Detecting translational regulation by change point analysis of ribosome profiling data sets

RNA

Volumn 20, Issue 10, 2014, Pages 1507-1518

  Zupanic, Anze ^a,b   Meplan, Catherine ^a   Grellscheid, Sushma N ^c   Mathers, John C ^a   Kirkwood, Tom B L ^a   Hesketh, John E ^a   Shanley, Daryl P ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^c DURHAM UNIVERSITY   (United Kingdom)

Author keywords

Change point analysis; Mathematical modeling; Ribosome profiling; Translation regulation

Indexed keywords

GLUTATHIONE PEROXIDASE 1; MESSENGER RNA; SELENOPROTEIN;

ALTERNATIVE RNA SPLICING; ANIMAL CELL; ARTICLE; CELL DENSITY; CODON; EMBRYONIC STEM CELL; MOUSE; NONHUMAN; OPEN READING FRAME; PROTEIN SYNTHESIS; RIBOSOME; RNA SEQUENCE; RNA TRANSLATION; STEREOSPECIFICITY; STOP CODON; TRANSLATION REGULATION; ALGORITHM; ANIMAL; CELL CULTURE; CYTOLOGY; GENE EXPRESSION REGULATION; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; METABOLISM; POLYSOME; THEORETICAL MODEL;

ALGORITHMS; ANIMALS; CELLS, CULTURED; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; MODELS, THEORETICAL; POLYRIBOSOMES; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER;

EID: 84907219361     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.045286.114     Document Type: Article

References (50)

1. Arava Y, Boas F, Brown P, Herschlag D. 2005. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 33: 2421-2432.
2. Barrett T, Edgar R. 2006. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411: 352-369.
3. Barry D, Hartigan JA. 1993. A Bayesian-analysis for change point problems. J Am Stat Assoc 88: 309-319.
4. Bazzini A, Lee M, Giraldez A. 2012. Ribosome profiling shows that miR- 430 reduces translation before causing mRNA decay in zebrafish. Science 336: 233-237.
5. Bohnert R, Ratsch G. 2010. rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res 38: W348-W351.
6. Bonderoff JM, Lloyd RE. 2010. Time-dependent increase in ribosome processivity. Nucleic Acids Res 38: 7054-7067.
7. Brockmann R, Beyer A, Heinisch JJ, Wilhelm T. 2007. Posttranscriptional expression regulation: what determines translation rates? PLoS Comput Biol 3: 531-539.
8. Buchan JR, Stansfield I. 2007. Halting a cellular production line: responses to ribosomal pausing during translation. Biol Cell 99: 475-487.
9. Cho PF, Gamberi C, Cho-Park YA, Cho-Park IB, Lasko P, Sonenberg N. 2006. Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos. Curr Biol 16: 2035-2041.
10. Dana A, Tuller T. 2012. Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol 8: e1002755.
11. Dittmar K, Goodenbour J, Pan T. 2006. Tissue-specific differences in human transfer RNA expression. PLoS Genet 2: e221.
12. Driscoll D, Copeland P. 2003. Mechanism and regulation of selenoprotein synthesis. Annu Rev Nutr 23: 17-40.
13. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. 2009. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: doi: 10.1186/1471-2105-10-48.
14. Erdman C, Emerson JW. 2008. A fast Bayesian change point analysis for the segmentation of microarray data. Bioinformatics 24: 2143-2148.
15. Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, et al. 2012. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res 22: 2208-2218.
16. Gillespie DT. 1977. Exact stochastic simulation of coupled chemical-reactions. J Phys Chem 81: 2340-2361.
17. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
18. Hansen KD, Brenner SE, Dudoit S. 2010. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38: e131.
19. Hesketh J. 2008. Nutrigenomics and selenium: gene expression patterns, physiological targets, and genetics. Annu Rev Nutr 28: 157-177.
20. Howard MT, Carlson BA, Anderson CB, Hatfield DL. 2013. Translational redefinition of UGA codons is regulated by selenium availability. J Biol Chem 288: 19401-19413.
21. Ingolia NT. 2014. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15: 205-213.
22. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.
23. Ingolia N, Lareau L, Weissman J. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802.
24. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. 2012. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7: 1534-1550.
25. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-D496.
26. Kozak M. 1989. The scanning model for translation: an update. J Cell Biol 108: 229-241.
27. Kudla G, Murray A, Tollervey D, Plotkin J. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258.
28. Kurland CG. 1992. Translational accuracy and the fitness of bacteria. Annu Rev Genet 26: 29-50.
29. Lakatos G, Chou T. 2003. Totally asymmetric exclusion processes with particles of arbitrary size. J Phys A Math Gen 36: 2027-2041.
30. Lee S, Liu B, Lee S, Huang S-X, Shen B, Qian S-B. 2012. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci 109: E2424-E2432.
31. Leprivier G, Remke M, Rotblat B, Dubuc A, Mateo AR, Kool M, Agnihotri S, El-Naggar A, Yu B, Somasekharan SP, et al. 2013. The eEF2 kinase confers resistance to nutrient deprivation by blocking translation elongation. Cell 153: 1064-1079.
32. Li GW, Oh E, Weissman JS. 2012. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538-541.
33. Liu B, Han Y, Qian SB. 2013. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol Cell 49: 453-463.
34. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al. 2013. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41: D64-D69.
35. Michel A, Choudhury K, Firth A, Ingolia N, Atkins J, Baranov P. 2012. Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res 22: 2219-2229.
36. R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
37. Richter JD, Sonenberg N. 2005. Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433: 477-480.
38. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. 2011. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12: R22.
39. Rogers AN, Chen D, McColl G, Czerwieniec G, Felkey K, Gibson BW, Hubbard A, Melov S, Lithgow GJ, Kapahi P. 2011. Life span extension via eIF4G inhibition is mediated by posttranscriptional remodeling of stress response gene expression in C. elegans. Cell Metab 14: 55-66.
40. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. 2011. Global quantification of mammalian gene expression control. Nature 473: 337-342.
41. Shaw L, Zia R, Lee K. 2003. Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys Rev E 68: 21910.
42. Sonenberg N, Hinnebusch A. 2009. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136: 731-745.
43. Stadler M, Fire A. 2011. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA 17: 2063-2073.
44. Starck SR, Ow YK, Jiang V, Tokuyama M, Rivera M, Qi X, Roberts RW, Shastri N. 2008. A distinct translation initiation mechanism generates cryptic peptides for immune surveillance. PLoS One 3: e3460.
45. Suo C, Calza S, Salim A, Pawitan Y. 2013. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. Bioinformatics 30: 506-513.
46. Sutton MA, Taylor AM, Ito HT, Pham A, Schuman EM. 2007. Postsynaptic decoding of neural activity: eEF2 as a biochemical sensor coupling miniature synaptic transmission to local protein synthesis. Neuron 55: 648-661.
47. Tian Q, Stepaniants S, Mao M, Weng L, Feetham M, Doyle M, Yi E, Dai H, Thorsson V, Eng J, et al. 2004. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics 3: 960-969.
48. Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y. 2010. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141: 344-354.
49. Vattem KM, Wek RC. 2004. Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci 101: 11269-11274.
50. Vogel C, Abreu R, Ko D, Le S-Y, Shapiro B, Burns S, Sandhu D, Boutz D, Marcotte E, Penalva L. 2010. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 6: 400.