEW Passos, D.O. and R. Parker (2008) Analysis of Cytoplasmic mRNA Decay in Saccharomyces cerevisiae. Methods in Enzymology 448:409-427
REVIEW Nissan, T. and R. Parker (2008) Analyzing P-bodies in Saccharomyces cerevisiae. Methods in Enzymology 448:507-520

RESEARCH

Buchan, J.R., Muhlrad, D, and R. Parker. (2008) P-bodies promote Stress Granule assembly in Saccharomyces cerevisiae. Journal of Cell Biology 183:441-455

RESEARCH

Thompson, D.M., Lu, C., Green, P.J. and R. Parker. (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes.  RNA 14:2095-2103

RESEARCH

Pedro-Segura, E., Vergara, S.V., Rodríguez-Navarro, S., Parker, R., Thiele, D.J. and S. Puig (2008) The Cth2 are-binding protein recruits the Dhh1 helicase to promote the decay of succinate dehydrogenase SDH4 mRNA in response to iron deficiency. Journal of Biological Chemistry 283:28527-28535

RESEARCH

Ling, S.H., Decker, C.J., Walsh, M.A., She, M., Parker, R. and H. Song (2008) Crystal structure of human Edc3 and its functional implications. Molecular and Cellular Biology 28:5965-5976

REVIEW

Hilliker, A., and R. Parker (2008) "Stressed out?  Make some modifications!" Nature Cell Biology 10:1129-1130

RESEARCH

Nissan, T. and R. Parker.  Computtional analysis of miRNA-mediated repression of translation:  Implications for models of translaton initiation inhibition. RNA 14:1480-1491

RESEARCH

She, M., Decker, C., Svergun, D.I., Round, A., Chen, N., Muhlrad, D., Parker, R., and H. Song (2008) Structural basis of Dcp2 recognition and activation by Dcp1. Molecular Cell 29:337-349

Beckham, C.J. and R. Parker (2008) P Bodies, Stress Granules, and Viral Life Cycles. Cell Host & Microbe 3:206-212

Beckham, C.J., Hilliker, A., Cziko, A.-M., Noueiry, A., Ramaswami, M., and R. Parker. (2008) The DEAD-Box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies.  Molecular Biology of the Cell 19:984-993

Pilkington, G., and R. Parker (2008) Pat1p contains distinct functional domains that promote P-body assembly and activation of decapping.Molecular and Cellular Biology 28:1298-1312

Buchan, J.R. and R. Parker. (2007) The Two Faces of miRNA. Science 318:1877-1878   (Summary)    (Full Text)

Doma, M.K. and R. Parker. (2007) Diversity, Principles and Consequences of RNA Quality Control in Eukaryotes. Cell 131:660-668

Decker, C.J., Teixeira, D., and R. Parker (2007) Edc3p and a QN-rich domain of Lsm4p function in P-body Assembly in Saccharomyces cerevisiae. Journal of Cell Biology 179:437-449

Beckham, C.J., Light, H.R., Nissan, T.A., Ahlquist, P., Parker, R., and A. Nouiery (2007) Interactions between Brome Mosaic Virus RNAs and Cytoplasmic Processing Bodies Journal of Virology 81:9759-9768

Brengues, M. and R. Parker. (2007) Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae. Molecular Biology of the Cell 18:2592-2602

Teixeira, D. and R. Parker. (2007) Analysis of P-body Assembly in Saccharomyces cerevisiae. Molecular Biology of the Cell 18:2274-2287

Sheth, U., and R. Parker. (2007) P-bodies and the control of mRNA translation and degradation. Molecular Cell 25:635-646

Cheng, Z., Muhlrad, D., Lim, M.K., Parker, R. and H. Song (2007) Structural and functional insights into the human Upf1 helicase core. EMBO Journal 26:253-64

Thompson, D. M., and R. Parker. (2007) Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. MCB 27:92-101

