Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

PLoS Biology

Volumn 6, Issue 10, 2008, Pages 2297-2313

  Hogan, Daniel J ^a   Riordan, Daniel P ^a   Gerber, André P ^b   Herschlag, Daniel ^a   Brown, Patrick O ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA BINDING PROTEIN; TRANSCRIPTOME; SACCHAROMYCES CEREVISIAE PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; NONHUMAN; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN PROCESSING; PROTEIN TARGETING; REGULATORY MECHANISM; RNA SEQUENCE; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE; CHEMISTRY; DNA MICROARRAY; GENETICS; METABOLISM; PROTEIN DATABASE; PROTEIN DOMAIN; SIGNAL TRANSDUCTION; UNTRANSLATED REGION;

SACCHAROMYCES CEREVISIAE;

DATABASES, PROTEIN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; RNA, MESSENGER; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; UNTRANSLATED REGIONS;

EID: 54949148332     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0060255     Document Type: Article

References (160)

1. Hieronymus H, Silver PA (2004) A systems view of mRNP biology. Genes Dev 18: 2845-2860.
2. Moore MJ (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309: 1514-1518.
3. Halbeisen RE, Galgano A, Scherrer T, Gerber AP (2008) Post-transcriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci 65: 798-813.
4. Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8: 533-543.
5. Keene JD, Tenenbaum SA (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9: 1161-1167.
6. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
7. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
8. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
9. Blencowe BJ (2006) Alternative splicing: new insights from global analyses. Cell 126: 37-47.
10. Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C (2007) Rapid, transcript-specific changes in splicing in response to environmental stress. Mol Cell 27: 928-937.
11. Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C (2007) Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 5: e90. doi:10.1371/journal.pbio.0050090
12. Walter P, Johnson AE (1994) Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu Rev Cell Biol 10: 87-119.
13. Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, et al. (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131: 174-187.
14. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741.
15. Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-124.
16. Kuhn KM, DeRisi JL, Brown PO, Sarnow P (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol 21: 916-927.
17. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
18. Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, et al. (2003) Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res 13: 1863-1872.
19. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A 99: 5860-5865.
20. Shock JL, Fischer KF, DeRisi JL (2007) Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol 8: R134.
21. Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24: 5534-5547.
22. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG (1993) hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62: 289-321.
23. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416: 499-506.
24. Hieronymus H, Silver PA (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat Genet 33: 155-161.
25. Kim Guisbert K, Duncan K, Li H, Guthrie C (2005) Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. RNA 11: 383-393.
26. Gerber AP, Herschlag D, Brown PO (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2: E79.
27. Brown V, Jin P, Ceman S, Darnell JC, O'Donnell WT, et al. (2001) Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107: 477-487.
28. Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D (2006) Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A 103: 4487-4492.
29. Gray NK, Pantopoulos K, Dandekar T, Ackrell BA, Hentze MW (1996) Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements. Proc Natl Acad Sci U S A 93: 4925-4930.
30. Lal A, Mazan-Mamczarz K, Kawai T, Yang X, Martindale JL, et al. (2004) Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs. Embo J 23: 3092-3102.
31. Padmanabhan K, Richter JD (2006) Regulated Pumilio-2 binding controls RINGO/Spy mRNA translation and CPEB activation. Genes Dev 20: 199-209.
32. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, et al. (2003) Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A 100: 11429-11434.
33. Sonoda J, Wharton RP (1999) Recruitment of Nanos to hunchback mRNA by Pumilio. Genes Dev 13: 2704-2712.
34. Tenenbaum SA, Carson CC, Lager PJ, Keene JD (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A 97: 14085-14090.
35. Ule J, Ule A, Spencer J, Williams A, Hu JS, et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37: 844-852.
36. Duttagupta R, Tian B, Wilusz CJ, Khounh DT, Soteropoulos P, et al. (2005) Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol Cell Biol 25: 5499-5513.
37. Inada M, Guthrie C (2004) Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc Natl Acad Sci U S A 101: 434-439.
38. Johansson MJ, He F, Spatrick P, Li C, Jacobson A (2007) Association of yeast Upf1p with direct substrates of the NMD pathway. Proc Natl Acad Sci U S A 104: 20872-20877.
