Translatomics: The Global View of Translation
Abstract
:1. Introduction
2. Methods for Translatome Research
2.1. Method for Translating mRNA
2.1.1. Polysome Profiling
2.1.2. RNC-Seq
2.1.3. Ribo-Seq
2.1.4. TRAP-Seq
2.2. Methods for tRNAome
2.3. Methods for the Folding State of Nascent Polypeptides
2.4. Methods to Identify and to Quantify Nascent Peptides
2.5. Methods for Detecting mRNA Co-Translational Decay Intermediates
2.6. Visualization of Translation In Vivo
3. Translatomics in Fundamental Biology
3.1. The “Quantitative” Central Dogma of Molecular Biology
3.2. Translational Pausing Induces Co-Translational Folding
3.3. Two-Dimensional Translational Control Initiation and Elongation
3.4. Alternative Translation Start Sites and Readthrough
3.5. Ribosome Diversity
4. Translatomics in Biology/Disease-Relevant Studies
4.1. Perturbation of Global Translation in Cancer
4.2. Microbial Stress Resistance
4.3. Rhythmic Translation in Circadian Clock Regulation
4.4. Translational Control in Plants
5. Application of Translatomics
5.1. Missing Protein and New Protein Discovery
5.2. Enhancing Recombinant Protein Production
6. Internet Resources for Translatome
7. Conclusion and Perspectives
Author Contributions
Funding
Conflicts of Interest
Abbreviations
2-DE | 2-dimensional electrophoresis |
5Pseq | 5′-monophosphorylated ends sequencing |
AHA | Azidohomoalanine |
BONCAT/QuaNCAT | Bio-Orthogonal/Quantitative Non-Canonical Amino acid Tagging |
CDS | Coding sequence |
CVN | Cyanovirin-N, an antiviral protein originated from cyanobacteria |
FRET | Fluorescence resonance energy transfer |
GMUCT | Genome-wide mapping of uncapped and cleaved transcripts |
EVI | Translation elongation speed |
FDR | False discover rate |
HPP | The Human Proteome Project |
miRNA | MicroRNAs |
MS | Mass spectrometry |
ncRNA | Non-coding RNAs |
NCT | Nascent chain tracking |
NGS | Next-generation sequencing |
NGD | No-go decay |
NMD | Nonsense-mediated mRNA decay |
NMR | Nuclear magnetic resonance |
NSD | Non-stop decay |
ORF | Open reading frame |
PARE | parallel analysis of RNA ends |
PUNCH-P | PUromycin-associated Nascent CHain Proteomics |
pSILAC | Pulsed-SILAC, Pulsed Stable Isotope Labelling by Amino acids |
RFP | Ribosome footprints, equivalent to ribosome protected fragments, RPFs |
Ribo-seq | Ribosome profiling |
RNC | Ribosome nascent-chain complex |
RNC-mRNA | Translating mRNAs |
RNC-seq | Full-length translating mRNA profiling |
ROS | Reactive oxygen species |
SSU | Small subunit of ribosome |
TR | Translation initiation efficiency |
TRAP-seq | Translating ribosome affinity purification sequencing |
tRNA-seq | Full-length tRNA sequencing |
UTR | Untranslated regions of genes |
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Technical Aspects | Polysome Profiling | RNC-Seq | Ribo-Seq | TRAP-Seq |
---|---|---|---|---|
Recovery of RNC-mRNA | Full-length | Full-length | Ribosome protected fragments | Full-length |
Difficulty in Recovering translating mRNA | Demanding | Simple | Demanding | Simple |
High-throughput methods can be used | Microarray, NGS | Microarray, NGS | NGS | Microarray, NGS |
Throughput requirement | Low | Low | High | Low |
Read length | Any | Any | 22–35 nt | Any |
Detecting sequence variations | Simple | Simple | Demanding | Simple |
UTR | Yes | Yes | No | Yes |
Obtain the position of ribosome, densities, ORF, uORFs | No | No | Yes | No |
Obtaining the amount of ribosomes in single mRNA | Yes | No | No | No |
Tissue specific | No | No | No | Yes |
Under physiological conditions | Yes | Yes | Yes | No |
Required experimental steps | Simple | Simple | Complex | Complex |
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Zhao, J.; Qin, B.; Nikolay, R.; Spahn, C.M.T.; Zhang, G. Translatomics: The Global View of Translation. Int. J. Mol. Sci. 2019, 20, 212. https://doi.org/10.3390/ijms20010212
Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. International Journal of Molecular Sciences. 2019; 20(1):212. https://doi.org/10.3390/ijms20010212
Chicago/Turabian StyleZhao, Jing, Bo Qin, Rainer Nikolay, Christian M. T. Spahn, and Gong Zhang. 2019. "Translatomics: The Global View of Translation" International Journal of Molecular Sciences 20, no. 1: 212. https://doi.org/10.3390/ijms20010212