Doma, M.K., and R. Parker. (2006). Revenge of the NRD: preferential degradation of nonfunctional eukaryotic rRNA. Developmental Cell 11:757-758

Barbee, S.A., Estes, P.S., Cziko, A-M., Hillebrand, J., Luedeman, R.A., Coller, J.M., Johnson, N., Howlett, I.C., Geng, C., Ueda, R., Brand, A.H., Newbury, S.F., Wilhelm, J.E., Levine, R.B., Nakamura, A., Parker, R., and M. Ramaswami.  (2006)  Staufen- and FMRP-containing neuronal RNPs are structurally and functionally related to somatic P bodies. Neuron 52:997-1009

Valencia-Sanchez, M., Liu, J., Hannon, G.J. and R. Parker.  (2006)  Control of translation and mRNA degradation by miRNAs and siRNAs.  Genes and Development 20:515-524

Baker, K.E. and R. Parker. (2006) Conventional 3' end formation is not required for NMD substrate recognition in Saccharomyces cerevisiae RNA 12:1441-1445

Sheth, U., and R. Parker. (2006) Targeting of Aberrant mRNAs to Cytoplasmic Processing Bodies.  Cell 125:1095-1109

Segal, S.P., Dunckley, T.C., and R. Parker. Sbp1p promotes tranlsational repression and mRNA decapping in Saccharomyces cereivisiae MCB 26:5120-5130

Doma, M.K., and R. Parker.  (2006)  Endonucleolytic cleavage of eukaryotic mRNAs with translation elongation stalls. Nature 440:561-564

Decker, C.J. and R. Parker (2006)  CAR-1 and trailer hitch:  Driving mRNP granule function at the ER?  Journal of Cell Biology Journal of Cell Biology 173:159-163

Beliakova-Bethell, N., Beckham, C., Giddings Jr., T.H., Winey, M., Parker, R., and S. Sandmeyer.  (2006)  Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components. RNA 12:94-101

She, M., Decker, C.J., Chen, N., Tumati, S., Parker, R., and H. Song. (2006) Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe.Nature Structural & Molecular Biology (in press)

Liu, J., Rivas, F.V., Wohlschlegel, J., Yates III, J.R., Parker, R., and G.J. Hannon. (2005) A role for the P-body component GW182 in microRNA function. Nature Cell Biology 7:1261-1266

Coller, J. and R. Parker. (2005) General Translational Repression by Activators of mRNA Decapping. Cell 122:875-886

Brengues, M., Teixeria, D. and R. Parker (2005) Movement of Eukaryotic mRNAs Between Polysomes and Cytoplasmic Processing Bodies. Science 310:486-489 Click here for access to complete article at Science

Wilson, M., Meaux, S., Parker, R., and A. van Hoof. (2005).  Molecular mechanisms of [PSI+] induced phenotypic variation in yeast. Proc. Natl. Acad. Sci. USA 102:10244-10249

Liu, J., Sanchez, M.A.V., Hannon, G.J., and R. Parker. (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nature Cell Biology 7:719-723

Cheng, Z., Coller, J., Parker, R., and H. Song. (2005) Crystal structure and functional analysis of DEAD box helicase Dhh1p.  RNA 11:1258-1270

Tharun, S., Muhlrad, D., Chowdhury, A., and R. Parker. (2005) Mutations in the Saccharomyces cerevisiae LSM1 gene that affect mRNA decapping and 3' end protection. Genetics, 170:33-46

Teixeria, D., Sheth, U, Valencia-Sanchez, MA, Brengues, M., and R. Parker. (2005) Processing bodies require RNA for assembly and contain non-translating mRNAs. RNA 11:371-382

Muhlrad, D. and R. Parker. (2005) The yeast EDC1 mRNA undergoes deadenylation-independent decapping stimulated by Not2p, Not4p and Not5p. EMBO 24:1033-1045

