Top 5 Cited Papers from 2019 Featuring Ribosome Profiling
Number of citations obtained from Google Scholar on the 14th January 2020.
- Ribosome Profiling: Global Views of Translation | Times Cited: 37 | COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
By: Ingolia, Nicholas T.; Hussmann, Jeffrey A.; Weissman, Jonathan S.
This review, featuring Nicholas Ingolia and Jonathan Weissman who were involved in the development of the Ribo-Seq technology, discusses ribosome profiling approaches and how the emergence of novel techniques and improved protocols will allow us to gain further insights into translation and protein function.
The rich and quantitative nature of ribosome profiling data provides an unprecedented opportunity to explore and model complex cellular processes.
- High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress | Times Cited: 35 | MOLECULAR CELL
By: Wu, Colin Chih-Chien; Zinshteyn, Boris; Wehner, Karen A.; Green, Rachel.
This paper from the Rachel Green Lab utilises high-resolution ribosome profiling, including the use of multiple elongation-inhibiting antibiotics and chemical probing to examine the conformational states of ribosomes corresponding to ribosome-protected mRNA fragments (RPFs) of different sizes. They discovered that short RPFs of 20-22 or 27-29 nucleotides in fungi, worms, and mammals correspond to ribosomes with vacant or occupied ribosomal A-sites, respectively. This study also describes mechanisms of translation-elongation arrest during certain stress conditions, including oxidative and hyperosmotic stress.
The ability of ribosome profiling to define the functional state of ribosomes within the cell provides a powerful tool for deciphering cellular responses to a variety of stresses.
- The Translational Landscape of the Human Heart | Times Cited: 21 | CELL
By: van Heesch, Sebastiaan; Witte, Franziska; Schneider-Lunitz, Valentin; et al.
Ribo-Seq was used in this fascinating study on 80 human hearts to examine translation regulation and to investigate novel translation events. The tissue samples were from dilated cardiomyopathy (DCM) patients, as well as non-diseased controls. Some of the key findings describe extensive translational control of cardiac gene expression, ribosomes frequently translating mRNAs downstream of predicted disease-causing protein-truncated variants, and hundreds of previously undetected microproteins expressed from lncRNAs and circRNAs were identified in vivo, many of which locate to the mitochondria.
- An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells | Times Cited: 17 | NATURE MICROBIOLOGY
By: Lulla, Valeria; Dinan, Adam M.; Hosmillo, Myra; Chaudhry, Yasmin; Sherry, Lee; Irigoyen, Nerea; Nayak, Komal M.; Stonehouse, Nicola J.; Zilbauer, Matthias; Goodfellow, Ian; Firth, Andrew E.
This interesting study focuses on the highly infectious and environmentally stable mammalian pathogens of enteroviruses. It was previously thought that all enteroviral proteins were derived from the proteolytic processing of a single polyprotein in an open reading frame. This study reveals that an upstream open reading frame with strong purifying selection is present in enterovirus genomes, and the expression of uORF protein was confirmed in infected cells. Ribosome profiling was used to exhibit translation of the uORF in predominant human enterovirus species such as Enterovirus A, B, and C.
- Small is big in Arabidopsis mitochondrial ribosome | Times Cited: 17 | NATURE PLANTS
By: Waltz, Florent; Tan-Trung Nguyen; Arrive, Mathilde; Bochler, Anthony; Chicher, Johana; Hammann, Philippe; Kuhn, Lauriane; Quadrado, Martine; Mireau, Hakim ; Hashem, Yaser; Giegé, Philippe.
Translation remains the most elusive of the mitochondrial gene expression processes. In plants, gene expression involves various pentatricopeptide repeat (PPR) proteins, however their function in mitochondrial translation remains to be seen. This study describes the biochemical characterisation of Arabidopsis mitochondrial ribosomes, as well as revealing their protein subunit composition. Knockout mutations of ribosomal PPR (rPPR) genes result in certain macroscopic phenotypes such as lethality and growth delay. Ribosome profiling was used in this study for the molecular analysis of rppr1 mutants and further analysis of mitochondrial protein levels, where it was revealed that rPPR1 is a generic translation factor that is a novel function for PPR proteins.