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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.2K
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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Ribosomes01:27

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.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
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Ribosomes01:27

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.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
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Ribosomes01:27

Ribosomes

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Ribosomes01:27

Ribosomes

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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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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.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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Related Experiment Video

Updated: Apr 29, 2026

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
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Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Published on: May 17, 2014

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Ribosome-omics of the human ribosome.

Varun Gupta1, Jonathan R Warner1

  • 1Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

RNA (New York, N.Y.)
|May 27, 2014
PubMed
Summary

Ribosomal protein mRNA levels largely match equimolar needs after accounting for pseudogenes. However, differences suggest regulated translation or protein turnover, with some genes showing tissue-specific expression impacting ribosome structure.

Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • Ribosomes are essential for protein synthesis, requiring equimolar amounts of ribosomal proteins (RPs).
  • RNA-sequencing (RNA-seq) data provides transcriptome-wide insights but requires careful analysis due to complexities like pseudogenes.

Purpose of the Study:

  • To investigate whether messenger RNA (mRNA) abundance for ribosomal proteins (RPs) aligns with the equimolar requirements for ribosome assembly.
  • To analyze the impact of pseudogenes on RP mRNA abundance measurements.

Main Methods:

  • Analysis of RNA-sequencing data from ENCODE and other sources.
  • Correction for mapping ambiguities caused by RP mRNA-derived pseudogenes.
  • Examination of tissue-specific gene transcription and alternative splicing.
Keywords:
RNA-seqalternative splicingpseudogeneribosomal proteinribosome

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Main Results:

  • Initial analysis revealed up to 100-fold differences in RP mRNA levels.
  • After pseudogene correction, 80%-90% of RP mRNAs showed less than threefold variation in molar ratio, with minimal tissue specificity.
  • Seven RPs possess subsidiary genes, including three "rescued" pseudogenes with tissue-specific transcription (e.g., RPL10L in testis, RPL3L in muscle).
  • One intron out of 376 in RP genes exhibited tissue-specific alternative splicing.

Conclusions:

  • RP mRNA levels are generally consistent with equimolar needs, suggesting post-transcriptional regulation (translation or protein turnover).
  • Tissue-specific transcription of certain RP genes and subsidiary genes may lead to variations in ribosome structure across different tissues.
  • While most RP mRNAs are not tissue-specific, some exceptions indicate specialized ribosome populations.