39. Beilharz TH, Preiss T (2007) Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA 13: 982-997.
40. Li AM, Watson A, Fridovich-Keil JL (2003) Scp160p associates with specific mRNAs in yeast. Nucleic Acids Res 31: 1830-1837.
41. Hodges PE, McKee AH, Davis BP, Payne WE, Garrels JI (1999) The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res 27: 69-73.
42. Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, et al. (2005) CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res 33: D364-368.
43. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032.
44. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
45. Efron B, Tibshirani R (2002) Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol 23: 70-86.
46. Bonafe N, Gilmore-Hebert M, Folk NL, Azodi M, Zhou Y, et al. (2005) Glyceraldehyde-3-phosphate dehydrogenase binds to the AU-Rich 3′ untranslated region of colony-stimulating factor-1 (CSF-1) messenger RNA in human ovarian cancer cells: possible role in CSF-1 posttranscriptional regulation and tumor phenotype. Cancer Res 65: 3762-3771.
47. Hentze MW, Argos P (1991) Homology between IRE-BP, a regulatory RNA-binding protein, aconitase, and isopropylmalate isomerase. Nucleic Acids Res 19: 1739-1740.
48. Gangloff SP, Marguet D, Lauquin GJ (1990) Molecular cloning of the yeast mitochondrial aconitase gene (ACO1) and evidence of a synergistic regulation of expression by glucose plus glutamate. Mol Cell Biol 10: 3551-3561.
49. Chen XJ, Wang X, Kaufman BA, Butow RA (2005) Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science 307: 714-717.
50. Lang BD, Li A, Black-Brewster HD, Fridovich-Keil JL (2001) The brefeldin A resistance protein Bfr1p is a component of polyribosome-associated mRNP complexes in yeast. Nucleic Acids Res 29: 2567-2574.
51. Conrad NK, Wilson SM, Steinmetz EJ, Patturajan M, Brow DA, et al. (2000) A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154: 557-571.
52. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, et al. (1998) The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
53. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
54. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
55. Hinnebusch AG (1985) A hierarchy of trans-acting factors modulates translation of an activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. Mol Cell Biol 5: 2349-2360.
56. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
57. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
58. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
59. Xie Y, Varshavsky A (2001) RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc Natl Acad Sci U S A 98: 3056-3061.
60. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, et al. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-94.
61. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
62. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894.
63. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, et al. (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103: 5320-5325.
64. Sachs AB, Bond MW, Kornberg RD (1986) A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression. Cell 45: 827-835.
65. Kessler SH, Sachs AB (1998) RNA recognition motif 2 of yeast Pab1p is required for its functional interaction with eukaryotic translation initiation factor 4G. Mol Cell Biol 18: 51-57.
66. Preiss T, Muckenthaler M, Hentze MW (1998) Poly(A)-tail-promoted translation in yeast: implications for translational control. RNA 4: 1321-1331.
67. Irie K, Tadauchi T, Takizawa PA, Vale RD, Matsumoto K, et al. (2002) The Khd1 protein, which has three KH RNA-binding motifs, is required for proper localization of ASH1 mRNA in yeast. Embo J 21: 1158-1167.
68. Gao Q, Das B, Sherman F, Maquat LE (2005) Cap-binding protein 1-mediated and eukaryotic translation initiation factor 4E-mediated pioneer rounds of translation in yeast. Proc Natl Acad Sci U S A 102: 4258-4263.
69. Lewis JD, Gorlich D, Mattaj IW (1996) A yeast cap binding protein complex (yCBC) acts at an early step in pre-mRNA splicing. Nucleic Acids Res 24: 3332-3336.
70. Tardiff DF, Lacadie SA, Rosbash M (2006) A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell 24: 917-929.
71. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450.
72. Vasiljeva L, Buratowski S (2006) Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol Cell 21: 239-248.
73. Moriya H, Isono K (1999) Analysis of genetic interactions between DHH1, SSD1 and ELM1 indicates their involvement in cellular morphology determination in Saccharomyces cerevisiae. Yeast 15: 481-496.
74. Kaeberlein M, Guarente L (2002) Saccharomyces cerevisiae MPT5 and SSD1 function in parallel pathways to promote cell wall integrity. Genetics 160: 83-95.
