Related Experiment Video
Updated: Jul 6, 2026
13:16
Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
Published on: January 22, 2018
Using ribosomal protein genes as reference: a tale of caution
Lieven Thorrez1, Katrijn Van Deun, Léon-Charles Tranchevent
1Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium.
Plos One
|March 28, 2008
Summary
Ribosomal protein genes, while essential housekeeping genes, show significant tissue-dependent expression variation. Therefore, they are not suitable as reliable reference genes for normalizing gene expression data across different tissues.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Housekeeping genes are crucial for basic cellular functions and often used as reference genes for gene expression normalization.
- Traditionally, housekeeping genes were assumed to have stable expression across all cell types.
- Recent studies suggest ribosomal protein genes as potential reference genes, challenging this assumption.
Purpose of the Study:
- To distinguish between housekeeping genes and reference genes.
- To assess the expression stability of ribosomal protein genes across different tissues.
- To evaluate the suitability of ribosomal protein genes as reference genes for gene expression normalization.
Main Methods:
- Statistical analysis of a dataset comprising 70 microarrays from 22 different tissues.
- Application of one-way and two-way ANOVA to assess expression stability.
- Multidimensional unfolding analysis to visualize tissue-dependent expression patterns.
Main Results:
- Ribosomal protein genes confirmed as housekeeping genes with stable expression.
- Significant tissue-dependent expression variation observed in ribosomal protein genes.
- Multidimensional unfolding revealed distinct tissue-dependent expression behaviors.
Conclusions:
- Ribosomal protein genes exhibit considerable tissue-specific mRNA expression variability.
- Despite their stable expression relative to other genes, they are not ideal reference genes.
- The use of ribosomal protein genes for normalizing gene expression data requires careful consideration of tissue-specific effects.
Related Concept Videos
02:24Ribosome Profiling
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 helps...
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 helps...
02:53Ribosomal RNA Synthesis
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,...
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,...
02:53Ribosomal RNA Synthesis
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,...
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,...
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
02:28Leaky Scanning
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
01:34Directing Proteins to the Rough Endoplasmic Reticulum
The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...