Global analyses of mRNA translational control during early Drosophila embryogenesis

Genome Biology

Volumn 8, Issue 4, 2007, Pages

  Qin, Xiaoli ^a,b   Ahn, Soyeon ^c   Speed, Terence P ^c   Rubin, Gerald M ^a,d  

^a University of California Berkeley   (United States)

^b InterMune Inc   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Janelia Farm Research Campus   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBOSOME PROTEIN;

ANIMAL CELL; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DROSOPHILA; EGG LAYING; EMBRYO; EMBRYO DEVELOPMENT; GENE CONTROL; GENETIC ANALYSIS; NONHUMAN; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PROTEIN PROCESSING; RIBOSOME; RNA TRANSCRIPTION; RNA TRANSLATION; TRANSLATION REGULATION; ANIMAL; ANIMAL EMBRYO; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; POLYSOME; PRENATAL DEVELOPMENT; PROTEIN SYNTHESIS; TERMINAL OLIGOPYRIMIDINE TRACT;

ANIMALIA;

ANIMALS; CLUSTER ANALYSIS; DROSOPHILA; EMBRYO, NONMAMMALIAN; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; POLYRIBOSOMES; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA 5' TERMINAL OLIGOPYRIMIDINE SEQUENCE; RNA, MESSENGER;

EID: 34948889112     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-4-r63     Document Type: Article

References (35)

1. Edgar BA Schubiger G Parameters controlling transcriptional activation during early Drosophila development. Cell 1986, 44:871-877. 10.1016/ 0092-8674(86)90009-7 2420468
2. Foe VE Odell GM Edgar BA Mitosis and Morphogenesis in the Drosophila Embryo: Point and Counterpoint Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press 1993. 1
3. Wickens M Goodwin EB Kimble J Strickland S Hentze M Translational it control of Developmental Decisions Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press 2000.
4. Bergsten SE Huang T Chatterjee S Gavis ER Recognition and long-range interactions of a minimal nanos RNA localization signal element. Development 2001, 128:427-435. 11152641
5. Gavis ER Lehmann R Localization of nanos RNA controls embryonic polarity. Cell 1992, 71:301-313. 10.1016/0092-8674(92)90358-J 1423595
6. Mancebo R Zhou X Shillinglaw W Henzel W Macdonald PM BSF binds specifically to the bicoid mRNA 3′ untranslated region and contributes to stabilization of bicoid mRNA. Mol Cell Biol 2001, 21:3462-3471. 100268 11313472 10.1128/MCB.21.10.3462-3471.2001
7. Macdonald PM Struhl G Cis-acting sequences responsible for anterior localization of bicoid mRNA in Drosophila embryos. Nature 1988, 336:595-598. 10.1038/336595a0 3143913
8. Struhl G Struhl K Macdonald PM The gradient morphogen bicoid is a concentration-dependent transcriptional activator. Cell 1989, 57:1259-1273. 10.1016/0092-8674(89)90062-7 2567637
9. Mathews MB Sonenberg N Hershey JWB Origins and Principles of Translational Control Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press 2000.
10. Kuhn KM DeRisi JL Brown PO Sarnow P 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 2001, 21:916-927. 10.1128/MCB.21.3.916-927.2001 11154278 86682
11. Arava Y Wang Y Storey JD Liu CL Brown PO Herschlag D Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100:3889-3894. 153018 12660367 10.1073/ pnas.0635171100
12. Johannes G Carter MS Eisen MB Brown PO Sarnow P Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci USA 1999, 96:13118-13123. 23910 10557283 10.1073/pnas.96.23.13118
13. Sonenberg N Hershey J Mathews MB Translational Control of Gene Expression Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press 2000.
14. Arava Y Boas FE Brown PO Herschlag D Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 2005, 33:2421-2432. 1087779 15860778 10.1093/nar/gki331
15. Affymetrix I: NetAffx analyses tool http://www.Affymetrix.com
16. Meyuhas O Synthesis of the translational apparatus is regulated at the translational level. Eur J Biochem 2000, 267:6321-6330. 10.1046/ j.1432-1327.2000.01719.x 11029573
17. Pierandrei-Amaldi P Amaldi F Aspects of regulation of ribosomal protein synthesis in Xenopus laevis. Review. Genetica 1994, 94:181-193. 10.1007/ BF01443432 7896138
18. Groisman I Jung MY Sarkissian M Cao Q Richter JD Translational control of the embryonic cell cycle. Cell 2002, 109:473-483. 10.1016/ S0092-8674(02)00733-X 12086604
19. Yoshihama M Uechi T Asakawa S Kawasaki K Kato S Higa S Maeda N Minoshima S Tanaka T Shimizu N Kenmochi N The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res 2002, 12:379-390. 155282 11875025 10.1101/gr.214202
20. Jefferies HB Fumagalli S Dennis PB Reinhard C Pearson RB Thomas G Rapamycin suppresses 5′TOP mRNA translation through inhibition of p70s6k. EMBO J 1997, 16:3693-3704. 1169993 9218810 10.1093/emboj/ 16.12.3693
21. Ruvinsky I Sharon N Lerer T Cohen H Stolovich-Rain M Nir T Dor Y Zisman P Meyuhas O Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev 2005, 19:2199-2211. 1221890 16166381 10.1101/gad.351605
22. Montagne J Stewart MJ Stocker H Hafen E Kozma SC Thomas G Drosophila S6 kinase: A regulator of cell size. Science 1999, 285:2126-2129. 10.1126/ science.285.5436.2126 10497130
23. Tomancak P Beaton A Weiszmann R Kwan E Shu S Lewis SE Richards S Ashburner M Hartenstein V Celniker SE Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 2002, 3:rEsearch0088.1-0088.14. 10.1186/gb-2002-3-12-research0088
24. Tai YC Speed TP A multivariate empirical bayes statistic for replicated microarray time course data. Ann Statist 2006, 34:2387-2412. 10.1214/ 009053606000000759
25. Stebbings H Cytoskeleton-dependent transport and localization of mRNA. Int Rev Cytol 2001, 211:1-31. 11597002
26. Bashirullah A Cooperstock RL Lipshitz HD RNA localization in development. Annu Rev Biochem 1998, 67:335-394. 10.1146/ annurev.biochem.67.1.335 9759492
27. Clark IE Wyckoff D Gavis ER Synthesis of the posterior determinant Nanos is spatially restricted by a novel cotranslational regulatory mechanism. Curr Biol 2000, 10:1311-1314. 10.1016/S0960-9822(00)00754-5 11069116
28. Berkeley Drosophila Genome Project: Supplemental Datasets http://www.fruitfly.org/about/pubs/index.html
29. Qin X Sarnow P Preferential translation of internal ribosome entry site-containing mRNAs during the mitotic cycle in mammalian cells. J Biol Chem 2004, 279:13721-13728. 10.1074/jbc.M312854200 14739278
30. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249 12925520
31. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 545600 15461798 10.1186/gb-2004-5-10-r80
32. Gautier L Cope L Bolstad BM Irizarry RA affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315. 10.1093/bioinformatics/btg405 14960456
33. Smyth GK Wettenhall J Thorne N LIMMA: Linear Models for Microarray Data User's Guide 2005. http://bioinf.wehi.edu.au/limma
34. Liu G Loraine AE Shigeta R Cline M Cheng J Valmeekam V Sun S Kulp D Siani-Rose MA NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 2003, 31:82-86. 165568 12519953 10.1093/nar/gkg121
35. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/ 75556 10802651