75. Gari E, Volpe T, Wang H, Gallego C, Futcher B, et al. (2001) Whi3 binds the mRNA of the G1 cyclin CLN3 to modulate cell fate in budding yeast. Genes Dev 15: 2803-2808.
76. Nash RS, Volpe T, Futcher B (2001) Isolation and characterization of WHI3, a size-control gene of Saccharomyces cerevisiae. Genetics 157: 1469-1480.
77. Lee FJ, Moss J (1993) An RNA-binding protein gene (RBP1) of Saccharomyces cerevisiae encodes a putative glucose-repressible protein containing two RNA recognition motifs. J Biol Chem 268: 15080-15087.
78. Fujita A, Kikuchi Y, Kuhara S, Misumi Y, Matsumoto S, et al. (1989) Domains of the SFL1 protein of yeasts are homologous to Myc oncoproteins or yeast heat-shock transcription factor. Gene 85: 321-328.
79. de Bruin RA, Kalashnikova TI, Chahwan C, McDonald WH, Wohlschlegel J, et al. (2006) Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell 23: 483-496.
80. Loy CJ, Lydall D, Surana U (1999) NDD1, a high-dosage suppressor of cdc28-1N, is essential for expression of a subset of late-S-phase-specific genes in Saccharomyces cerevisiae. Mol Cell Biol 19: 3312-3327.
81. Pramila T, Miles S, GuhaThakurta D, Jemiolo D, Breeden LL (2002) Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev 16: 3034-3045.
82. Verna J, Lodder A, Lee K, Vagts A, Ballester R (1997) A family of genes required for maintenance of cell wall integrity and for the stress response in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 94: 13804-13809.
83. O'Rourke SM, Herskowitz I (2002) A third osmosensing branch in Saccharomyces cerevisiae requires the Msb2 protein and functions in parallel with the Sho1 branch. Mol Cell Biol 22: 4739-4749.
84. Brown JL, Jaquenoud M, Gulli MP, Chant J, Peter M (1997) Novel Cdc42-binding proteins Gic1 and Gic2 control cell polarity in yeast. Genes Dev 11: 2972-2982.
85. Michaelis S, Herskowitz I (1988) The a-factor pheromone of Saccharomyces cerevisiae is essential for mating. Mol Cell Biol 8: 1309-1318.
86. Grishin AV, Rothenberg M, Downs MA, Blumer KJ (1998) Mot3, a Zn finger transcription factor that modulates gene expression and attenuates mating pheromone signaling in Saccharomyces cerevisiae. Genetics 149: 879-892.
87. Raitt DC, Johnson AL, Erkine AM, Makino K, Morgan B, et al. (2000) The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol Biol Cell 11: 2335-2347.
88. Wittenberg C, Sugimoto K, Reed SI (1990) G1-specific cyclins of S. cerevisiae: cell cycle periodicity, regulation by mating pheromone, and association with the p34CDC28 protein kinase. Cell 62: 225-237.
89. Elemento O, Slonim N, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
90. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
91. Steinmetz EJ, Brow DA (1998) Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc Natl Acad Sci U S A 95: 6699-6704.
92. Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL (2004) Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol 24: 6241-6252.
93. Steinmetz EJ, Conrad NK, Brow DA, Corden JL (2001) RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413: 327-331.
94. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
95. Aviv T, Lin Z, Lau S, Rendl LM, Sicheri F, et al. (2003) The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Biol 10: 614-621.
96. Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol 13: 168-176.
97. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotech 24: 1429-1435.
98. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, et al. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215.
99. Uesono Y, Toh-e A, Kikuchi Y (1997) Ssd1p of Saccharomyces cerevisiae associates with RNA. J Biol Chem 272: 16103-16109.
100. Ibeas JI, Yun DJ, Damsz B, Narasimhan ML, Uesono Y, et al. (2001) Resistance to the plant PR-5 protein osmotin in the model fungus Saccharomyces cerevisiae is mediated by the regulatory effects of SSD1 on cell wall composition. Plant J 25: 271-280.
101. Kaeberlein M, Andalis AA, Liszt GB, Fink GR, Guarente L (2004) Saccharomyces cerevisiae SSD1-V confers longevity by a Sir2p-independent mechanism. Genetics 166: 1661-1672.