Chen, N., Walsh, M.A., Liu, Y., Parker, R., and H. Song. (2005) Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.  Journal of Molecular Biology 347:707-718

Cheng, Z., Liu, Y., Wang, C., Parker R., and H. Song.  (2004) Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recomination.  Protein Science 13:2673-2684

Baker, K.E., Coller, J.M., and R. Parker.  (2004)  Yeast Apq1p affects nucleocytoplasmic mRNA transport.  RNA 10:1352-1358

Kshirsagar, M., and R. Parker, (2004) Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae.  Genetics 166:729-739

She, M., Decker, C.J., Sundramurthy, K., Liu, Y., Chen, N., Parker, R. and H. Song. (2004) Crystal Structure of Dcp1p and Its Functional Implications in mRNA Decapping. Nature Structural and Molecular Biology 11:249-6

Baker, K.E., and R. Parker.  (2004)  Nonsense-mediated mRNA decay: terminating erroneous gene expression.  Current Opinion Cell Biology 16:293-9

Parker, R. and H. Song.  (2004) The Enzymes and Control of Eukaryotic mRNA Turnover. Nature Structural and Molecular Biology 11:121-127

Coller, J. and R. Parker.  (2004)  Eukaryotic mRNA decapping.  Annual Review of Biochmistry 73:861-890

Hilleren, P.J., and R. Parker.  (2003)  Cytoplasmic Degradation of Splice Defective pre-mRNAs and Intermediates Molecular Cell 12:1453-1465

Cao, D., and R. Parker.  (2003)  Computational Modeling and Experimental Analysis of Nonsense-Mediated Decay in Yeast.  Cell 113:533-545

Sheth, U., and R. Parker.  (2003)  Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science  300:805-808

Schwartz, D., Decker, C.J., and R. Parker. (2003) The Enhancer of Decapping Proteins, Edc1p and Edc2p, bind RNA and stimulate activity of the decapping enzyme. RNA 9:239-251

Decker, C.J. and R. Parker (2002) mRNA decay enzymes: Decappers conserved between yeast and mammals. Proc. Natl. Acad. Sci. USA 99:12512-12514

van Hoof, A., and R. Parker. (2002) Mammalian mRNA degradation: Beginning at the end. Current Biology 12:R285-R287

Steiger, M., Carr-Schmid, A., Schwartz, D.C., Kiledjian, M., and R. Parker. (2002) Analysis of recombinant yeast decapping enzyme. RNA 9:231-238

Steiger, M., and R. Parker (2002) Analyzing mRNA Decay in Saccharomyces cerevisiae. Methods in Enzymology 351:648-660

Decker, C.J. and R. Parker (2002) mRNA decay enzymes: Decappers conserved between yeast and mammals. Proc. Natl. Acad. Sci. USA 99:12512-12514

Frischmeyer, P.A., van Hoof, A., OíDonnell K., Guerrerio A.L., R. Parker and Dietz, H.C. (2002) An mRNA Surveillance Mechanism that Eliminates Transcripts Lacking Termination Codons. Science 295: 2258-2261

van Hoof, A., Frischmeyer, P.A., Dietz, H.C., and R. Parker. (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295: 2262-2264

Tucker, M., Staples, R.R., Valencia-Sanchez, M.A., Muhlrad, D., and R. Parker. (2002) Ccr4p is the catalytic sub-unit of a Ccr4/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO Journal 21:1427-1436

Wickens, M., Bernstein, D.S., Kimble, J., and R. Parker (2002) A PUF family portrait: 3íUTR regulation as a way of life. Trends in Genetics 18:150-157

Hilleren, P., McCarthy, T., Rosbash, M., Parker, R., and Jensen, T.H. (2001) Quality control of mRNA 3í-end processing is linked to the nuclear exosome. Nature 413:538 - 542

Coller, J.M., Tucker, M., Sheth, U., Valencia-Sanchez, M.A., and R. Parker. (2001) The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA 7:1717-27

