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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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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Ribosomal RNA Synthesis02:53

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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How Data are Classified: Categorical Data01:11

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A variable, usually notated by capital letters such as X and Y, is a characteristic or measurement that can be determined for each member of a population. Data are the actual values of variables. They may be numbers, or they may be words. Datum is a single value.
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HRPDviewer: human ribosome profiling data viewer.

Wei-Sheng Wu1, Yu-Xuan Jiang1, Jer-Wei Chang1

  • 1Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan.

Database : the Journal of Biological Databases and Curation
|July 17, 2018
PubMed
Summary
This summary is machine-generated.

Researchers developed the Human Ribosome Profiling Data viewer (HRPDviewer) to visualize ribosome profiling (ribo-seq) data. This tool aids in understanding human protein synthesis and translational regulation by aligning data to the transcriptome.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Translational regulation is crucial for protein synthesis, and its dysregulation is linked to diseases like cancer and inflammatory disorders.
  • Ribosome profiling (ribo-seq) is an advanced technique for capturing a snapshot of cellular translation by sequencing ribosome-protected mRNA fragments.
  • Existing ribo-seq databases (GWIPS-viz, RPFdb, TranslatomeDB) have limitations in data alignment and visualization capabilities.

Purpose of the Study:

  • To address the limitations of current ribo-seq databases by developing a novel data viewer.
  • To provide a resource for visualizing and comparing ribo-seq data across multiple mRNA transcripts.
  • To facilitate a deeper understanding of translational regulation in human cells.

Main Methods:

  • Developed the Human Ribosome Profiling Data viewer (HRPDviewer).
  • Integrated 610 published human ribo-seq datasets from the Gene Expression Omnibus.
  • Aligned ribo-seq data to the transcriptome, rather than the genome, for improved accuracy.
  • Implemented visualization tools for ribo-seq data on selected mRNA transcripts.

Main Results:

  • HRPDviewer successfully aligns ribo-seq data to the transcriptome.
  • The platform enables simultaneous visualization of ribo-seq data across multiple mRNA transcripts.
  • Researchers can now compare ribosome binding patterns for genes and transcripts within the HRPDviewer.

Conclusions:

  • HRPDviewer offers significant advantages over existing databases by aligning data to the transcriptome and providing enhanced visualization.
  • The tool allows for comparative analysis of translational activity across different mRNA transcripts, crucial for understanding protein synthesis.
  • HRPDviewer is a valuable resource for researchers investigating translational regulation in humans.