Translation regulation gets its 'omics' moment

Wiley Interdisciplinary Reviews: RNA

Volumn 4, Issue 6, 2013, Pages 617-630

  Kuersten, Scott ^a   Radek, Agnes ^a   Vogel, Christine ^b   Penalva, Luiz O F ^c  

^a ILLUMINA INC   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRE RECOMBINASE; MESSENGER RNA; MICRORNA; RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; UNTRANSLATED RNA;

BIOGENESIS; CELL FUNCTION; CELL GROWTH; CELL MOTILITY; CELL PROLIFERATION; EMBRYONIC STEM CELL; GENE CONTROL; GENE EXPRESSION REGULATION; HUMAN; IMMUNOPRECIPITATION; NONHUMAN; OPEN READING FRAME; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FOOTPRINTING; PROTEIN RNA BINDING; PROTEIN SYNTHESIS; PROTEOMICS; REVIEW; RNA DEGRADATION; RNA PROCESSING; RNA STABILITY; START CODON; STEADY STATE; STOP CODON; SYSTEMS BIOLOGY; TRANSCRIPTION ELONGATION; TRANSLATION INITIATION; TRANSLATION REGULATION;

GENE EXPRESSION REGULATION; MICRORNAS; PROTEIN BIOSYNTHESIS; PROTEOMICS; RIBONUCLEOPROTEINS; RIBOSOMES; RNA-BINDING PROTEINS;

EID: 84885815730     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1173     Document Type: Review

References (64)

1. Costa FF. Non-coding RNAs: meet thy masters. Bioessays 2010, 32:599-608. doi: 10.1002/bies.200900112.
2. Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 2010, 6:400.
3. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.
4. Castello A, Fischer B, Hentze MW, Preiss T. RNA-binding proteins in Mendelian disease. Trends Genet 2013, 29:318-327.
5. Melamed D, Arava Y. Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol 2007, 431:177-201.
6. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324:218-223.
7. Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods Enzymol 2010, 470:119-142.
8. Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147:789-802.
9. Kolle G, Shepherd JL, Gardiner B, Kassahn KS, Cloonan N, Wood DL, Nourbakhsh E, Taylor DF, Wani S, Chy HS, et al. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells. Genome Res 2011, 21:2014-2025.
10. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 2012, 7:1534-1550.
11. Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 2010, 141:344-354.
12. Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y. A role for codon order in translation dynamics. Cell 2010, 141:355-367. Erratum in: Cell 2010;141:728.
13. Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 2011, 12:32-42.
14. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840.
15. Li GW, Oh E, Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 2012, 484:538-541.
16. Efeyan A, Zoncu R, Sabatini DM. Amino acids and mTORC1: from lysosomes to disease. Trends Mol Med 2012, 18:524-533. doi: 10.1016/j.molmed.2012.05.007.
17. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 2010, 18:11-22.
18. Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 2012, 485:55-61.
19. Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 2012, 13:227-232.
20. Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Paabo S, Mann M. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011, 7:548.
21. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
22. Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
23. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2006, 5:144-156.
24. Brewis IA, Brennan P. Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 2010, 80:1-44.
25. Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2007, 25:117-124.
26. de Sousa Abreu R, Penalva LO, Marcotte E, Vogel C. Global signatures of protein and mRNA expression levels. Mol Biosyst 2009, 5:1512.
27. Schwanhausser B, Gossen M, Dittmar G, Selbach M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics 2009, 9:205-209.
28. Lackner DH, Schmidt MW, Wu S, Wolf DA, Bahler J. Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol 2012, 13:R25.
29. Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol 2011, 7:514.
30. Olsen PH, Ambros V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 1999, 216:671-680.
31. Seggerson K, Tang L, Moss EG. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol 2002, 243:215-225.
32. Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, et al. MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol 2011, 12:R126.
33. Huntzinger E, Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 2011, 12:99-110.
34. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006, 20:515-524.
35. Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012, 336:233-237.
36. Djuranovic S, Nahvi A, Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 2012, 336:237-240.
37. Nottrott S, Simard MJ, Richter JD. Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nat Struct Mol Biol 2006, 13:1108-1114.
38. Stadler M, Artiles K, Pak J, Fire A. Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets. Genome Res 2012, 22:2418-2426.
39. Thermann R, Hentze MW. Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 2007, 447:875-878.
40. Ankö ML, Neugebauer KM. RNA-protein interactions in vivo: global gets specific. Trends Biochem Sci 2012, 37:255-262.
41. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406.
42. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 2012, 46:674-690.
43. Tenenbaum SA, Carson CC, Lager PJ, Keene JD. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A 2000, 97:14085-14090.
44. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003, 302:1212-1215.
45. Morris AR, Mukherjee N, Keene JD. Systematic analysis of posttranscriptional gene expression. WIREs Syst Biol Med 2010, 2:162-180.
46. König J, Zarnack K, Luscombe NM, Ule J. Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 2012, 13:77-83. doi: 10.1038/nrg3141.
47. Kapeli K, Yeo GW. Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. Front Neurosci. 2012, 6:144.
48. Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, et al. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 2012, 150:710-724.
49. Komili S, Farny NG, Roth FP, Silver PA. Functional specificity among ribosomal proteins regulates gene expression. Cell 2007, 131:557-571.
50. Galante PA, Sandhu D, de Sousa Abreu R, Gradassi M, Slager N, Vogel C, de Souza SJ, Penalva LO. A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: identification of potential players in tumor formation. RNA Biol 2009, 6:426-433.
51. Li C, Ge M, Yin Y, Luo M, Chen D. Silencing expression of ribosomal protein L26 and L29 by RNA interfering inhibits proliferation of human pancreatic cancer PANC-1 cells. Mol Cell Biochem 2012, 370(1-2):127-139.
52. Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suárez-Fariñas M, Schwarz C, Stephan DA, Surmeier DJ, et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 2008, 135:738-748.
53. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, Bupp S, Shrestha P, Shah RD, Doughty ML, et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 2008, 135:749-762. Erratum in: Cell. 2009;139:1022.
54. Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS. Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci U S A 2009, 106:13939-13944.
55. Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, et al. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res 2012, 22:2208-2218.
56. Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A 2012, 109:E2424-E2432.
57. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 2012, 335:552-557.
58. Gerashchenko MV, Lobanov AV, Gladyshev VN. Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc Natl Acad Sci U S A 2012, 109:17394-17399.
59. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, et al. Decoding human cytomegalovirus. Science 2012, 338:1088-1093.
60. Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, et al. Proto-genes and de novo gene birth. Nature 2012, 487:370-374.
61. Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 2011, 9:34.
62. Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 2009, 10:264.
63. Liu S, Lin L, Jiang P, Wang D, Xing Y. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res 2011, 39:578-588.
64. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.