The DOI matches its Crossref record; 98 of the 98 references it cites were found in a registry or an index.
Ribosome Footprint Profiling of Translation throughout the Genome
Open accessAbstract
Ribosome profiling has emerged as a technique for measuring translation comprehensively and quantitatively by deep sequencing of ribosome-protected mRNA fragments. By identifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into the composition and regulation of the expressed proteome, including delineating potentially functional micropeptides, revealing pervasive translation on cytosolic RNAs, and identifying differences in elongation rates driven by codon usage or other factors. This Primer looks at important experimental and analytical concerns for executing ribosome profiling experiments and surveys recent examples where the approach was developed to explore protein biogenesis and homeostasis.
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Citations
Cites
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Mass spectrometry-based proteomics
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Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
Vogel, C., & Marcotte, E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3185 · Cited by 4,195
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Self-citationRegulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets
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Exploring the new world of the genome with DNA microarrays
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Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011) · Cell · doi:10.1016/j.cell.2011.10.002 · Cited by 2,187
Self-citationImproving RNA-Seq expression estimates by correcting for fragment bias
Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology · doi:10.1186/gb-2011-12-3-r22 · Cited by 1,725
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Cited by
Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis
Khajuria, R. K., Munschauer, M., Ulirsch, J. C., Fiorini, C., Ludwig, L. S., McFarland, S. K., Abdulhay, N. J., Specht, H., Keshishian, H., Mani, D. R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.036 · Cited by 416
“See also Figure S4 and Tables S3 and S4. primary human HSPCs undergoing erythroid lineage commitment, we performed ribosome profiling (Ingolia, 2016; Mills et al., 2016).”
BackgroundMethodInfluentialTranslation affects mRNA stability in a codon-dependent manner in human cells
Wu, Q., Medina, S. G., Kushawah, G., DeVore, M. L., Castellano, L. A., Hand, J. M., Wright, M., & Bazzini, A. A. (2019) · eLife · doi:10.7554/elife.45396 · Cited by 283
An Updated Overview on the Regulation of Seed Germination
Carrera-Castaño, G., Calleja-Cabrera, J., Pernas, M., Gómez, L., & Oñate-Sánchez, L. (2020) · Plants · doi:10.3390/plants9060703 · Cited by 269
IRES-mediated cap-independent translation, a path leading to hidden proteome
Yang, Y., & Wang, Z. (2019) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjz091 · Cited by 260
Spatially resolved single-cell translatomics at molecular resolution
(2023) · doi:10.1126/science.add3067 · Cited by 198
Metadata
- Authors
- Ingolia, N. T.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-03
- Volume
- 165
- Issue
- 1
- Pages
- 22-33
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2306137721
- Cited by
- 409
- References
- 98
- FWCI
- 23.62
- Type
- journal article
- Language
- en
- Open access
- bronze
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
