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Profiling Ribosome Dynamics [PDF]
Nature Reviews Molecular Cell Biology, 2016 Eytan Zlotorynski
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2022
Selective Ribosome Profiling (SeRP) is an emerging methodology, developed to capture cotranslational interactions in vivo. To date, SeRP is the only method that can directly capture, in near-codon resolution, ribosomes in action. Thus, SeRP allows us to study the mechanisms of protein synthesis and the network of protein-protein interactions that are ...
Hagit, Bar-Yosef +3 more
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Selective Ribosome Profiling (SeRP) is an emerging methodology, developed to capture cotranslational interactions in vivo. To date, SeRP is the only method that can directly capture, in near-codon resolution, ribosomes in action. Thus, SeRP allows us to study the mechanisms of protein synthesis and the network of protein-protein interactions that are ...
Hagit, Bar-Yosef +3 more
openaire +2 more sources
Analysis of Ribosome Profiling Data
2022Ribosome profiling methods are based on high-throughput sequencing of ribosome-protected mRNA footprints and allow to study in detail translational changes. Bioinformatic and statistical tools are necessary to analyze sequencing data. Here, we describe our developed methods for a fast and reliable quality control of ribosome profiling data, to ...
Carine Legrand +2 more
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Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling
2021The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218-223, 2009), ribosome
Alexander L, Cope +5 more
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Transcriptome-Wide Measurement of Ribosomal Occupancy by Ribosome Profiling
Methods, 2015Gene expression profiling provides a tool to analyze the internal states of cells or organisms, and their responses to perturbations. While global measurements of mRNA levels have thus been widely used for many years, it is only through the recent development of the ribosome profiling technique that an analogous examination of global mRNA translation ...
Christoph Dieterich, Helge Grosshans
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2017
Ribosome profiling (also known as Ribo-seq) provides a genome-wide, high-resolution, and quantitative accounting of mRNA segments that are occupied by ribosomes in vivo. The method has been used to address numerous questions in bacteria, yeast, and metazoa, but its application to questions in plant biology is just beginning.
Prakitchai, Chotewutmontri +3 more
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Ribosome profiling (also known as Ribo-seq) provides a genome-wide, high-resolution, and quantitative accounting of mRNA segments that are occupied by ribosomes in vivo. The method has been used to address numerous questions in bacteria, yeast, and metazoa, but its application to questions in plant biology is just beginning.
Prakitchai, Chotewutmontri +3 more
openaire +2 more sources
Tissue-Specific Ribosome Profiling in Drosophila
2021Robust mechanisms exist that serve to dynamically regulate the translation of mRNA into proteins across heterogeneous tissues. These processes ensure timely generation of proteins in quantities that scale with the demands of specific cell types.
Xun, Chen, Dion, Dickman
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Ribosome Profiling in Trypanosomatids
2019Ribosomes are the machinery responsible for reading mRNAs and translating them into proteins. The ribosome profiling approach is based on high-throughput sequencing of ribosome-protected mRNAs. RNAs not harboring ribosomes are removed by nuclease digestion leaving the so-called ribosome "footprints." The purified "footprint" RNA molecules are processed
Amelie J, Kraus, Raúl O, Cosentino
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Transcriptome-Wide Measurement of Translation by Ribosome Profiling
Methods, 2017 Translation is one of the fundamental processes of life. It comprises the assembly of polypeptides whose amino acid sequence corresponds to the codon sequence of an mRNA's ORF. Translation is performed by the ribosome; therefore, in order to understand translation and its regulation we must be able to determine the numbers and locations of ribosomes on
Nicholas Ingolia, Nicholas J McGlincy
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2016
In the last decade gene expression profiling by microarrays (Brown and Botstein 1999), and more recently by RNA-Seq (Mortazavi et al. 2008), has become one of the most important and widely used tools of molecular biology. However, recent studies have shown that mRNA levels only imperfectly correlate with protein levels (Vogel et al.
Zupanic, Anze +1 more
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In the last decade gene expression profiling by microarrays (Brown and Botstein 1999), and more recently by RNA-Seq (Mortazavi et al. 2008), has become one of the most important and widely used tools of molecular biology. However, recent studies have shown that mRNA levels only imperfectly correlate with protein levels (Vogel et al.
Zupanic, Anze +1 more
openaire +2 more sources