Estimation of ribosome profiling performance and reproducibility at various levels of resolution
Tóm tắt
Ribosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects. The main promise of the approach is its ability to detect ribosome densities over an entire transcriptome in high resolution of single codons. Indeed, dozens of ribo-seq studies have included results related to local ribosome densities in different parts of the transcript; nevertheless, the performance of Ribo-seq has yet to be quantitatively evaluated and reported in a large-scale multi-organismal and multi-protocol study of currently available datasets. Here we provide the first objective evaluation of Ribo-seq at the resolution of a single nucleotide(s) using clear, interpretable measures, based on the analysis of 15 experiments, 6 organisms, and a total of 612, 961 transcripts. Our major conclusion is that the ability to infer signals of ribosomal densities at nucleotide scale is considerably lower than previously thought, as signals at this level are not reproduced well in experimental replicates. In addition, we provide various quantitative measures that connect the expected error rate with Ribo-seq analysis resolution. The analysis of Ribo-seq data at the resolution of codons and nucleotides provides a challenging task, calls for task-specific statistical methods and further protocol improvements. We believe that our results are important for every researcher studying translation and specifically for researchers analyzing data generated by the Ribo-seq approach. This article was reviewed by Dmitrij Frishman, Eugene Koonin and Frank Eisenhaber.
Tài liệu tham khảo
Vogel C, Abreu R de S, Ko D, Le S-Y, Shapiro BA, Burns SC, et al. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol. 2010;6:400.
Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, et al. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 2004;3:960–9.
Calkhoven CF, Müller C, Leutz A. Translational control of gene expression and disease. Trends Mol Med. 2002;8:577–83.
Silvera D, Formenti SC, Schneider RJ. Translational control in cancer. Nat Rev Cancer. 2010;10:254–66.
Harding HP, Calfon M, Urano F, Novoa I, Ron D. Transcriptional and Translational Control in the Mammalian Unfolded Protein Response. Annu Rev Cell Dev Biol. 2002;18:575–99.
Gebauer F, Hentze MW. Molecular mechanisms of translational control. Nat Rev Mol Cell Biol. 2004;5:827–35.
Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, et al. Global quantification of mammalian gene expression control. Nature. 2011;473:337–42.
Russell JB, Cook GM. Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol Rev. 1995;59:48–62.
Buttgereit F, Brand MD. A hierarchy of ATP-consuming processes in mammalian cells. Biochem J. 1995;312:163–7.
Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science. 2009;324:218–23.
Dana A, Tuller T. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res. 2014;42:9171–81.
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;335:552–7.
Sabi R, Tuller T. A comparative genomics study on the effect of individual amino acids on ribosome stalling. BMC Genomics. 2015;16:S5.
Bazzini AA, Lee MT, Giraldez AJ. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science. 2012;336:233–7.
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–27.
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011;477:295–300.
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;7:1534–50.
Aeschimann F, Xiong J, Arnold A, Dieterich C, Großhans H. Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling. Methods. 2015;85:75–89.
Hussmann JA, Patchett S, Johnson A, Sawyer S, Press WH. Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast. PLoS Genet. 2015;11:e1005732.
Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. Cell Rep. 2016;14:1787–99.
Artieri CG, Fraser HB. Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation. Genome Res. 2014;24:2011-2021.
Bartholomäus A, Del CC, Ignatova Z. Mapping the non-standardized biases of ribosome profiling. Biol Chem. 2015;397:23–35.
Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, et al. Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo. Cell. 2011;147:1295–308.
Gingold H, Pilpel Y. Determinants of translation efficiency and accuracy. Mol Syst Biol. 2011;7:481.
Tuller T, Veksler-Lublinsky I, Gazit N, Kupiec M, Ruppin E, Ziv-Ukelson M. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol. 2011;12:R110.
Stadler M, Fire A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA. 2011;17:2063–73.
Thomas LK, Dix DB, Thompson RC. Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro. Proc Natl Acad Sci U S A. 1988;85:4242–6.
Kato M, Nishikawa K, Uritani M, Miyazaki M, Takemura S. The difference in the type of codon-anticodon base pairing at the ribosomal P-site is one of the determinants of the translational rate. J Biochem. 1990;107:242–7.
Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, et al. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol. 2014;10:770–0.
Charneski CA, Hurst LD. Positively Charged Residues Are the Major Determinants of Ribosomal Velocity. PLoS Biol. 2013;11:e1001508.
Lu J, Deutsch C. Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol. 2008;384:73–86.
Dana A, Tuller T. Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells. PLoS Comput Biol. 2012;8:e1002755.
Yang J-R, Chen X, Zhang J. Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding. PLoS Biol. 2014;12:e1001910.
Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science. 2006;314:1930–3.
Gardin J, Yeasmin R, Yurovsky A, Cai Y, Skiena S, Futcher B. Measurement of average decoding rates of the 61 sense codons in vivo. Elife. 2014;3:e03735.
Li G-W, Oh E, Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature. 2012;484:538–41.
Qian W, Yang J-R, Pearson NM, Maclean C, Zhang J. Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency. PLoS Genet. 2012;8:e1002603.
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.
Ben-Yehezkel T, Atar S, Zur H, Diament A, Goz E, Marx T, et al. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants. RNA Biol. 2015;12:972–84.
Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M. High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells. PLoS Biol. 2006;4:e180.
Lithwick G, Margalit H. Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation. Genome Res. 2003;13:2665–73.
Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, et al. A Role for Codon Order in Translation Dynamics. Cell. 2010;141:355–67.
Artieri CG, Fraser HB. Evolution at two levels of gene expression in yeast. Genome Res. 2014;24:411–21.
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;22:2418–26.
Liu B, Han Y, Qian S-B. Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes. Mol Cell. 2013;49:453–63.
Gerashchenko MV, Gladyshev VN. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res. 2014;42:e134–4.
Gritsenko AA, Hulsman M, Reinders MJT, de Ridder D. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. PLoS Comput Biol. 2015;11:e1004336.
Andreev DE, O’Connor PBF, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, et al. Translation of 5’ leaders is pervasive in genes resistant to eIF2 repression. Elife. 2015;4:e03971.
McManus CJ, May GE, Spealman P, Shteyman A. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res. 2014;24:422–30.
Stumpf CR, Moreno MV, Olshen AB, Taylor BS, Ruggero D. The Translational Landscape of the Mammalian Cell Cycle. Mol Cell. 2013;52:574–82.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42:D749–55.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17:10–2.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Lee S, Liu B, Lee S, Huang S-X, Shen B, Qian S-B. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A. 2012;109:E2424–32.