A review of Ribosome profiling and tools used in Ribo-seq data analysis [PDF]
Computational and Structural Biotechnology JournalTranslational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of the methods to study translation and its regulation.
Mingso Sherma Limbu +2 more
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RiboPlotR: a visualization tool for periodic Ribo-seq reads [PDF]
Plant Methods, 2021 Background Ribo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time.
Hsin-Yen Larry Wu, Polly Yingshan Hsu
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Structured RNA Contaminants in Bacterial Ribo-Seq [PDF]
mSphere, 2020 Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes.
Brayon J. Fremin, Ami S. Bhatt
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Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq [PDF]
STAR Protocols, 2023 Summary: Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the “translational fitness” of a given mRNA in response to environmental or developmental cues with high resolution.
Isabel Cristina Vélez-Bermúdez +4 more
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Ribo-Seq and RNA-Seq of TMA46 (DFRP1) and GIR2 (DFRP2) knockout yeast strains [version 1; peer review: 3 approved] [PDF]
F1000Research, 2021 In eukaryotes, stalled and collided ribosomes are recognized by several conserved multicomponent systems, which either block protein synthesis in situ and resolve the collision locally, or trigger a general stress response. Yeast ribosome-binding GTPases
Alexander I. Alexandrov +9 more
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Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases [PDF]
Cells, 2022 RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases.
Atefeh Bagheri +3 more
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Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture [PDF]
Plant Methods, 2021 Background Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational ...
Amir Mahboubi +3 more
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Optimization of carbon and energy utilization through differential translational efficiency [PDF]
Nature Communications, 2018 Microorganisms must regulate allocation of resources in nutrient-limited conditions. Here, the authors combine Ribo-seq, RNA-seq and TSS-seq to study resource allocation in the acetogen C.
Mahmoud M. Al-Bassam +7 more
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Comparative survey of the relative impact of mRNA features on local ribosome profiling read density [PDF]
Nature Communications, 2016 Ribosome profiling data can suffer from uneven coverage which hampers estimation of elongation rates. Connor et al.present an enhanced data smoothing method for Ribo-seq data and highlight significant variability in sequence determinants of ribosome ...
Patrick B. F. O’Connor +2 more
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Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni [PDF]
Nature CommunicationsIn contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here,
Kathrin Froschauer +13 more
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