102. Reinke A, Anderson S, McCaffery JM, Yates J 3rd, Aronova S, et al. (2004) TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae. J Biol Chem 279: 14752-14762.
103. Wheeler RT, Kupiec M, Magnelli P, Abeijon C, Fink GR (2003) A Saccharomyces cerevisiae mutant with increased virulence. Proc Natl Acad Sci U S A 100: 2766-2770.
104. Costigan C, Gehrung S, Snyder M (1992) A synthetic lethal screen identifies SLK1, a novel protein kinase homolog implicated in yeast cell morphogenesis and cell growth. Mol Cell Biol 12: 1162-1178.
105. Kurischko C, Weiss G, Ottey M, Luca FC (2005) A role for the Saccharomyces cerevisiae regulation of Ace2 and polarized morphogenesis signaling network in cell integrity. Genetics 171: 443-455.
106. Phatnani HP, Jones JC, Greenleaf AL (2004) Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 43: 15702-15719.
107. Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, et al. (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34: D169-172.
108. Beltzer JP, Chang LF, Hinkkanen AE, Kohlhaw GB (1986) Structure of yeast LEU4. The 5′ flanking region contains features that predict two modes of control and two productive translation starts. J Biol Chem 261: 5160-5167.
109. Delbecq P, Werner M, Feller A, Filipkowski RK, Messenguy F, et al. (1994) A segment of mRNA encoding the leader peptide of the CPA1 gene confers repression by arginine on a heterologous yeast gene transcript. Mol Cell Biol 14: 2378-2390.
110. di Blasi F, Carra E, de Vendittis E, Masturzo P, Burderi E, et al. (1993) The SCH9 protein kinase mRNA contains a long 5′ leader with a small open reading frame. Yeast 9: 21-32.
111. Hinnebusch AG (1984) Evidence for translational regulation of the activator of general amino acid control in yeast. Proc Natl Acad Sci U S A 81: 6442-6446.
112. Kebaara B, Nazarenus T, Taylor R, Forch A, Atkin AL (2003) The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5′-UTR and first 92 ORF nucleotides. Nucleic Acids Res 31: 3157-3165.
113. Krummeck G, Gottenof T, Rodel G (1991) AUG codons in the RNA leader sequences of the yeast PET genes CBS1 and SCO1 have no influence on translation efficiency. Curr Genet 20: 465-469.
114. Strick CA, Fox TD (1987) Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5′ leader. Mol Cell Biol 7: 2728-2734.
115. Vilela C, Linz B, Rodrigues-Pousada C, McCarthy JE (1998) The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Res 26: 1150-1159.
116. Sachs MS, Geballe AP (2006) Downstream control of upstream open reading frames. Genes Dev 20: 915-921.
117. Gilbert WV, Zhou K, Butler TK, Doudna JA (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317: 1224-1227.
118. Iizuka N, Najita L, Franzusoff A, Sarnow P (1994) Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol Cell Biol 14: 7322-7330.
119. Spriggs KA, Stoneley M, Bushell M, Willis AE (2008) Re-programming of translation following cell stress allows IRES-mediated translation to predominate. Biol Cell 100: 27-38.
120. Cox JS, Walter P (1996) A Novel mechanism for regulating activity of a transcription factor that controls the unfolded protein response. Cell 87: 391-404.
121. Rüegsegger U, Leber JH, Walter P (2001) Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 107: 103-114.
122. Czaplinski K, Singer RH (2006) Pathways for mRNA localization in the cytoplasm. Trends Biochem Sci 31: 687-693.
123. Groisman I, Huang YS, Mendez R, Cao Q, Theurkauf W, et al. (2000) CPEB, maskin, and cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. Cell 103: 435-447.
124. Huang YS, Richter JD (2004) Regulation of local mRNA translation. Curr Opin Cell Biol 16: 308-313.
125. Kosik KS, Krichevsky AM (2002) The message and the messenger: delivering RNA in neurons. Sci STKE 2002: PE16.
126. Lambert JD, Nagy LM (2002) Asymmetric inheritance of centrosomally localized mRNAs during embryonic cleavages. Nature 420: 682-686.