Tharun, S., and R. Parker. (2001) Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Molecular Cell 8:1075-83

Cao, D., and R. Parker (2001) Computational modeling of eukaryotic mRNA turnover. RNA 7:1192-1212

He, W. and R. Parker (2001) The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation. Genetics 158:1445-1455

Tucker M., Valencia-Sanchez M.A., Staples R., Chen J., Denis C.L., and R. Parker (2001) The transcription factor associated proteins Ccr4 and Caf1 are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104:377-386

Dunckley T., Tucker, M., and R. Parker (2001) Two related proteins, Edc1p and Edc2p, stimulate mRNA decapping in Saccharomyces cerevisiae. Genetics 157:27-37

Hilleren P., and R. Parker (2001) Defects in the mRNA export factors Rat7p, Gle1p, Mex67p and Rat8p cause hyperadenylation during 3'-end formation of nascent transcripts. RNA 7:753-64

Dunckley, T., and R. Parker (2001) Yeast mRNA Decapping Enzyme. Methods Enzymology 342:226-33

Olivas, W. and R. Parker (2000) The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast EMBO Journal 19:6602-6611

van Hoof, A., Staples, R. R., Baker, R. E. and R. Parker (2000)Function of the Ski4p (Csl4p) and Ski7p proteins in 3'-to-5' degradation of mRNA. Molecular and Cellular Biology 20:8230-8243

Schwartz, D. and R. Parker (2000) mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Molecular and Cellular Biology 20:7933-7942

Jacobs, J.S.J. and R. Parker (2000) Computational Identification of Cis-acting Elements Affecting Post-Transcriptional Control of Gene Expression in Saccharomyces cerevisiae. Nucleic Acids Research 28:1604-1617

Tharun, S., He, W., Mayes, A.E., Lennertz, P., Beggs, J.D., and R. Parker (2000) Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404:515-518

van Hoof, A., Lennertz, P., and R. Parker. (2000) Three conserved members ofthe RNase D family have unique and overlapping functions inthe processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO Journal 19: 1357-1365

van Hoof, A., Lennertz, P. and R. Parker (2000) Yeast Exosome Mutants Accumulate 3'-Extended Polyadenylated Forms of U4 Small Nuclear RNA and Small Nucleolar RNAs. Molecular and Cellular Biology 20:441-452

Tucker, M. and R. Parker. (2000) Mechanisms and Control of mRNA Decapping in Saccharomyces cerevisiae. Annual Review of Biochemistry 69:571-95

He, W. and Parker R. (2000) Functions of Lsm proteins in mRNA degradation and splicing. Current Opinion in Cell Biology 12:346-350

Muhlrad, D. and R. Parker (1999) Aberrant mRNAs with extended 3¹ UTRs are substrates for rapid degradation by mRNA surveillance. RNA 5:1299-1307

Muhlrad, D. and R. Parker. (1999) Recognition of Yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: Implications for the control of mRNA decapping. Molecular Biology of the Cell 10: 3971-3978

Dunckley, T. and R. Parker (1999) The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functinal MutT motif. EMBO Journal 18: 5411-5422

Schwartz, D. and R. Parker (1999) Mutations in Translation Initiation Factors lead to increased rates of deadenylation and decapping of yeast mRNAs. Molecular and Cellular Biology 19:5247-56

LaGrandeur, T. and R. Parker. (1999) The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast includes the context of the translational short codon. RNA 5:420-33

Hilleren, P. and R. Parker. (1999) Mechanisms of mRNA Surveillance in Eukaryotes. Annual Review of Genetics 3:229-260

van Hoof, A. and R. Parker. (1999) The exosome: A proteasome for RNA? Cell 99:347-50

Tharun, S. and R. Parker. (1999) Analysis of mutations in the yeast mRNA decapping enzyme. Genetics 151:1273-1285

