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Related Concept Videos

Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

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Related Experiment Video

Updated: May 23, 2026

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity
07:46

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity

Published on: October 8, 2018

A role for tRNA modifications in genome structure and codon usage.

Eva Maria Novoa1, Mariana Pavon-Eternod, Tao Pan

  • 1Institute for Research in Biomedicine, c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain.

Cell
|April 3, 2012
PubMed
Summary
This summary is machine-generated.

Two specific transfer RNA (tRNA) modifications significantly influenced genome composition across all life kingdoms. Accounting for these modifications reveals correlations between codon usage and tRNA gene frequencies, impacting gene expression.

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An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity
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Published on: October 8, 2018

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry
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A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli
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A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli

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Area of Science:

  • Genomics and Molecular Biology
  • Bioinformatics and Comparative Genomics
  • Gene Expression and Regulation

Background:

  • Transfer RNA (tRNA) gene content is a key genomic feature influencing translational efficiency.
  • Principles governing tRNA gene copy number and codon composition across different life kingdoms remain unclear.
  • Previous studies suggested a lack of correlation between genomic codon usage and tRNA gene frequencies.

Purpose of the Study:

  • To investigate the impact of specific tRNA modifications on genome structure and composition.
  • To identify key tRNA modifications that differentiate archaeal, bacterial, and eukaryal genomes.
  • To re-evaluate the correlation between codon usage and tRNA gene frequencies in light of tRNA modifications.

Main Methods:

  • Comparative genomic analysis of over 500 diverse genomes.
  • Identification and characterization of kingdom-specific tRNA modifications.
  • Statistical analysis correlating tRNA gene composition, codon usage, and gene expression patterns.
  • Experimental validation of findings in human gene expression.

Main Results:

  • Two specific tRNA modifications were identified as major drivers shaping the tRNA gene composition of archaeal, bacterial, and eukaryal genomes.
  • Genomic codon usage and tRNA gene frequencies show a strong correlation across all kingdoms when these two modifications are considered.
  • The presence or absence of these modifications explains previously observed patterns in gene expression.
  • Experimental data confirmed that human gene expression correlates with genomic codon composition when these modifications are accounted for.

Conclusions:

  • Specific tRNA modifications are fundamental determinants of genome architecture and tRNA gene composition.
  • These modifications reconcile discrepancies in codon usage-tRNA gene frequency correlations across life.
  • Understanding these tRNA modifications provides crucial insights into the regulation of gene expression and genome evolution.