127. Martin KC (2004) Local protein synthesis during axon guidance and synaptic plasticity. Curr Opin Neurobiol 14: 305-310.
128. Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25: 635-646.
129. Smith R (2004) Moving molecules: mRNA trafficking in Mammalian oligodendrocytes and neurons. Neuroscientist 10: 495-500.
130. St Johnston D (2005) Moving messages: the intracellular localization of mRNAs. Nat Rev Mol Cell Biol 6: 363-375.
131. Sylvestre J, Vialette S, Corral Debrinski M, Jacq C (2003) Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria. Genome Biol 4: R44.
132. Aronov S, Gelin-Licht R, Zipor G, Haim L, Safran E, et al. (2007) mRNAs encoding polarity and exocytosis factors are cotransported with the cortical endoplasmic reticulum to the incipient bud in Saccharomyces cerevisiae. Mol Cell Biol 27: 3441-3455.
133. Gerst JE (2008) Message on the web: mRNA and ER co-trafficking. Trends Cell Biol 18: 68-76.
134. Long RM, Singer RH, Meng X, Gonzalez I, Nasmyth K, et al. (1997) Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA. Science 277: 383-387.
135. Takizawa PA, Sil A, Swedlow JR, Herskowitz I, Vale RD (1997) Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast. Nature 389: 90-93.
136. Takizawa PA, Vale RD (2000) The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. Proc Natl Acad Sci U S A 97: 5273-5278.
137. Olivier C, Poirier G, Gendron P, Boisgontier A, Major F, et al. (2005) Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol Cell Biol 25: 4752-4766.
138. Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, et al. (2005) Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 102: 18005-18010.
139. Hurt E, Luo MJ, Rother S, Reed R, Strasser K (2004) Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc Natl Acad Sci U S A 101: 1858-1862.
140. Ciesla J (2006) Metabolic enzymes that bind RNA: yet another level of cellular regulatory network? Acta Biochim Pol 53: 11-32.
141. Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ (2006) Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev 20: 1294-1307.
142. Lee HK, Jeong S (2006) Beta-catenin stabilizes cyclooxygenase-2 mRNA by interacting with AU-rich elements of 3′-UTR. Nucleic Acids Res 34: 5705-5714.
143. Rother S, Strasser K (2007) The RNA polymerase II CTD kinase Ctk1 functions in translation elongation. Genes Dev 21: 1409-1421.
144. Shetty S, Velusamy T, Idell S, Shetty P, Mazar AP, et al. (2007) Regulation of urokinase receptor expression by p53: novel role in stabilization of uPAR mRNA. Mol Cell Biol 27: 5607-5618.
145. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-251.
146. Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5: R2.
147. Hurowitz EH, Drori I, Stodden VC, Donoho DL, Brown PO (2007) Virtual Northern analysis of the human genome. PLoS ONE 2: e460. doi:10.1371/journal. pone.0000460
148. de Hoog CL, Foster LJ, Mann M (2004) RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. Cell 117: 649-662.
149. Mili S, Moissoglu K, Macara IG (2008) Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions. Nature 453: 115-119.
150. Rodriguez AJ, Czaplinski K, Condeelis JS, Singer RH (2008) Mechanisms and cellular roles of local protein synthesis in mammalian cells. Curr Opin Cell Biol 20: 144-149.
151. Willis DE, van Niekerk EA, Sasaki Y, Mesngon M, Merianda TT, et al. (2007) Extracellular stimuli specifically regulate localized levels of individual neuronal mRNAs. J Cell Biol 178: 965-980.
152. Kapust RB, Tozser J, Fox JD, Anderson DE, Cherry S, et al. (2001) Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 14: 993-1000.
153. Branham WS, Melvin CD, Han T, Desai VG, Moland CL, et al. (2007) Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol 7: 8.
154. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75: 4672-4675.
155. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, et al. (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35: D766-770.
156. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
157. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
158. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, et al. (2004) GO::Term-Finder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715.
159. Gish W, States DJ (1993) Identification of protein coding regions by database similarity search. Nat Genet 3: 266-272.
160. Sheather SJ, Jones MC (1991) A reliable data-based bandwidth selection method for kernel density estimation. J R Stat Soc B 53: 683-690.