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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Updated: Nov 3, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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A tool for analyzing and visualizing ribo-seq data at the isoform level.

Wei-Sheng Wu1, Yi-Hong Tsao2, Sheng-Cian Shiue3

  • 1Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan. wessonwu@mail.ncku.edu.tw.

BMC Bioinformatics
|June 1, 2021
PubMed
Summary
This summary is machine-generated.

Researchers can now analyze ribosome profiling data at the isoform level using RPiso, a new software tool. This tool offers more accurate isoform abundance estimation and interactive visualization, aiding in understanding translational regulation and disease.

Keywords:
Isoform-levelPipelineRibo-seqRibosome profilingSoftwareToolVisualization

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Translational regulation is crucial for gene expression, with its dysregulation linked to various diseases.
  • Ribosome profiling (RP) is a key technique for studying translation by sequencing ribosome-protected mRNA fragments.
  • Existing RP tools primarily analyze data at the gene level, limiting isoform-specific insights.

Purpose of the Study:

  • To develop an accessible software tool, RPiso, for isoform-level ribosome profiling analysis.
  • To provide researchers with a method for more detailed investigation of translational regulation.

Main Methods:

  • Implementation of a previously developed pipeline for analyzing ribosome profiling data at the isoform level.
  • Development of RPiso as an easy-to-install and execute software tool.
  • Integration of a web-based viewer for interactive data visualization.

Main Results:

  • RPiso offers more accurate estimation of isoform abundance compared to existing tools like Ribomap.
  • The software supports analyses across a wider range of species.
  • RPiso provides an interactive web-based viewer for visualizing ribosome profiling data on specific mRNA isoforms.

Conclusions:

  • RPiso is a user-friendly software tool for isoform-level ribosome profiling analysis.
  • The tool facilitates the analysis and visualization of ribosome profiling data, enhancing research in translational regulation.
  • RPiso is expected to be a valuable resource for researchers studying gene expression and disease.