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Single-cell Ribo-seq reveals cell cycle-dependent translational pausing
Nature, 2021Single-cell sequencing methods have enabled in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These tools focus predominantly on sequencing the genomes1, epigenomes2 and transcriptomes3 of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution4 ...
Michael VanInsberghe +4 more
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Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density
Nature Methods, 2021In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its ...
Johanna Schott +2 more
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Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction
2021Ribosome profiling is a powerful technique that enables researchers to monitor translational events across the transcriptome. It provides a snapshot of ribosome positions and density across the transcriptome at a sub-codon resolution. Here we describe the whole procedure of profiling ribosome footprints in mammalian cells.
Jingfan, Qiu, Shu-Bing, Qian
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A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants
2022Protein production from mRNA is one of the fundamental molecular processes in a cell. Accurate genome-wide information on the levels of translation and ribosome distribution on mRNA can be gathered by carrying out ribosome footprinting, aka Ribo-seq.
Hao, Chen +2 more
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
Journal of Visualized Experiments, 2021The ribosome profiling technique (RIBO-seq) is currently the most effective tool for studying the process of protein synthesis in vivo. The advantage of this method, in comparison to other approaches, is its ability to monitor translation by precisely mapping the position and number of ribosomes on a mRNA transcript.
Natalia, Kopik +4 more
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Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome
Trends in Genetics, 2017By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling (Ribo-seq) has established its role as a powerful tool to study gene expression. Several laboratories have introduced modifications to the experimental protocol and expanded the repertoire of biochemical methods to study translation transcriptome-wide. However,
Lorenzo Calviello, Uwe Ohler
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Ribo-seq analysis of B16/F10 WT and Ythdf1 KO group
2022To identify the efficiency of downstream translation regulated by Ythdf1 in an m6A-dependent manner, we performed Ribo-seq analysis of WT and Ythdf1 KO group.
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Computational methods for translation regulation analysis from Ribo-seq data
2019Since its inception, Ribo-seq, a technique for deep sequencing the ribosome protected fragments (RPFs) of mRNA, has greatly expanded our knowledge of translation. With Ribo-seq, the coding potentials of the transcripts are re-evaluated, thousands of novel open reading frames (ORFs) are found translating, especially within those previously presumed non ...
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