Hilleren, P. and R. Parker. (1999) mRNA Surveillance in Eukaryotes: Kinetic Proofreading of Proper Translation Termination as assessed by mRNP Domain Organization? RNA 5:711-719

He, W. and R. Parker. (1999) Analysis of mRNA Decay Pathway in S. Cerevisiae. Methods 17:3-10

LaGrandeur, T. E. and R. Parker. (1998) Isolation and Characterization of Dcp1p, the yeast mRNA decapping enzyme. EMBO Journal 17:1487-1496

Anderson, J. S. J. and R. Parker. (1998) The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO Journal 17:1497-1506

Olivas, W. M., Muhlrad, D., and Parker, R. (1997). Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res 25:4619-4625

LaGrandeur, T. E. and R. Parker. (1997) mRNA decapping activities and their biological roles. Biochemie 78:1049-1055

Caponigro, G., and Parker, R. (1996) mRNA turnover in yeast promoted by the MATalpha1 instability element. Nucleic Acids Res 24:4304-4312

Hatfield, L., Beelman, C. A., Stevens, A., and Parker, R. (1996) Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol 16:5830-5838

Anderson, J. S., and Parker, R. (1996) RNA turnover: the helicase story unwinds. Curr Biol 6:780-782

Caponigro, G., and Parker, R. (1996) Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol Rev 60:233-249

Beelman, C. A., Stevens, A., Caponigro, G., LaGrandeur, T. E., Hatfield, L., Fortner, D., and Parker, R. (1996) An essential component of the decapping enzyme required for normal rates of mRNA decay in yeast. Nature 382:642-6

Mandart, E., and Parker, R. (1995) Effects of mutations in the Saccharomyces cerevisiae RNA14, RNA15, and PAP1 genes on polyadenylation in vivo. Mol Cell Biol 15:6979-6986

Decker C. J., and Parker, R. (1995) Diversity of cytoplasmic functions for the 3' untranslated region of eukaryotic transcripts. Curr Opin Cell Biol 7:386-392

Muhlrad D., Decker C. J., and Parker, R. (1995) Turnover mechanisms of the stable yeast PGK1 mRNA. Mol Cell Biol 15:2145-2156

Beelman, C. A. and Parker, R. (1995) Degradation of mRNA in eukaryotes. Cell 81:179-183

Caponigro, G. and Parker, R. (1995) Multiple functions of the Poly(A) binding protein in mRNA decapping and deadenylation. Genes Dev 9:2421-2432

Decker C. J., and Parker, R. (1994) Mechanisms of mRNA degradation in eukaryotes. Trends Biochem Sci 19:336-340

Beelman C. A., and 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

Muhlrad, D., and Parker, R. (1994) Premature translational termination triggers mRNA decapping. Nature 340:578-581

Muhlrad, D., Decker, C. J., and Parker, R. (1994) Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5' to 3' degradation of the transcript. Genes Dev 8:855-866

Decker, C. J., and Parker, R. (1993) A turnover pathway for stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev 7:1632-1643

Parker, R. and P. Siliciano (1993) Evidence for a non-Watson Crick interaction between the first and last nucleotides of a nuclear pre-mRNA intron. Nature 361:660-662

Caponigro, G., Muhlrad, D., and Parker, R. (1993) A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons. Mol Cell Biol 13:5141-5148

Muhlrad, D., and Parker, R. (1992) Mutations affecting stability and deadenylation of the yeast MFA2 transcript. Genes Dev 6:2100-2111

Heaton, B., Decker, C., Muhlrad, D., Donahue, J., Jacobson, A., and Parker, R. (1992) Analysis of chimeric mRNAs derived from the STE3 mRNA identifies multiple regions within yeast mRNAs that modulate mRNA decay. Nucleic Acids Res 20:5365-5373

Muhlrad, D., Hunter, R., and Parker, R. (1992) A rapid method for localized mutagenesis of yeast genes. Yeast 8:79-82

 


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